Publications for All Faculty

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.

Mallick H, Franzosa EA, Mclver LJ, Banerjee S, Sirota-Madi A, Kostic AD, Clish CB, Vlamakis H, Xavier RJ, Huttenhower C
Nat Commun. 2019;10(1):3136 - PMID: 31316056 - PMCID: PMC6637180 - DOI: 10.1038/s41467-019-10927-1

Template-directed Nonenzymatic Primer Extension Using 2-methylimidazole-activated Morpholino Derivatives of Guanosine and Cytidine.

Zhang W, Pal A, Ricardo A, Szostak JW
J Am Chem Soc. 2019;141(30):12159-12166 - PMID: 31298852 - DOI: 10.1021/jacs.9b06453

A 96-Week Multinational Randomized Double-Blind Parallel-Group Clinical Trial Evaluating the Safety and Effectiveness of Bexagliflozin as a Monotherapy for Adults with Type 2 Diabetes.

Halvorsen YD, Walford GA, Massaro J, Aftring RP, Freeman MW
Diabetes Obes Metab. 2019;:ePub - PMID: 31297965 - DOI: 10.1111/dom.13833

Allele-specific gene editing prevents deafness in a model of dominant progressive hearing loss.

György B, Nist-Lund C, Pan B, Asai Y, Karavitaki KD, Kleinstiver BP, Garcia SP, Zaborowski MP, Solanes P, Spataro S, Schneider BL, Joung JK, Géléoc GSG, Holt JR, Corey DP
Nat Med. 2019;25(7):1123-1130 - PMID: 31270503 - DOI: 10.1038/s41591-019-0500-9

Case 22-2019: A 65-Year-Old Woman with Weakness, Dark Urine, and Dysphagia.

Freeman MW, Singh AK, Guidon AC, Arvikar SL, Goldstein RH, Clement NF
N Engl J Med. 2019;381(3):275-283 - PMID: 31314973 - DOI: 10.1056/NEJMcpc1900589

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.

Smillie CS, Biton M, Ordovas-Montanes J, Sullivan KM, Burgin G, Graham DB, Herbst RH, Rogel N, Slyper M, Waldman J, Sud M, Andrews E, Velonias G, Haber AL, Jagadeesh K, Vickovic S, Yao J, Stevens C, Dionne D, Nguyen LT, Villani AC, Hofree M, Creasey EA, Huang H, Rozenblatt-Rosen O, Garber JJ, Khalili H, Desch AN, Daly MJ, Ananthakrishnan AN, Shalek AK, Xavier RJ, Regev A
Cell. 2019;178(3):714-730.e22 - PMID: 31348891 - PMCID: PMC6662628 - DOI: 10.1016/j.cell.2019.06.029

Microbial genes and pathways in inflammatory bowel disease.

Schirmer M, Garner A, Vlamakis H, Xavier RJ
Nat Rev Microbiol. 2019;17(8):497-511 - PMID: 31249397 - DOI: 10.1038/s41579-019-0213-6

Mutations in pmrB confer cross-resistance between the LptD inhibitor POL7080 and colistin in Pseudomonas aeruginosa.

Romano KP, Warrier T, Poulsen BE, Nguyen PH, Loftis AR, Saebi A, Pentelute BL, Hung DT
Antimicrob Agents Chemother. 2019;:ePub - PMID: 31235628 - DOI: 10.1128/AAC.00511-19

Large-scale chemical-genetics yields new M. tuberculosis inhibitor classes.

Johnson EO, LaVerriere E, Office E, Stanley M, Meyer E, Kawate T, Gomez JE, Audette RE, Bandyopadhyay N, Betancourt N, Delano K, Da Silva I, Davis J, Gallo C, Gardner M, Golas AJ, Guinn KM, Kennedy S, Korn R, McConnell JA, Moss CE, Murphy KC, Nietupski RM, Papavinasasundaram KG, Pinkham JT, Pino PA, Proulx MK, Ruecker N, Song N, Thompson M, Trujillo C, Wakabayashi S, Wallach JB, Watson C, Ioerger TR, Lander ES, Hubbard BK, Serrano-Wu MH, Ehrt S, Fitzgerald M, Rubin EJ, Sassetti CM, Schnappin ...
Nature. 2019;571(7763):72-78 - PMID: 31217586 - DOI: 10.1038/s41586-019-1315-z

Nucleic Acid Extraction and Sequencing from Low-Biomass Synthetic Mars Analog Soils for In Situ Life Detection.

Mojarro A, Hachey J, Bailey R, Brown M, Doebler R, Ruvkun G, Zuber MT, Carr CE
Astrobiology. 2019;:ePub - PMID: 31204862 - DOI: 10.1089/ast.2018.1929

Nonenzymatic template-directed synthesis of mixed-sequence 3'-NP-DNA up to 25 nucleotides long inside model protocells.

O'Flaherty DK, Zhou L, Szostak JW
J Am Chem Soc. 2019;141(26):10481-10488 - PMID: 31180644 - DOI: 10.1021/jacs.9b04858

Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide.

Henke MT, Kenny DJ, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J
Proc Natl Acad Sci U S A. 2019;116(26):12672-12677 - PMID: 31182571 - PMCID: PMC6601261 - DOI: 10.1073/pnas.1904099116

A 24-week, randomized, double-blind, active-controlled clinical trial comparing bexagliflozin to sitagliptin as an adjunct to metformin for the treatment of type 2 diabetes in adults.

Halvorsen YD, Lock JP, Zhou W, Zhu F, Freeman MW
Diabetes Obes Metab. 2019;:ePub - PMID: 31161692 - DOI: 10.1111/dom.13801

Regulation of Caenorhabditis elegans neuronal polarity by heterochronic genes.

Armakola M, Ruvkun G
Proc Natl Acad Sci U S A. 2019;116(25):12327-12336 - PMID: 31164416 - PMCID: PMC6589651 - DOI: 10.1073/pnas.1820928116

Akkermansia muciniphila induces intestinal adaptive immune responses during homeostasis.

Ansaldo E, Slayden LC, Ching KL, Koch MA, Wolf NK, Plichta DR, Brown EM, Graham DB, Xavier RJ, Moon JJ, Barton GM
Science. 2019;364(6446):1179-1184 - PMID: 31221858 - PMCID: PMC6645389 - DOI: 10.1126/science.aaw7479

Correction: Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population.

Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, International IBD Genetics Consortium, NIDDK IBD Genetics Consortium, T2D-GENES Consortium, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkk ...
PLoS Genet. 2019;15(5):e1008190 - PMID: 31145742 - PMCID: PMC6542503 - DOI: 10.1371/journal.pgen.1008190

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.

Lloyd-Price J, Arze C, Ananthakrishnan AN, Schirmer M, Avila-Pacheco J, Poon TW, Andrews E, Ajami NJ, Bonham KS, Brislawn CJ, Casero D, Courtney H, Gonzalez A, Graeber TG, Hall AB, Lake K, Landers CJ, Mallick H, Plichta DR, Prasad M, Rahnavard G, Sauk J, Shungin D, Vázquez-Baeza Y, White RA, IBDMDB Investigators, Braun J, Denson LA, Jansson JK, Knight R, Kugathasan S, McGovern DPB, Petrosino JF, Stappenbeck TS, Winter HS, Clish CB, Franzosa EA, Vlamakis H, Xavier RJ, Huttenhower C
Nature. 2019;569(7758):655-662 - PMID: 31142855 - PMCID: PMC6650278 - DOI: 10.1038/s41586-019-1237-9

Conservation of the structure and function of bacterial tryptophan synthases.

Michalska K, Gale J, Joachimiak G, Chang C, Hatzos-Skintges C, Nocek B, Johnston SE, Bigelow L, Bajrami B, Jedrzejczak RP, Wellington S, Hung DT, Nag PP, Fisher SL, Endres M, Joachimiak A
IUCrJ. 2019;6(Pt 4):649-664 - PMID: 31316809 - PMCID: PMC6608616 - DOI: 10.1107/S2052252519005955

Induction of the metal transporter ZIP8 by interferon gamma in intestinal epithelial cells: Potential role of metal dyshomeostasis in Crohn's disease.

Melia JMP, Lin R, Xavier RJ, Thompson RB, Fu D, Wan F, Sears CL, Donowitz M
Biochem Biophys Res Commun. 2019;515(2):325-331 - PMID: 31151823 - DOI: 10.1016/j.bbrc.2019.05.137

Safety and Effectiveness of Bexagliflozin in Patients With Type 2 Diabetes Mellitus and Stage 3a/3b CKD.

Allegretti AS, Zhang W, Zhou W, Thurber TK, Rigby SP, Bowman-Stroud C, Trescoli C, Serusclat P, Freeman MW, Halvorsen YC
Am J Kidney Dis. 2019;:ePub - PMID: 31101403 - DOI: 10.1053/j.ajkd.2019.03.417

Default activation and nuclear translocation of the plant cellular energy sensor SnRK1 regulate metabolic stress responses and development.

Ramon M, Dang TVT, Broeckx T, Hulsmans S, Crepin N, Sheen J, Rolland FA
Plant Cell. 2019;31(7):1614-1632 - PMID: 31123051 - PMCID: PMC6635846 - DOI: 10.1105/tpc.18.00500

Meiotic gatekeeper STRA8 suppresses autophagy by repressing Nr1d1 expression during spermatogenesis in mice.

Ferder IC, Fung L, Ohguchi Y, Zhang X, Lassen KG, Capen D, Brown D, Xavier RJ, Wang N
PLoS Genet. 2019;15(5):e1008084 - PMID: 31059511 - PMCID: PMC6502318 - DOI: 10.1371/journal.pgen.1008084

Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis.

Brown EM, Ke X, Hitchcock D, Jeanfavre S, Avila-Pacheco J, Nakata T, Arthur TD, Fornelos N, Heim C, Franzosa EA, Watson N, Huttenhower C, Haiser HJ, Dillow G, Graham DB, Finlay BB, Kostic AD, Porter JA, Vlamakis H, Clish CB, Xavier RJ
Cell Host Microbe. 2019;25(5):668-680.e7 - PMID: 31071294 - PMCID: PMC6544385 - DOI: 10.1016/j.chom.2019.04.002

Publisher Correction: Definitions and guidelines for research on antibiotic persistence.

Balaban NQ, Helaine S, Lewis K, Ackermann M, Aldridge B, Andersson DI, Brynildsen MP, Bumann D, Camilli A, Collins JJ, Dehio C, Fortune S, Ghigo JM, Hardt WD, Harms A, Heinemann M, Hung DT, Jenal U, Levin BR, Michiels J, Storz G, Tan MW, Tenson T, Van Melderen L, Zinkernagel A
Nat Rev Microbiol. 2019;17(7):460 - PMID: 31036919 - DOI: 10.1038/s41579-019-0207-4

Defining the core essential genome of Pseudomonas aeruginosa.

Poulsen BE, Yang R, Clatworthy AE, White T, Osmulski SJ, Li L, Penaranda C, Lander ES, Shoresh N, Hung DT
Proc Natl Acad Sci U S A. 2019;116(20):10072-10080 - PMID: 31036669 - PMCID: PMC6525520 - DOI: 10.1073/pnas.1900570116

Hypoxia Rescues Frataxin Loss by Restoring Iron Sulfur Cluster Biogenesis.

Ast T, Meisel JD, Patra S, Wang H, Grange RMH, Kim SH, Calvo SE, Orefice LL, Nagashima F, Ichinose F, Zapol WM, Ruvkun G, Barondeau DP, Mootha VK
Cell. 2019;177(6):1507-1521.e16 - PMID: 31031004 - DOI: 10.1016/j.cell.2019.03.045

Tetraspanin CD82 Organizes Dectin-1 into Signaling Domains to Mediate Cellular Responses to Candida albicans.

Tam JM, Reedy JL, Lukason DP, Kuna SG, Acharya M, Khan NS, Negoro PE, Xu S, Ward RA, Feldman MB, Dutko RA, Jeffery JB, Sokolovska A, Wivagg CN, Lassen KG, Le Naour F, Matzaraki V, Garner EC, Xavier RJ, Kumar V, van de Veerdonk FL, Netea MG, Miranti CK, Mansour MK, Vyas JM
J Immunol. 2019;202(11):3256-3266 - PMID: 31010852 - PMCID: PMC6529278 - DOI: 10.4049/jimmunol.1801384

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors.

Grünewald J, Zhou R, Garcia SP, Iyer S, Lareau CA, Aryee MJ, Joung JK
Nature. 2019;569(7756):433-437 - PMID: 30995674 - PMCID: PMC6657343 - DOI: 10.1038/s41586-019-1161-z

Adaptive Evolution within Gut Microbiomes of Healthy People.

Zhao S, Lieberman TD, Poyet M, Kauffman KM, Gibbons SM, Groussin M, Xavier RJ, Alm EJ
Cell Host Microbe. 2019;25(5):656-667.e8 - PMID: 31028005 - DOI: 10.1016/j.chom.2019.03.007

Endoplasmic reticulum-associated SKN-1A/Nrf1 mediates a cytoplasmic unfolded protein response and promotes longevity.

Lehrbach NJ, Ruvkun G
Elife. 2019;8:ePub - PMID: 30973820 - PMCID: PMC6459674 - DOI: 10.7554/eLife.44425

Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk: A Cross-Sectional Study.

Kurilshikov A, van den Munckhof IC, Chen L, Bonder MJ, Schraa K, Rutten J, Riksen NP, de Graaf J, Oosting M, Sanna S, Joosten LA, van der Graaf M, Brand T, Koonen DP, van Faassen MJ, Slagboom PE, Xavier RJ, Kuipers F, Hofker M, Wijmenga C, Netea MG, Zhernakova A, Fu J
Circ Res. 2019;124(12):1808-1820 - PMID: 30971183 - DOI: 10.1161/CIRCRESAHA.118.314642

Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease.

Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ
Nat Microbiol. 2019;4(5):898 - PMID: 30971771 - DOI: 10.1038/s41564-019-0442-5

Protein Sequence Editing of SKN-1A/Nrf1 by Peptide:N-Glycanase Controls Proteasome Gene Expression.

Lehrbach NJ, Breen PC, Ruvkun G
Cell. 2019;177(3):737-750.e15 - PMID: 31002798 - PMCID: PMC6574124 - DOI: 10.1016/j.cell.2019.03.035

Gut Microbiota Regulation of T Cells During Inflammation and Autoimmunity.

Brown EM, Kenny DJ, Xavier RJ
Annu Rev Immunol. 2019;37:599-624 - PMID: 31026411 - DOI: 10.1146/annurev-immunol-042718-041841

Clinical and biological predictors of response to standardised paediatric colitis therapy (PROTECT): a multicentre inception cohort study.

Hyams JS, Davis Thomas S, Gotman N, Haberman Y, Karns R, Schirmer M, Mo A, Mack DR, Boyle B, Griffiths AM, LeLeiko NS, Sauer CG, Keljo DJ, Markowitz J, Baker SS, Rosh J, Baldassano RN, Patel A, Pfefferkorn M, Otley A, Heyman M, Noe J, Oliva-Hemker M, Rufo PA, Strople J, Ziring D, Guthery SL, Sudel B, Benkov K, Wali P, Moulton D, Evans J, Kappelman MD, Marquis MA, Sylvester FA, Collins MH, Venkateswaran S, Dubinsky M, Tangpricha V, Spada KL, Saul B, Wang J, Serrano J, Hommel K, Marigorta UM, ...
Lancet. 2019;393(10182):1708-1720 - PMID: 30935734 - PMCID: PMC6501846 - DOI: 10.1016/S0140-6736(18)32592-3

The mechanism of nonenzymatic template copying with imidazole-activated nucleotides.

Walton T, Zhang W, Li L, Tam CP, Szostak JW
Angew Chem Int Ed Engl. 2019;58(32):10812-10819 - PMID: 30908802 - DOI: 10.1002/anie.201902050

Molybdenum cofactor transfer from bacteria to nematode mediates sulfite detoxification.

Warnhoff K, Ruvkun G
Nat Chem Biol. 2019;15(5):480-488 - PMID: 30911177 - PMCID: PMC6470025 - DOI: 10.1038/s41589-019-0249-y

Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA.

Bhattacharyya RP, Walker M, Boykin R, Son SS, Liu J, Hachey AC, Ma P, Wu L, Choi K, Cummins KC, Benson M, Skerry J, Ryu H, Wong SY, Goldberg MB, Han J, Pierce VM, Cosimi LA, Shoresh N, Livny J, Beechem J, Hung DT
Sci Rep. 2019;9(1):4516 - PMID: 30872641 - PMCID: PMC6418090 - DOI: 10.1038/s41598-019-40792-3

Transfer of Sequence Information and Replication of Diimine Duplexes.

Strom KR, Szostak JW, Prywes N
J Org Chem. 2019;84(7):3754-3761 - PMID: 30855962 - DOI: 10.1021/acs.joc.9b00095

Salt-Inducible Kinases: Physiology, Regulation by cAMP, and Therapeutic Potential: (Trends Endocrinol. Metab. 29, 723-735, 2018).

Wein MN, Foretz M, Fisher DE, Xavier RJ, Kronenberg HM
Trends Endocrinol Metab. 2019;30(6):407 - PMID: 30837108 - DOI: 10.1016/j.tem.2019.01.009

Adopt a moratorium on heritable genome editing.

Lander ES, Baylis F, Zhang F, Charpentier E, Berg P, Bourgain C, Friedrich B, Joung JK, Li J, Liu D, Naldini L, Nie JB, Qiu R, Schoene-Seifert B, Shao F, Terry S, Wei W, Winnacker EL
Nature. 2019;567(7747):165-168 - PMID: 30867611 - DOI: 10.1038/d41586-019-00726-5

CRISPResso2 provides accurate and rapid genome editing sequence analysis.

Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L
Nat Biotechnol. 2019;37(3):224-226 - PMID: 30809026 - PMCID: PMC6533916 - DOI: 10.1038/s41587-019-0032-3

Mitochondrial Dysfunction in C. elegans Activates Mitochondrial Relocalization and Nuclear Hormone Receptor-Dependent Detoxification Genes.

Mao K, Ji F, Breen P, Sewell A, Han M, Sadreyev R, Ruvkun G
Cell Metab. 2019;29(5):1182-1191.e4 - PMID: 30799287 - PMCID: PMC6506380 - DOI: 10.1016/j.cmet.2019.01.022

Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing.

Kleinstiver BP, Sousa AA, Walton RT, Tak YE, Hsu JY, Clement K, Welch MM, Horng JE, Malagon-Lopez J, Scarfò I, Maus MV, Pinello L, Aryee MJ, Joung JK
Nat Biotechnol. 2019;37(3):276-282 - PMID: 30742127 - PMCID: PMC6401248 - DOI: 10.1038/s41587-018-0011-0

Spatial and Temporal Mapping of Human Innate Lymphoid Cells Reveals Elements of Tissue Specificity.

Yudanin NA, Schmitz F, Flamar AL, Thome JJC, Tait Wojno E, Moeller JB, Schirmer M, Latorre IJ, Xavier RJ, Farber DL, Monticelli LA, Artis D
Immunity. 2019;50(2):505-519.e4 - PMID: 30770247 - PMCID: PMC6594374 - DOI: 10.1016/j.immuni.2019.01.012

Rhizobium induces DNA damage in Caenorhabditis elegans intestinal cells.

Kniazeva M, Ruvkun G
Proc Natl Acad Sci U S A. 2019;116(9):3784-3792 - PMID: 30808764 - PMCID: PMC6397575 - DOI: 10.1073/pnas.1815656116

Integration of nutrient, energy, light and hormone signalling via TOR in plants.

Wu Y, Shi L, Li L, Fu L, Liu Y, Xiong Y, Sheen J
J Exp Bot. 2019;70(8):2227-2238 - PMID: 30715492 - PMCID: PMC6463029 - DOI: 10.1093/jxb/erz028

SLC39A8 missense variant is associated with Crohn's disease but does not have a major impact on gut microbiome composition in healthy subjects.

Collij V, Imhann F, Vich Vila A, Fu J, Dijkstra G, Festen EAM, Voskuil MD, Daly MJ, Xavier RJ, Wijmenga C, Zhernakova A, Weersma RK
PLoS One. 2019;14(1):e0211328 - PMID: 30703110 - PMCID: PMC6354981 - DOI: 10.1371/journal.pone.0211328

Single-Cell RNA Sequencing to Understand Host-Pathogen Interactions.

Penaranda C, Hung DT
ACS Infect Dis. 2019;5(3):336-344 - PMID: 30702856 - DOI: 10.1021/acsinfecdis.8b00369

Using Imaging Flow Cytometry to Quantify and Optimize Giant Vesicle Production by Water-in-oil Emulsion Transfer Methods.

Matsushita-Ishiodori Y, Hanczyc MM, Wang A, Szostak JW, Yomo T
Langmuir. 2019;35(6):2375-2382 - PMID: 30645943 - DOI: 10.1021/acs.langmuir.8b03635

Prospective Validation of a Transcriptomic Metric in Severe Trauma.

Raymond SL, Hawkins RB, Wang Z, Mira JC, Stortz JA, Han F, Lanz JD, Hennessy LV, Brumback BA, Baker HV, Efron PA, Brakenridge SC, Xiao W, Tompkins RG, Cuschieri J, Moore FA, Maier RV, Moldawer LL
Ann Surg. 2019;:ePub - PMID: 30688688 - PMCID: PMC6656642 - DOI: 10.1097/SLA.0000000000003204

A defined commensal consortium elicits CD8 T cells and anti-cancer immunity.

Tanoue T, Morita S, Plichta DR, Skelly AN, Suda W, Sugiura Y, Narushima S, Vlamakis H, Motoo I, Sugita K, Shiota A, Takeshita K, Yasuma-Mitobe K, Riethmacher D, Kaisho T, Norman JM, Mucida D, Suematsu M, Yaguchi T, Bucci V, Inoue T, Kawakami Y, Olle B, Roberts B, Hattori M, Xavier RJ, Atarashi K, Honda K
Nature. 2019;565(7741):600-605 - PMID: 30675064 - DOI: 10.1038/s41586-019-0878-z

The Crohn's disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response.

Lavoie S, Conway KL, Lassen KG, Jijon HB, Pan H, Chun E, Michaud M, Lang JK, Gallini Comeau CA, Dreyfuss JM, Glickman JN, Vlamakis H, Ananthakrishnan A, Kostic A, Garrett WS, Xavier RJ
Elife. 2019;8:ePub - PMID: 30666959 - PMCID: PMC6342529 - DOI: 10.7554/eLife.39982

Noncanonical ATG8-ABS3 interaction controls senescence in plants.

Jia M, Liu X, Xue H, Wu Y, Shi L, Wang R, Chen Y, Xu N, Zhao J, Shao J, Qi Y, An L, Sheen J, Yu F
Nat Plants. 2019;5(2):212-224 - PMID: 30664732 - PMCID: PMC6368864 - DOI: 10.1038/s41477-018-0348-x

Coenzyme Q10 protects against burn-induced mitochondrial dysfunction and impaired insulin signaling in mouse skeletal muscle.

Nakazawa H, Ikeda K, Shinozaki S, Yasuhara S, Yu YM, Martyn JAJ, Tompkins RG, Yorozu T, Inoue S, Kaneki M
FEBS Open Bio. 2019;9(2):348-363 - PMID: 30761259 - PMCID: PMC6356165 - DOI: 10.1002/2211-5463.12580

Core-Shell Modeling of Light Scattering by Vesicles: Effect of Size, Contents, and Lamellarity.

Wang A, Chan Miller C, Szostak JW
Biophys J. 2019;116(4):659-669 - PMID: 30686489 - PMCID: PMC6382849 - DOI: 10.1016/j.bpj.2019.01.006

Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.

Haberman Y, Karns R, Dexheimer PJ, Schirmer M, Somekh J, Jurickova I, Braun T, Novak E, Bauman L, Collins MH, Mo A, Rosen MJ, Bonkowski E, Gotman N, Marquis A, Nistel M, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, Leleiko NS, Heyman MB, Grifiths AM, Patel AS, Noe JD, Aronow BJ, Kugathasan S, Walters TD, Gibson G, Thomas SD, Mollen K, Shen-Orr S, Huttenhower C, Xavier RJ, Hyams JS, Denson LA
Nat Commun. 2019;10(1):38 - PMID: 30604764 - PMCID: PMC6318335 - DOI: 10.1038/s41467-018-07841-3

Template-directed catalysis of a multi-step reaction pathway for nonenzymatic RNA primer extension.

Walton T, Pazienza L, Szostak JW
Biochemistry. 2018;58(6):755-762 - PMID: 30566332 - DOI: 10.1021/acs.biochem.8b01156

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.

Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJ
Nat Microbiol. 2018;4(3):470-479 - PMID: 30559407 - PMCID: PMC6384140 - DOI: 10.1038/s41564-018-0321-5

Mitogen-activated protein kinases MPK3 and MPK6 are required for stem cell maintenance in the Arabidopsis shoot apical meristem.

Lee H, Jun YS, Cha OK, Sheen J
Plant Cell Rep. 2018;38(3):311-319 - PMID: 30552452 - PMCID: PMC6573032 - DOI: 10.1007/s00299-018-2367-5

Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis.

Haberman Y, Schirmer M, Dexheimer PJ, Karns R, Braun T, Kim MO, Walters TD, Baldassano RN, Noe JD, Rosh J, Markowitz J, Crandall WV, Mack DR, Griffiths AM, Heyman MB, Baker SS, Kellermayer R, Moulton D, Patel AS, Gulati AS, Steiner SJ, LeLeiko N, Otley A, Oliva-Hemker M, Ziring D, Kirschner BS, Keljo DJ, Guthery SL, Cohen SA, Snapper S, Evans J, Dubinsky M, Aronow B, Hyams JS, Kugathasan S, Huttenhower C, Xavier RJ, Denson LA
Mucosal Immunol. 2018;12(2):491-502 - PMID: 30542108 - PMCID: PMC6375755 - DOI: 10.1038/s41385-018-0114-4

Gut microbiome structure and metabolic activity in inflammatory bowel disease.

Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ
Nat Microbiol. 2018;4(2):293-305 - PMID: 30531976 - PMCID: PMC6342642 - DOI: 10.1038/s41564-018-0306-4

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Kim SC, O'Flaherty DK, Zhou L, Lelyveld VS, Szostak JW
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CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data.

Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L
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Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.

Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK
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Proc Natl Acad Sci U S A. 2018;115(50):12823-12828 - PMID: 30482859 - PMCID: PMC6294885 - DOI: 10.1073/pnas.1809526115

An ATG16L1-dependent pathway promotes plasma membrane repair and limits Listeria monocytogenes cell-to-cell spread.

Tan JMJ, Mellouk N, Osborne SE, Ammendolia DA, Dyer DN, Li R, Brunen D, van Rijn JM, Huang J, Czuczman MA, Cemma MA, Won AM, Yip CM, Xavier RJ, MacDuff DA, Reggiori F, Debnath J, Yoshimori T, Kim PK, Fairn GD, Coyaud E, Raught B, Muise AM, Higgins DE, Brumell JH
Nat Microbiol. 2018;3(12):1472-1485 - PMID: 30478389 - DOI: 10.1038/s41564-018-0293-5

Single-cell RNA Sequencing of Blood and Ileal T cells From Patients With Crohn's Disease Reveals Tissue-specific Characteristics and Drug Targets.

Uniken Venema WT, Voskuil MD, Vich Vila A, van der Vries G, Jansen BH, Jabri B, Faber KN, Dijkstra G, Xavier RJ, Wijmenga C, Graham DB, Weersma RK, Festen EA
Gastroenterology. 2018;156(3):812-815.e22 - PMID: 30391472 - DOI: 10.1053/j.gastro.2018.10.046

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.

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Stewart CJ, Ajami NJ, O'Brien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni H, Metcalf GA, Muzny D, Gibbs RA, Vatanen T, Huttenhower C, Xavier RJ, Rewers M, Hagopian W, Toppari J, Ziegler AG, She JX, Akolkar B, Lernmark A, Hyoty H, Vehik K, Krischer JP, Petrosino JF
Nature. 2018;562(7728):583-588 - PMID: 30356187 - PMCID: PMC6415775 - DOI: 10.1038/s41586-018-0617-x

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study.

Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ
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DAF-16/FOXO and HLH-30/TFEB function as combinatorial transcription factors to promote stress resistance and longevity.

Lin XX, Sen I, Janssens GE, Zhou X, Fonslow BR, Edgar D, Stroustrup N, Swoboda P, Yates JR, Ruvkun G, Riedel CG
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A non-canonical autophagy-dependent role of the ATG16L1T300A variant in urothelial vesicular trafficking and uropathogenic Escherichia coli persistence.

Wang C, Bauckman KA, Ross ASB, Symington JW, Ligon MM, Scholtes G, Kumar A, Chang HW, Twentyman J, Fashemi BE, Xavier RJ, Mysorekar IU
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Jin L, Engelhart AE, Zhang W, Adamala KP, Szostak JW
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Endoplasmic Reticulum Homeostasis Is Modulated by the Forkhead Transcription Factor FKH-9 During Infection of Caenorhabditis elegans.

Tillman EJ, Richardson CE, Cattie DJ, Reddy KC, Lehrbach NJ, Droste R, Ruvkun G, Kim DH
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Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course.

Schirmer M, Denson L, Vlamakis H, Franzosa EA, Thomas S, Gotman NM, Rufo P, Baker SS, Sauer C, Markowitz J, Pfefferkorn M, Oliva-Hemker M, Rosh J, Otley A, Boyle B, Mack D, Baldassano R, Keljo D, LeLeiko N, Heyman M, Griffiths A, Patel AS, Noe J, Kugathasan S, Walters T, Huttenhower C, Hyams J, Xavier RJ
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Discovery of heterocyclic replacements for the coumarin core of anti-tubercular FadD32 inhibitors.

Fang C, Lee KK, Nietupski R, Bates RH, Fernandez-Menendez R, Lopez-Roman EM, Guijarro-Lopez L, Yin Y, Peng Z, Gomez JE, Fisher S, Barros-Aguirre D, Hubbard BK, Serrano-Wu MH, Hung DT
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In vivo CRISPR editing with no detectable genome-wide off-target mutations.

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Nature. 2018;561(7723):416-419 - PMID: 30209390 - PMCID: PMC6194229 - DOI: 10.1038/s41586-018-0500-9

Tracing My Roots: How I Became a Plant Biologist.

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Annu Rev Genet. 2018;52:1-20 - PMID: 30192637 - DOI: 10.1146/annurev-genet-120417-031722

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Cold Spring Harb Perspect Biol. 2018;10(9):ePub - PMID: 30181195 - DOI: 10.1101/cshperspect.a034801

Salt-Inducible Kinases: Physiology, Regulation by cAMP, and Therapeutic Potential.

Wein MN, Foretz M, Fisher DE, Xavier RJ, Kronenberg HM
Trends Endocrinol Metab. 2018;29(10):723-735 - PMID: 30150136 - PMCID: PMC6151151 - DOI: 10.1016/j.tem.2018.08.004

Discovery and Optimization of nTZDpa as an Antibiotic Effective Against Bacterial Persisters.

Kim W, Steele AD, Zhu W, Csatary EE, Fricke N, Dekarske MM, Jayamani E, Pan W, Kwon B, Sinitsa IF, Rosen JL, Conery AL, Fuchs BB, Vlahovska PM, Ausubel FM, Gao H, Wuest WM, Mylonakis E
ACS Infect Dis. 2018;4(11):1540-1545 - PMID: 30132650 - PMCID: PMC6468991 - DOI: 10.1021/acsinfecdis.8b00161

Carbapenem resistance caused by high-level expression of OXA-663 β-lactamase in an OmpK36-deficient Klebsiella pneumoniae clinical isolate.

Ma P, Laibinis HH, Ernst CM, Hung DT
Antimicrob Agents Chemother. 2018;62(11):ePub - PMID: 30126962 - PMCID: PMC6201135 - DOI: 10.1128/AAC.01281-18

TMEM41B is a novel regulator of autophagy and lipid mobilization.

Moretti F, Bergman P, Dodgson S, Marcellin D, Claerr I, Goodwin JM, DeJesus R, Kang Z, Antczak C, Begue D, Bonenfant D, Graff A, Genoud C, Reece-Hoyes JS, Russ C, Yang Z, Hoffman GR, Mueller M, Murphy LO, Xavier RJ, Nyfeler B
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Harnessing CRISPR Effectors for Infectious Disease Diagnostics.

Bhattacharyya RP, Thakku SG, Hung DT
ACS Infect Dis. 2018;4(9):1278-1282 - PMID: 30113801 - DOI: 10.1021/acsinfecdis.8b00170

Acceleration profiles and processing methods for parabolic flight.

Carr CE, Bryan NC, Saboda KN, Bhattaru SA, Ruvkun G, Zuber MT
NPJ Microgravity. 2018;4:14 - PMID: 30109261 - PMCID: PMC6081456 - DOI: 10.1038/s41526-018-0050-3

An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities.

Gehrke JM, Cervantes O, Clement MK, Wu Y, Zeng J, Bauer DE, Pinello L, Joung JK
Nat Biotechnol. 2018;36(10):977-982 - PMID: 30059493 - PMCID: PMC6181770 - DOI: 10.1038/nbt.4199

Impaired Aryl Hydrocarbon Receptor Ligand Production by the Gut Microbiota Is a Key Factor in Metabolic Syndrome.

Natividad JM, Agus A, Planchais J, Lamas B, Jarry AC, Martin R, Michel ML, Chong-Nguyen C, Roussel R, Straube M, Jegou S, McQuitty C, Le Gall M, da Costa G, Lecornet E, Michaudel C, Modoux M, Glodt J, Bridonneau C, Sovran B, Dupraz L, Bado A, Richard ML, Langella P, Hansel B, Launay JM, Xavier RJ, Duboc H, Sokol H
Cell Metab. 2018;28(5):737-749.e4 - PMID: 30057068 - DOI: 10.1016/j.cmet.2018.07.001

TOR signaling in plants: conservation and innovation.

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Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs.

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Genetics. 2018;209(3):651-673 - PMID: 29967059 - PMCID: PMC6028246 - DOI: 10.1534/genetics.118.300291

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.

Yassour M, Jason E, Hogstrom LJ, Arthur TD, Tripathi S, Siljander H, Selvenius J, Oikarinen S, Hyöty H, Virtanen SM, Ilonen J, Ferretti P, Pasolli E, Tett A, Asnicar F, Segata N, Vlamakis H, Lander ES, Huttenhower C, Knip M, Xavier RJ
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Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes.

Graham DB, Jasso GJ, Mok A, Goel G, Ng ACY, Kolde R, Varma M, Doench JG, Root DE, Clish CB, Carr SA, Xavier RJ
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The causes and consequences of variation in human cytokine production in health.

Schirmer M, Kumar V, Netea MG, Xavier RJ
Curr Opin Immunol. 2018;54:50-58 - PMID: 29913309 - DOI: 10.1016/j.coi.2018.05.012

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Zhang W, Walton T, Li L, Szostak JW
Elife. 2018;7:ePub - PMID: 29851379 - PMCID: PMC5980232 - DOI: 10.7554/eLife.36422

Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population.

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PLoS Genet. 2018;14(5):e1007329 - PMID: 29795570 - PMCID: PMC5967709 - DOI: 10.1371/journal.pgen.1007329

Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses.

Bakker OB, Aguirre-Gamboa R, Sanna S, Oosting M, Smeekens SP, Jaeger M, Zorro M, Võsa U, Withoff S, Netea-Maier RT, Koenen HJPM, Joosten I, Xavier RJ, Franke L, Joosten LAB, Kumar V, Wijmenga C, Netea MG, Li Y
Nat Immunol. 2018;19(7):776-786 - PMID: 29784908 - PMCID: PMC6022810 - DOI: 10.1038/s41590-018-0121-3

Long-term effects of patiromer for hyperkalaemia treatment in patients with mild heart failure and diabetic nephropathy on angiotensin-converting enzymes/angiotensin receptor blockers: results from AMETHYST-DN.

Pitt B, Bakris GL, Weir MR, Freeman MW, Lainscak M, Mayo MR, Garza D, Zawadzki R, Berman L, Bushinsky DA
ESC Heart Fail. 2018;5(4):592-602 - PMID: 29767459 - PMCID: PMC6073017 - DOI: 10.1002/ehf2.12292

Sequencing nothing: Exploring failure modes of nanopore sensing and implications for life detection.

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Life Sci Space Res (Amst). 2018;18:80-86 - PMID: 30100151 - DOI: 10.1016/j.lssr.2018.05.004

The surveillance of pre-mRNA splicing is an early step in C. elegans RNAi of endogenous genes.

Newman MA, Ji F, Fischer SEJ, Anselmo A, Sadreyev RI, Ruvkun G
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Genetic Markers Predict Primary Nonresponse and Durable Response to Anti-Tumor Necrosis Factor Therapy in Ulcerative Colitis.

Burke KE, Khalili H, Garber JJ, Haritunians T, McGovern DPB, Xavier RJ, Ananthakrishnan AN
Inflamm Bowel Dis. 2018;24(8):1840-1848 - PMID: 29718226 - PMCID: PMC6128143 - DOI: 10.1093/ibd/izy083

Platelet transfusion increases risk for acute respiratory distress syndrome in non-massively transfused blunt trauma patients.

Kasotakis G, Starr N, Nelson E, Sarkar B, Burke PA, Remick DG, Tompkins RG, Inflammation and Host Response to Injury Investigators
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J Am Chem Soc. 2018;140(15):5171-5178 - PMID: 29608310 - DOI: 10.1021/jacs.8b00639

Without Adaptive Immunity, There's a Cost to Responding STAT.

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Cell Metab. 2018;27(4):705-707 - PMID: 29617636 - DOI: 10.1016/j.cmet.2018.03.011

Impact of Genetic Variation on CRISPR-Cas Targeting.

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Lareau CA, Clement K, Hsu JY, Pattanayak V, Joung JK, Aryee MJ, Pinello L
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A new class of synthetic retinoid antibiotics effective against bacterial persisters.

Kim W, Zhu W, Hendricks GL, Van Tyne D, Steele AD, Keohane CE, Fricke N, Conery AL, Shen S, Pan W, Lee K, Rajamuthiah R, Fuchs BB, Vlahovska PM, Wuest WM, Gilmore MS, Gao H, Ausubel FM, Mylonakis E
Nature. 2018;556(7699):103-107 - PMID: 29590091 - PMCID: PMC6462414 - DOI: 10.1038/nature26157

A common mechanism links activities of butyrate in the colon.

Verma MS, Fink MJ, Salmon GL, Fornelos N, Ohara TE, Ryu SH, Vlamakis H, Xavier RJ, Stappenbeck TS, Whitesides GM
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CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing.

Mojarro A, Hachey J, Ruvkun G, Zuber MT, Carr CE
BMC Bioinformatics. 2018;19(1):108 - PMID: 29587645 - PMCID: PMC5872496 - DOI: 10.1186/s12859-018-2124-3

Whole-organism phenotypic screening for anti-infectives promoting host health.

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Nat Chem Biol. 2018;14(4):331-341 - PMID: 29556098 - DOI: 10.1038/s41589-018-0018-3

Quorum-sensing regulator RhlR but not its autoinducer RhlI enablesPseudomonasto evade opsonization.

Haller S, Franchet A, Hakkim A, Chen J, Drenkard E, Yu S, Schirmeier S, Li Z, Martins N, Ausubel FM, Liégeois S, Ferrandon D
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Fatty Acid/Phospholipid Blended Membranes: A Potential Intermediate State in Protocellular Evolution.

Jin L, Kamat NP, Jena S, Szostak JW
Small. 2018;14(15):e1704077 - PMID: 29479815 - PMCID: PMC6278924 - DOI: 10.1002/smll.201704077

Both live and dead Enterococci activate Caenorhabditis elegans host defense via immune and stress pathways.

Yuen GJ, Ausubel FM
Virulence. 2018;9(1):0 - PMID: 29436902 - PMCID: PMC5955442 - DOI: 10.1080/21505594.2018.1438025

Preparation, Purification, and Use of Fatty Acid-containing Liposomes.

Jin L, Engelhart AE, Adamala KP, Szostak JW
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The expanding diversity of Mycobacterium tuberculosis drug targets.

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A structural rationale for the enhanced catalysis of nonenzymatic RNA primer extension by a downstream oligonucleotide.

Zhang W, Tam CP, Zhou L, Oh SS, Wang J, Szostak JW
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C1orf106 is a colitis risk gene that regulates stability of epithelial adherens junctions.

Mohanan V, Nakata T, Desch AN, Lévesque C, Boroughs A, Guzman G, Cao Z, Creasey E, Yao J, Boucher G, Charron G, Bhan AK, Schenone M, Carr SA, Reinecker HC, Daly MJ, Rioux JD, Lassen KG, Xavier RJ
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Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation.

Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, Sadowsky MJ, Allegretti JR, Smith MB, Xavier RJ, Alm EJ
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Host genetic variation and its microbiome interactions within the Human Microbiome Project.

Kolde R, Franzosa EA, Rahnavard G, Hall AB, Vlamakis H, Stevens C, Daly MJ, Xavier RJ, Huttenhower C
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Loss of Response to Anti-Tumor Necrosis Factor Alpha Therapy in Crohn's Disease Is Not Associated with Emergence of Novel Inflammatory Pathways.

Luther J, Gala M, Patel SJ, Dave M, Borren N, Xavier RJ, Ananthakrishnan AN
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Genomic and expression analyses identify a disease modifying variant for fibrostenotic Crohn's disease.

Visschedijk MC, Spekhorst LM, Cheng SC, van Loo ES, Jansen BHD, Blokzijl T, Kil H, de Jong DJ, Pierik M, Maljaars JPWJ, van der Woude CJ, van Bodegraven AA, Oldenburg B, Löwenberg M, Nieuwenhuijs VB, Imhann F, van Sommeren S, Alberts R, Xavier RJ, Dijkstra G, Faber KN, Aldaz CM, Weersma RK, Festen EAM
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Solvated-electron production using cyanocuprates is compatible with the UV-environment on a Hadean-Archaean Earth.

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Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C
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Gene therapy comes of age.

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TMEM258 Is a Component of the Oligosaccharyltransferase Complex Controlling ER Stress and Intestinal Inflammation

Graham DB, Lefkovith A, Deelen P, de Klein N, Varma M, Boroughs A, Desch AN, Ng ACY, Guzman G, Schenone M, Petersen CP, Bhan AK, Rivas MA, Daly MJ, Carr SA, Wijmenga C, Xavier RJ
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Kazis LE, Sheridan RL, Shapiro GD, Lee AF, Liang MH, Ryan CM, Schneider JC, Lydon M, Soley-Bori M, Sonis LA, Dore EC, Palmieri T, Herndon D, Meyer W, Warner P, Kagan R, Stoddard FJ, Murphy M, Tompkins RG
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Mechanisms and Function of Autophagy in Intestinal Disease.

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A Mechanistic Explanation for the Regioselectivity of Nonenzymatic RNA Primer Extension.

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Jia TZ, Fahrenbach AC, Kamat NP, Adamala KP, Szostak JW
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A role for bacterial urease in gut dysbiosis and Crohn's disease.

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Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens.

Haney CH, Wiesmann CL, Shapiro LR, O'Sullivan LR, Khorasani S, Melnyk RA, Xiao L, Han J, Bush J, Carrillo J, Pierce NE, Ausubel FM
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scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing.

Avital G, Avraham R, Fan A, Hashimshony T, Hung DT, Yanai I
Genome Biol. 2017;18(1):200 - PMID: 29073931 - PMCID: PMC5658913 - DOI: 10.1186/s13059-017-1340-x

Transcription factor TFEB cell-autonomously modulates susceptibility to intestinal epithelial cell injury in vivo.

Murano T, Najibi M, Paulus GLC, Adiliaghdam F, Valencia-Guerrero A, Selig M, Wang X, Jeffrey K, Xavier RJ, Lassen KG, Irazoqui JE
Sci Rep. 2017;7(1):13938 - PMID: 29066772 - PMCID: PMC5655326 - DOI: 10.1038/s41598-017-14370-4

A kinetic model of nonenzymatic RNA polymerization by cytidine-5'-phosphoro-2-aminoimidazolide.

Walton T, Szostak JW
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p40 (phox) -Deficient Mice Exhibit Impaired Bacterial Clearance and Enhanced Pro-inflammatory Responses during Salmonella enterica serovar Typhimurium Infection.

Li Y, Lv M, Su C, Long S, Zhang W, Conway KL, Li W, Xavier RJ, Shi HN
Front Immunol. 2017;8:1270 - PMID: 29062317 - PMCID: PMC5640886 - DOI: 10.3389/fimmu.2017.01270

Small-molecule inhibitors directly target CARD9 and mimic its protective variant in inflammatory bowel disease.

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Dual CLAVATA3 Peptides in Arabidopsis Shoot Stem Cell Signaling.

Kim HJ, Wu CY, Yu HM, Sheen J, Lee H
J Plant Biol. 2017;60(5):506-512 - PMID: 30310351 - PMCID: PMC6176727 - DOI: 10.1007/s12374-017-0083-2

Dual CLAVATA3 Peptides in Arabidopsis Shoot Stem Cell Signaling

Kim HJ, Wu CY, Yu HM, Sheen J, Lee H1.
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SHANK3 Regulates Intestinal Barrier Function Through Modulating ZO-1 Expression Through the PKCε-dependent Pathway.

Wei SC, Yang-Yen HF, Tsao PN, Weng MT, Tung CC, Yu LCH, Lai LC, Hsiao JH, Chuang EY, Shun CT, Ni YH, Xavier RJ, Podolsky DK, Yen JJY, Wong JM
Inflamm Bowel Dis. 2017;23(10):1730-1740 - PMID: 28906292 - DOI: 10.1097/MIB.0000000000001250

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation.

Atarashi K, Suda W, Luo C, Kawaguchi T, Motoo I, Narushima S, Kiguchi Y, Yasuma K, Watanabe E, Tanoue T, Thaiss CA, Sato M, Toyooka K, Said HS, Yamagami H, Rice SA, Gevers D, Johnson RC, Segre JA, Chen K, Kolls JK, Elinav E, Morita H, Xavier RJ, Hattori M, Honda K
Science. 2017;358(6361):359-365 - PMID: 29051379 - PMCID: PMC5682622 - DOI: 10.1126/science.aan4526

Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars.

Pontefract A, Zhu TF, Walker VK, Hepburn H, Lui C, Zuber MT, Ruvkun G, Carr CE
Front Microbiol. 2017;8:1819 - PMID: 29018418 - PMCID: PMC5623196 - DOI: 10.3389/fmicb.2017.01819

Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution.

Ransey E, Björkbom A, Lelyveld VS, Biecek P, Pantano L, Szostak JW, Sliz P
RNA Biol. 2017;14(12):0 - PMID: 28945502 - PMCID: PMC5731800 - DOI: 10.1080/15476286.2017.1356566

Enhanced proofreading governs CRISPR-Cas9 targeting accuracy.

Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, Sternberg SH, Joung JK, Yildiz A, Doudna JA
Nature. 2017;550(7676):407-410 - PMID: 28931002 - PMCID: PMC5918688 - DOI: 10.1038/nature24268

An Anti-Persister Strategy for the Treatment of Chronic Pseudomonas aeruginosa Infections.

Koeva M, Gutu AD, Hebert W, Wager JD, Yonker LM, O'Toole GA, Ausubel FM, Moskowitz SM, Joseph-McCarthy D
Antimicrob Agents Chemother. 2017;61(12):ePub - PMID: 28923873 - PMCID: PMC5700368 - DOI: 10.1128/AAC.00987-17

Autophagy-Independent Lysosomal Targeting Regulated by ULK1/2-FIP200 and ATG9.

Goodwin JM, Dowdle WE, DeJesus R, Wang Z, Bergman P, Kobylarz M, Lindeman A, Xavier RJ, McAllister G, Nyfeler B, Hoffman G, Murphy LO
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The Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis and Anti-tuberculous Host Defense.

Franco LH, Nair VR, Scharn CR, Xavier RJ, Torrealba JR, Shiloh MU, Levine B
Cell Host Microbe. 2017;22(3):421-423 - PMID: 28910640 - PMCID: PMC5818210 - DOI: 10.1016/j.chom.2017.08.005

Investment in secreted enzymes during nutrient-limited growth is utility dependent.

Cezairliyan B, Ausubel FM
Proc Natl Acad Sci U S A. 2017;114(37):E7796-E7802 - PMID: 28847943 - PMCID: PMC5604031 - DOI: 10.1073/pnas.1708580114

SHANK3 Regulates Intestinal Barrier Function Through Modulating ZO-1 Expression Through the PKCε-dependent Pathway.

Wei SC, Yang-Yen HF, Tsao PN, Weng MT, Tung CC, Yu LCH, Lai LC, Hsiao JH, Chuang EY, Shun CT, Ni YH, Xavier RJ, Podolsky DK, Yen JJY, Wong JM
Inflamm Bowel Dis. 2017;:ePub - PMID: 28922251

Human genetic variation and the gut microbiome in disease.

Hall AB, Tolonen AC, Xavier RJ
Nat Rev Genet. 2017;18(11):690-699 - PMID: 28824167 - DOI: 10.1038/nrg.2017.63

Erratum: E3 Ubiquitin ligase ZNRF4 negatively regulates NOD2 signalling and induces tolerance to MDP.

Bist P, Cheong WS, Ng A, Dikshit N, Kim BH, Pulloor NK, Khameneh HJ, Hedl M, Shenoy AR, Balamuralidhar V, Malik NBA, Hong M, Neutzner A, Chin KC, Kobayashi KS, Bertoletti A, Mortellaro A, Abraham C, MacMicking JD, Xavier RJ, Sukumaran B
Nat Commun. 2017;8:16141 - PMID: 28820178 - PMCID: PMC5562926 - DOI: 10.1038/ncomms16141

Small-molecule studies identify CDK8 as a regulator of IL-10 in myeloid cells.

Johannessen L, Sundberg TB, O'Connell DJ, Kolde R, Berstler J, Billings KJ, Khor B, Seashore-Ludlow B, Fassl A, Russell CN, Latorre IJ, Jiang B, Graham DB, Perez JR, Sicinski P, Phillips AJ, Schreiber SL, Gray NS, Shamji AF, Xavier RJ
Nat Chem Biol. 2017;13(10):1102-1108 - PMID: 28805801 - PMCID: PMC5693369 - DOI: 10.1038/nchembio.2458

NIH Centers for Accelerated Innovations Program: principles, practices, successes and challenges.

Antman EM, Di Corleto PE, Freeman MW, Ganz T, Golan DE, Kitterman R, Loscalzo J, Low M, McKenna E, O'Connor AC, Palazzolo M, Parrish J, Reizes O, Ross RS, Vaughan C, Vince DG, Watts L, NIH Centers for Accelerated Innovations
Nat Rev Drug Discov. 2017;16(10):663-664 - PMID: 28775338 - PMCID: PMC5963257 - DOI: 10.1038/nrd.2017.131

Paneth cells secrete lysozyme via secretory autophagy during bacterial infection of the intestine.

Bel S, Pendse M, Wang Y, Li Y, Ruhn KA, Hassell B, Leal T, Winter SE, Xavier RJ, Hooper LV
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Burn-induced muscle metabolic derangements and mitochondrial dysfunction are associated with activation of HIF-1α and mTORC1: Role of protein farnesylation.

Nakazawa H, Ikeda K, Shinozaki S, Kobayashi M, Ikegami Y, Fu M, Nakamura T, Yasuhara S, Yu YM, Martyn JAJ, Tompkins RG, Shimokado K, Yorozu T, Ito H, Inoue S, Kaneki M
Sci Rep. 2017;7(1):6618 - PMID: 28747716 - PMCID: PMC5529411 - DOI: 10.1038/s41598-017-07011-3

Nucleic Acid Extraction from Synthetic Mars Analog Soils for in situ Life Detection.

Mojarro A, Ruvkun G, Zuber MT, Carr CE
Astrobiology. 2017;17(8):747-760 - PMID: 28704064 - PMCID: PMC5567878 - DOI: 10.1089/ast.2016.1535

UV-light-driven prebiotic synthesis of iron-sulfur clusters.

Bonfio C, Valer L, Scintilla S, Shah S, Evans DJ, Jin L, Szostak JW, Sasselov DD, Sutherland JD, Mansy SS
Nat Chem. 2017;9(12):1229-1234 - PMID: 29168482 - PMCID: PMC5808832 - DOI: 10.1038/nchem.2817

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children.

Zhao G, Vatanen T, Droit L, Park A, Kostic AD, Poon TW, Vlamakis H, Siljander H, Härkönen T, Hämäläinen AM, Peet A, Tillmann V, Ilonen J, Wang D, Knip M, Xavier RJ, Virgin HW
Proc Natl Acad Sci U S A. 2017;114(30):E6166-E6175 - PMID: 28696303 - PMCID: PMC5544325 - DOI: 10.1073/pnas.1706359114

A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase.

Wellington S, Nag PP, Michalska K, Johnston SE, Jedrzejczak RP, Kaushik VK, Clatworthy AE, Siddiqi N, McCarren P, Bajrami B, Maltseva NI, Combs S, Fisher SL, Joachimiak A, Schreiber SL, Hung DT
Nat Chem Biol. 2017;13(9):943-950 - PMID: 28671682 - DOI: 10.1038/nchembio.2420

Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex.

Zhang W, Tam CP, Walton T, Fahrenbach AC, Birrane G, Szostak JW
Proc Natl Acad Sci U S A. 2017;114(29):7659-7664 - PMID: 28673998 - PMCID: PMC5530681 - DOI: 10.1073/pnas.1704006114

Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation.

Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW, Heim CE, Krastel P, Schmitt EK, Omar AS, Creasey EA, Garner AL, Mohammadi S, O'Connell DJ, Abubucker S, Arthur TD, Franzosa EA, Huttenhower C, Murphy LO, Haiser HJ, Vlamakis H, Porter JA, Xavier RJ
Cell Host Microbe. 2017;22(1):25-37.e6 - PMID: 28704649 - PMCID: PMC5672633 - DOI: 10.1016/j.chom.2017.06.007

Fine-mapping inflammatory bowel disease loci to single-variant resolution.

Huang H, Fang M, Jostins L, Umićević Mirkov M, Boucher G, Anderson CA, Andersen V, Cleynen I, Cortes A, Crins F, D'Amato M, Deffontaine V, Dmitrieva J, Docampo E, Elansary M, Farh KK, Franke A, Gori AS, Goyette P, Halfvarson J, Haritunians T, Knight J, Lawrance IC, Lees CW, Louis E, Mariman R, Meuwissen T, Mni M, Momozawa Y, Parkes M, Spain SL, Théâtre E, Trynka G, Satsangi J, van Sommeren S, Vermeire S, Xavier RJ, International Inflammatory Bowel Disease Genetics Consortium, Weersma RK, Due ...
Nature. 2017;547(7662):173-178 - PMID: 28658209 - PMCID: PMC5511510 - DOI: 10.1038/nature22969

E3 Ubiquitin ligase ZNRF4 negatively regulates NOD2 signalling and induces tolerance to MDP.

Bist P, Cheong WS, Ng A, Dikshit N, Kim BH, Pulloor NK, Khameneh HJ, Hedl M, Shenoy AR, Balamuralidhar V, Malik NBA, Hong M, Neutzner A, Chin KC, Kobayashi KS, Bertoletti A, Mortellaro A, Abraham C, MacMicking JD, Xavier RJ, Sukumaran B
Nat Commun. 2017;8:15865 - PMID: 28656966 - PMCID: PMC5493756 - DOI: 10.1038/ncomms15865

Characterization of a Francisella tularensis-Caenorhabditis elegans pathosystem for the evaluation of therapeutic compounds.

Jayamani E, Tharmalingam N, Rajamuthiah R, Coleman JJ, Kim W, Okoli I, Hernandez AM, Lee K, Nau GJ, Ausubel FM, Mylonakis E
Antimicrob Agents Chemother. 2017;61(9):ePub - PMID: 28652232 - PMCID: PMC5571314 - DOI: 10.1128/AAC.00310-17

Common and Potentially Prebiotic Origin for Precursors of Nucleotide Synthesis and Activation.

Fahrenbach AC, Giurgiu C, Tam CP, Li L, Hongo Y, Aono M, Szostak JW
J Am Chem Soc. 2017;139(26):8780-8783 - PMID: 28640999 - PMCID: PMC6326526 - DOI: 10.1021/jacs.7b01562

Dissecting the human microbiome with single-cell genomics.

Tolonen AC, Xavier RJ
Genome Med. 2017;9(1):56 - PMID: 28615076 - PMCID: PMC5471897 - DOI: 10.1186/s13073-017-0448-7

Genome editing of factor X in zebrafish reveals unexpected tolerance of severe defects in the common pathway.

Hu Z, Liu Y, Huarng MC, Menegatti M, Reyon D, Rost MS, Norris ZG, Richter CE, Stapleton AN, Chi NC, Peyvandi F, Joung JK, Shavit JA
Blood. 2017;130(5):666-676 - PMID: 28576875 - PMCID: PMC5542852 - DOI: 10.1182/blood-2017-02-765206

Selective Induction of Homeostatic Th17 Cells in the Murine Intestine by Cholera Toxin Interacting with the Microbiota.

Zhao Q, Harbour SN, Kolde R, Latorre IJ, Tun HM, Schoeb TR, Turner H, Moon JJ, Khafipour E, Xavier RJ, Weaver CT, Elson CO
J Immunol. 2017;199(1):312-322 - PMID: 28539431 - PMCID: PMC5539960 - DOI: 10.4049/jimmunol.1700171

Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides.

Stairs S, Nikmal A, Bucar DK, Zheng SL, Szostak JW, Powner MW
Nat Commun. 2017;8:15270 - PMID: 28524845 - PMCID: PMC5454461 - DOI: 10.1038/ncomms15270

Adult-onset, chronic, cyclic thrombocytopenia in a Rhesus macaque (Macaca mulatta) after dengue virus vaccination and viral challenge.

Frydman GH, Metcalf Pate KA, Marini RP, de Laforcade AM, Bosch I, Bakthavatchalu V, Muthupalani S, Swennes AG, Lyons CE, Tompkins RG, Fox JG
Vet Clin Pathol. 2017;46(2):238-247 - PMID: 28518476 - PMCID: PMC5977396 - DOI: 10.1111/vcp.12497

The Narrow Road to the Deep Past.

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Angew Chem Int Ed Engl. 2017;56(37):11037-11043 - PMID: 28514493 - DOI: 10.1002/anie.201704048

Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence.

Barczak AK, Avraham R, Singh S, Luo SS, Zhang WR, Bray MA, Hinman AE, Thompson M, Nietupski RM, Golas A, Montgomery P, Fitzgerald M, Smith RS, White DW, Tischler AD, Carpenter AE, Hung DT
PLoS Pathog. 2017;13(5):e1006363 - PMID: 28505176 - PMCID: PMC5444860 - DOI: 10.1371/journal.ppat.1006363

Epitope-specific immunotherapy targeting CD4-positive T cells in coeliac disease: two randomised, double-blind, placebo-controlled phase 1 studies.

Goel G, King T, Daveson AJ, Andrews JM, Krishnarajah J, Krause R, Brown GJE, Fogel R, Barish CF, Epstein R, Kinney TP, Miner PB, Tye-Din JA, Girardin A, Taavela J, Popp A, Sidney J, Mäki M, Goldstein KE, Griffin PH, Wang S, Dzuris JL, Williams LJ, Sette A, Xavier RJ, Sollid LM, Jabri B, Anderson RP
Lancet Gastroenterol Hepatol. 2017;2(7):479-493 - PMID: 28506538 - PMCID: PMC5676538 - DOI: 10.1016/S2468-1253(17)30110-3

Discovery of nitrate-CPK-NLP signalling in central nutrient-growth networks.

Liu KH, Niu Y, Konishi M, Wu Y, Du H, Sun Chung H, Li L, Boudsocq M, McCormack M, Maekawa S, Ishida T, Zhang C, Shokat K, Yanagisawa S, Sheen J
Nature. 2017;545(7654):311-316 - PMID: 28489820 - PMCID: PMC5823009 - DOI: 10.1038/nature22077

CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets.

Tsai SQ, Nguyen NT, Malagon-Lopez J, Topkar VV, Aryee MJ, Joung JK
Nat Methods. 2017;14(6):607-614 - PMID: 28459458 - PMCID: PMC5924695 - DOI: 10.1038/nmeth.4278

Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases.

Ananthakrishnan AN, Luo C, Yajnik V, Khalili H, Garber JJ, Stevens BW, Cleland T, Xavier RJ
Cell Host Microbe. 2017;21(5):603-610.e3 - PMID: 28494241 - PMCID: PMC5705050 - DOI: 10.1016/j.chom.2017.04.010

Nucleic acid detection with CRISPR-Cas13a/C2c2.

Gootenberg JS, Abudayyeh OO, Lee JW, Essletzbichler P, Dy AJ, Joung J, Verdine V, Donghia N, Daringer NM, Freije CA, Myhrvold C, Bhattacharyya RP, Livny J, Regev A, Koonin EV, Hung DT, Sabeti PC, Collins JJ, Zhang F
Science. 2017;356(6336):438-442 - PMID: 28408723 - PMCID: PMC5526198 - DOI: 10.1126/science.aam9321

Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease.

Bouziat R, Hinterleitner R, Brown JJ, Stencel-Baerenwald JE, Ikizler M, Mayassi T, Meisel M, Kim SM, Discepolo V, Pruijssers AJ, Ernest JD, Iskarpatyoti JA, Costes LM, Lawrence I, Palanski BA, Varma M, Zurenski MA, Khomandiak S, McAllister N, Aravamudhan P, Boehme KW, Hu F, Samsom JN, Reinecker HC, Kupfer SS, Guandalini S, Semrad CE, Abadie V, Khosla C, Barreiro LB, Xavier RJ, Ng A, Dermody TS, Jabri B
Science. 2017;356(6333):44-50 - PMID: 28386004 - PMCID: PMC5506690 - DOI: 10.1126/science.aah5298

Camptothecin resistance is determined by the regulation of topoisomerase I degradation mediated by ubiquitin proteasome pathway.

Ando K, Shah AK, Sachdev V, Kleinstiver BP, Taylor-Parker J, Welch MM, Hu Y, Salgia R, White FM, Parvin JD, Ozonoff A, Rameh LE, Joung JK, Bharti AK
Oncotarget. 2017;8(27):43733-43751 - PMID: 28415827 - PMCID: PMC5546437 - DOI: 10.18632/oncotarget.16376

An Alpha7 Nicotinic Acetylcholine Receptor Agonist (GTS-21) Promotes C2C12 Myonuclear Accretion in Association with Release of Interleukin-6 (IL-6) and Improves Survival in Burned Mice.

Khan MA, Khan MF, Kashiwagi S, Kem WR, Yasuhara S, Kaneki M, Tompkins RG, Martyn JA
Shock. 2017;48(2):227-235 - PMID: 28282360 - PMCID: PMC5511057 - DOI: 10.1097/SHK.0000000000000849

Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140.

Mehta S, Cronkite DA, Basavappa M, Saunders TL, Adiliaghdam F, Amatullah H, Morrison SA, Pagan JD, Anthony RM, Tonnerre P, Lauer GM, Lee JC, Digumarthi S, Pantano L, Ho Sui SJ, Ji F, Sadreyev R, Zhou C, Mullen AC, Kumar V, Li Y, Wijmenga C, Xavier RJ, Means TK, Jeffrey KL
Sci Immunol. 2017;2(9):ePub - PMID: 28783698 - PMCID: PMC5549562 - DOI: 10.1126/sciimmunol.aag3160

Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study.

Kugathasan S, Denson LA, Walters TD, Kim MO, Marigorta UM, Schirmer M, Mondal K, Liu C, Griffiths A, Noe JD, Crandall WV, Snapper S, Rabizadeh S, Rosh JR, Shapiro JM, Guthery S, Mack DR, Kellermayer R, Kappelman MD, Steiner S, Moulton DE, Keljo D, Cohen S, Oliva-Hemker M, Heyman MB, Otley AR, Baker SS, Evans JS, Kirschner BS, Patel AS, Ziring D, Trapnell BC, Sylvester FA, Stephens MC, Baldassano RN, Markowitz JF, Cho J, Xavier RJ, Huttenhower C, Aronow BJ, Gibson G, Hyams JS, Dubinsky MC
Lancet. 2017;389(10080):1710-1718 - PMID: 28259484 - PMCID: PMC5719489 - DOI: 10.1016/S0140-6736(17)30317-3

US immigration order strikes against biotech.

Levin JM, Holtzman SH, Maraganore J, Hastings PJ, Cohen R, Dahiyat B, Adams J, Adams C, Ahrens B, Albers J, Aspinall MG, Audia JE, Babler M, Barrett P, Barry Z, Bermingham N, Bloch S, Blum RI, Bolno PB, Bonney MW, Booth B, Bradbury DM, Brauer SK, Byers B, Cagnoni PJ, Cali BM, Ciechanover I, Clark C, Clayman MD, Cleland JL, Cobb P, Cooper R, Currie MG, Diekman J, Dobmeier EL, Doerfler D, Donley EL, Dunsire D, During M, Eckstein JW, Elenko E, Exter NA, Fleming JJ, Flesher GJ, Formela JF, Forre ...
Nat Biotechnol. 2017;35(3):204-206 - PMID: 28267733 - DOI: 10.1038/nbt.3824

A Microbiome Foundation for the Study of Crohn's Disease.

Gevers D, Kugathasan S, Knights D, Kostic AD, Knight R, Xavier RJ
Cell Host Microbe. 2017;21(3):301-304 - PMID: 28279336 - PMCID: PMC5684696 - DOI: 10.1016/j.chom.2017.02.012

Local and Systemic Changes Associated with Long-term, Percutaneous, Static Implantation of Titanium Alloys in Rhesus Macaques (Macaca mulatta).

Frydman GH, Marini RP, Bakthavatchalu V, Biddle KE, Muthupalani S, Vanderburg CR, Lai B, Bendapudi PK, Tompkins RG, Fox JG
Comp Med. 2017;67(2):165-175 - PMID: 28381317 - PMCID: PMC5402736

Corrigendum: SIKs control osteocyte responses to parathyroid hormone.

Wein MN, Liang Y, Goransson O, Sundberg TB, Wang J, Williams EA, O'Meara MJ, Govea N, Beqo B, Nishimori S, Nagano K, Brooks DJ, Martins JS, Corbin B, Anselmo A, Sadreyev R, Wu JY, Sakamoto K, Foretz M, Xavier RJ, Baron R, Bouxsein ML, Gardella TJ, Divieti-Pajevic P, Gray NS, Kronenberg HM
Nat Commun. 2017;8:14745 - PMID: 28224982 - PMCID: PMC5322529 - DOI: 10.1038/ncomms14745

Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment.

Gomez JE, Kaufmann-Malaga BB, Wivagg CN, Kim PB, Silvis MR, Renedo N, Ioerger TR, Ahmad R, Livny J, Fishbein S, Sacchettini JC, Carr SA, Hung DT
Elife. 2017;6:ePub - PMID: 28220755 - PMCID: PMC5319836 - DOI: 10.7554/eLife.20420

MAPK Assays in Arabidopsis MAMP-PRR Signal Transduction.

Chung HS, Sheen J
Methods Mol Biol. 2017;1578:155-166 - PMID: 28220422 - DOI: 10.1007/978-1-4939-6859-6_12

Enhanced Nonenzymatic RNA Copying with 2-Aminoimidazole Activated Nucleotides.

Li L, Prywes N, Tam CP, O'Flaherty DK, Lelyveld VS, Izgu EC, Pal A, Szostak JW
J Am Chem Soc. 2017;139(5):1810-1813 - PMID: 28117989 - PMCID: PMC6326525 - DOI: 10.1021/jacs.6b13148

iNOS as a Driver of Inflammation and Apoptosis in Mouse Skeletal Muscle after Burn Injury: Possible Involvement of Sirt1 S-Nitrosylation-Mediated Acetylation of p65 NF-?B and p53.

Nakazawa H, Chang K, Shinozaki S, Yasukawa T, Ishimaru K, Yasuhara S, Yu YM, Martyn JA, Tompkins RG, Shimokado K, Kaneki M
PLoS One. 2017;12(1):e0170391 - PMID: 28099528 - PMCID: PMC5242494 - DOI: 10.1371/journal.pone.0170391

Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks.

Cerqueira GC, Earl AM, Ernst CM, Grad YH, Dekker JP, Feldgarden M, Chapman SB, Reis-Cunha JL, Shea TP, Young S, Zeng Q, Delaney ML, Kim D, Peterson EM, O'Brien TF, Ferraro MJ, Hooper DC, Huang SS, Kirby JE, Onderdonk AB, Birren BW, Hung DT, Cosimi LA, Wortman JR, Murphy CI, Hanage WP
Proc Natl Acad Sci U S A. 2017;114(5):1135-1140 - PMID: 28096418 - PMCID: PMC5293017 - DOI: 10.1073/pnas.1616248114

The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events.

Urbach JM, Ausubel FM
Proc Natl Acad Sci U S A. 2017;114(5):1063-1068 - PMID: 28096345 - PMCID: PMC5293065 - DOI: 10.1073/pnas.1619730114

ATP Binding Cassette Transporter ABCA7 Regulates NKT Cell Development and Function by Controlling CD1d Expression and Lipid Raft Content.

Nowyhed HN, Chandra S, Kiosses W, Marcovecchio P, Andary F, Zhao M, Fitzgerald ML, Kronenberg M, Hedrick CC
Sci Rep. 2017;7:40273 - PMID: 28091533 - PMCID: PMC5238393 - DOI: 10.1038/srep40273

Downstream Oligonucleotides Strongly Enhance the Affinity of GMP to RNA Primer-Template Complexes.

Tam CP, Fahrenbach AC, Björkbom A, Prywes N, Izgu EC, Szostak JW
J Am Chem Soc. 2017;139(2):571-574 - PMID: 28055190 - DOI: 10.1021/jacs.6b09760

Influence of maternal breast milk ingestion on acquisition of the intestinal microbiome in preterm infants.

Gregory KE, Samuel BS, Houghteling P, Shan G, Ausubel FM, Sadreyev RI, Walker WA
Microbiome. 2016;4(1):68 - PMID: 28034306 - PMCID: PMC5200970 - DOI: 10.1186/s40168-016-0214-x

The Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis and Anti-tuberculous Host Defense.

Franco LH, Nair VR, Scharn CR, Xavier RJ, Torrealba JR, Shiloh MU, Levine B
Cell Host Microbe. 2016;21(1):59-72 - PMID: 28017659 - PMCID: PMC5699477 - DOI: 10.1016/j.chom.2016.11.002

N-Carboxyanhydride-Mediated Fatty Acylation of Amino Acids and Peptides for Functionalization of Protocell Membranes.

Izgu EC, Björkbom A, Kamat NP, Lelyveld VS, Zhang W, Jia TZ, Szostak JW
J Am Chem Soc. 2016;138(51):16669-16676 - PMID: 27959544 - DOI: 10.1021/jacs.6b08801

Tribbles ortholog NIPI-3 and bZIP transcription factor CEBP-1 regulate a Caenorhabditis elegans intestinal immune surveillance pathway.

McEwan DL, Feinbaum RL, Stroustrup N, Haas W, Conery AL, Anselmo A, Sadreyev R, Ausubel FM
BMC Biol. 2016;14(1):105 - PMID: 27927200 - PMCID: PMC5143455 - DOI: 10.1186/s12915-016-0334-6

DNA-binding Specificity Is a Major Determinant of the Activity and Toxicity of Zinc-finger Nucleases.

Cornu TI, Thibodeau-Beganny S, Guhl E, Alwin S, Eichtinger M, Joung JK, Cathomen T
Mol Ther. 2016;16(2):352-358 - PMID: 28178540 - DOI: 10.1038/sj.mt.6300357

Genome Editing Technologies: Defining a Path to Clinic: Genomic Editing: Establishing Preclinical Toxicology Standards, Bethesda, Maryland 10 June 2014.

Corrigan-Curay J, O'Reilly M, Kohn DB, Cannon PM, Bao G, Bushman FD, Carroll D, Cathomen T, Joung JK, Roth D, Sadelain M, Scharenberg AM, von Kalle C, Zhang F, Jambou R, Rosenthal E, Hassani M, Singh A, Porteus MH
Mol Ther. 2016;23(5):796-806 - PMID: 28142000

Hold the Pendulum: Rates of Acute Kidney Injury are Increased in Patients Who Receive Resuscitation Volumes Less than Predicted by the Parkland Equation.

Mason SA, Nathens AB, Finnerty CC, Gamelli RL, Gibran NS, Arnoldo BD, Tompkins RG, Herndon DN, Jeschke MG,
Ann Surg. 2016;264(6):1142-1147 - PMID: 27828823 - PMCID: PMC5111808 - DOI: 10.1097/SLA.0000000000001615

The Role of the Histone Methyltransferase Enhancer of Zeste Homolog 2 (EZH2) in the Pathobiological Mechanisms Underlying Inflammatory Bowel Disease (IBD).

Sarmento OF, Svingen PA, Xiong Y, Sun Z, Bamidele AO, Mathison AJ, Smyrk TC, Nair AA, Gonzalez MM, Sagstetter MR, Baheti S, McGovern DP, Friton JJ, Papadakis KA, Gautam G, Xavier RJ, Urrutia RA, Faubion WA
J Biol Chem. 2016;292(2):706-722 - PMID: 27909059 - PMCID: PMC5241744 - DOI: 10.1074/jbc.M116.749663

The Csk-Associated Adaptor PAG Inhibits Effector T Cell Activation in Cooperation with Phosphatase PTPN22 and Dok Adaptors.

Davidson D, Zhong MC, Pandolfi PP, Bolland S, Xavier RJ, Seed B, Li X, Gu H, Veillette A
Cell Rep. 2016;17(10):2776-2788 - PMID: 27926878 - PMCID: PMC5656005 - DOI: 10.1016/j.celrep.2016.11.035

TMEM258 Is a Component of the Oligosaccharyltransferase Complex Controlling ER Stress and Intestinal Inflammation.

Graham DB, Lefkovith A, Deelen P, de Klein N, Varma M, Boroughs A, Desch AN, Ng AC, Guzman G, Schenone M, Petersen CP, Bhan AK, Rivas MA, Daly MJ, Carr SA, Wijmenga C, Xavier RJ
Cell Rep. 2016;17(11):2955-2965 - PMID: 27974209 - PMCID: PMC5661940 - DOI: 10.1016/j.celrep.2016.11.042

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LA, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ
Cell. 2016;167(7):1897 - PMID: 27984736 - DOI: 10.1016/j.cell.2016.11.046

Visceral Adiposity, Genetic Susceptibility, and Risk of Complications Among Individuals with Crohn's Disease.

Van Der Sloot KW, Joshi AD, Bellavance DR, Gilpin KK, Stewart KO, Lochhead P, Garber JJ, Giallourakis C, Yajnik V, Ananthakrishnan AN, Alizadeh BZ, Xavier RJ, Khalili H
Inflamm Bowel Dis. 2016;23(1):82-88 - PMID: 27893544 - PMCID: PMC5177457 - DOI: 10.1097/MIB.0000000000000978

Erratum to: Vedolizumab Therapy Is Associated with an Improvement in Sleep Quality and Mood in Inflammatory Bowel Diseases.

Stevens BW, Borren NZ, Velonias G, Conway G, Cleland T, Andrews E, Khalili H, Garber JJ, Xavier RJ, Yajnik V, Ananthakrishnan AN
Dig Dis Sci. 2016;62(2):552 - PMID: 27864657 - DOI: 10.1007/s10620-016-4380-2

Glutaminolysis and Fumarate Accumulation Integrate Immunometabolic and Epigenetic Programs in Trained Immunity.

Arts RJ, Novakovic B, Ter Horst R, Carvalho A, Bekkering S, Lachmandas E, Rodrigues F, Silvestre R, Cheng SC, Wang SY, Habibi E, Gonçalves LG, Mesquita I, Cunha C, van Laarhoven A, van de Veerdonk FL, Williams DL, van der Meer JW, Logie C, O'Neill LA, Dinarello CA, Riksen NP, van Crevel R, Clish C, Notebaart RA, Joosten LA, Stunnenberg HG, Xavier RJ, Netea MG
Cell Metab. 2016;24(6):807-819 - PMID: 27866838 - PMCID: PMC5742541 - DOI: 10.1016/j.cmet.2016.10.008

Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits.

Aguirre-Gamboa R, Joosten I, Urbano PC, van der Molen RG, van Rijssen E, van Cranenbroek B, Oosting M, Smeekens S, Jaeger M, Zorro M, Withoff S, van Herwaarden AE, Sweep FC, Netea RT, Swertz MA, Franke L, Xavier RJ, Joosten LA, Netea MG, Wijmenga C, Kumar V, Li Y, Koenen HJ
Cell Rep. 2016;17(9):2474-2487 - PMID: 27818087 - PMCID: PMC5130901 - DOI: 10.1016/j.celrep.2016.10.053

Unusual Base-Pairing Interactions in Monomer-Template Complexes.

Zhang W, Tam CP, Wang J, Szostak JW
ACS Cent Sci. 2016;2(12):916-926 - PMID: 28058281 - PMCID: PMC5200924 - DOI: 10.1021/acscentsci.6b00278

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LA, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ
Cell. 2016;167(4):1125-1136.e8 - PMID: 27814509 - PMCID: PMC5131922 - DOI: 10.1016/j.cell.2016.10.020

Host and Environmental Factors Influencing Individual Human Cytokine Responses.

Ter Horst R, Jaeger M, Smeekens SP, Oosting M, Swertz MA, Li Y, Kumar V, Diavatopoulos DA, Jansen AF, Lemmers H, Toenhake-Dijkstra H, van Herwaarden AE, Janssen M, van der Molen RG, Joosten I, Sweep FC, Smit JW, Netea-Maier RT, Koenders MM, Xavier RJ, van der Meer JW, Dinarello CA, Pavelka N, Wijmenga C, Notebaart RA, Joosten LA, Netea MG
Cell. 2016;167(4):1111-1124.e13 - PMID: 27814508 - PMCID: PMC5787854 - DOI: 10.1016/j.cell.2016.10.018

A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans.

Li Y, Oosting M, Smeekens SP, Jaeger M, Aguirre-Gamboa R, Le KT, Deelen P, Ricaño-Ponce I, Schoffelen T, Jansen AF, Swertz MA, Withoff S, van de Vosse E, van Deuren M, van de Veerdonk F, Zhernakova A, van der Meer JW, Xavier RJ, Franke L, Joosten LA, Wijmenga C, Kumar V, Netea MG
Cell. 2016;167(4):1099-1110.e14 - PMID: 27814507 - DOI: 10.1016/j.cell.2016.10.017

RNF166 Determines Recruitment of Adaptor Proteins during Antibacterial Autophagy.

Heath RJ, Goel G, Baxt LA, Rush JS, Mohanan V, Paulus GL, Jani V, Lassen KG, Xavier RJ
Cell Rep. 2016;17(9):2183-2194 - PMID: 27880896 - PMCID: PMC5192565 - DOI: 10.1016/j.celrep.2016.11.005

Vedolizumab Therapy Is Associated with an Improvement in Sleep Quality and Mood in Inflammatory Bowel Diseases.

Stevens BW, Borren NZ, Velonias G, Conway G, Cleland T, Andrews E, Khalili H, Garber JG, Xavier RJ, Yajnik V, Ananthakrishnan AN
Dig Dis Sci. 2016;62(1):197-206 - PMID: 27796768 - PMCID: PMC5218976 - DOI: 10.1007/s10620-016-4356-2

KERIS: kaleidoscope of gene responses to inflammation between species.

Li P, Tompkins RG, Xiao W,
Nucleic Acids Res. 2016;45(D1):D908-D914 - PMID: 27789704 - PMCID: PMC5210651 - DOI: 10.1093/nar/gkw974

SIKs control osteocyte responses to parathyroid hormone.

Wein MN, Liang Y, Goransson O, Sundberg TB, Wang J, Williams EA, O'Meara MJ, Govea N, Beqo B, Nishimori S, Nagano K, Brooks DJ, Martins JS, Corbin B, Anselmo A, Sadreyev R, Wu JY, Sakamoto K, Foretz M, Xavier RJ, Baron R, Bouxsein ML, Gardella TJ, Divieti-Pajevic P, Gray NS, Kronenberg HM
Nat Commun. 2016;7:13176 - PMID: 27759007 - PMCID: PMC5075806 - DOI: 10.1038/ncomms13176

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease.

Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RW, Huttenhower C, Dijkstra G, Xavier RJ, Festen EA, Wijmenga C, Zhernakova A, Weersma RK
Gut. 2016;67(1):108-119 - PMID: 27802154 - PMCID: PMC5699972 - DOI: 10.1136/gutjnl-2016-312135

TNF-?/IL-10 Ratio Correlates with Burn Severity and May Serve as a Risk Predictor of Increased Susceptibility to Infections.

Tsurumi A, Que YA, Ryan CM, Tompkins RG, Rahme LG
Front Public Health. 2016;4:216 - PMID: 27761434 - PMCID: PMC5050217 - DOI: 10.3389/fpubh.2016.00216

Corrigendum: Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi.

Li Y, Oosting M, Deelen P, Ricaño-Ponce I, Smeekens S, Jaeger M, Matzaraki V, Swertz MA, Xavier RJ, Franke L, Wijmenga C, Joosten LA, Kumar V, Netea MG
Nat Med. 2016;22(10):1192 - PMID: 27711068 - DOI: 10.1038/nm1016-1192b

The metabolic stress response to burn trauma: current understanding and therapies.

Porter C, Tompkins RG, Finnerty CC, Sidossis LS, Suman OE, Herndon DN
Lancet. 2016;388(10052):1417-1426 - PMID: 27707498 - PMCID: PMC5753602 - DOI: 10.1016/S0140-6736(16)31469-6

A perspective on single cell behavior during infection.

Avraham R, Hung DT
Gut Microbes. 2016;7(6):0 - PMID: 27658058 - PMCID: PMC5153611 - DOI: 10.1080/19490976.2016.1239001

Succinate Dehydrogenase Supports Metabolic Repurposing of Mitochondria to Drive Inflammatory Macrophages.

Mills EL, Kelly B, Logan A, Costa AS, Varma M, Bryant CE, Tourlomousis P, Däbritz JH, Gottlieb E, Latorre I, Corr SC, McManus G, Ryan D, Jacobs HT, Szibor M, Xavier RJ, Braun T, Frezza C, Murphy MP, O'Neill LA
Cell. 2016;167(2):457-470.e13 - PMID: 27667687 - PMCID: PMC5863951 - DOI: 10.1016/j.cell.2016.08.064

Changes in neutrophil migration patterns upon contact with platelets in a microfluidic assay.

Frydman GH, Le A, Ellett F, Jorgensen J, Fox JG, Tompkins RG, Irimia D
J Leukoc Biol. 2016;101(3):797-806 - PMID: 27630219 - PMCID: PMC5295852 - DOI: 10.1189/jlb.1TA1115-517RR

Erratum: A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.

Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC, , , MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Fä ...
Nat Commun. 2016;7:12869 - PMID: 27619887 - PMCID: PMC5027274 - DOI: 10.1038/ncomms12869

Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease.

Vaughn BP, Vatanen T, Allegretti JR, Bai A, Xavier RJ, Korzenik J, Gevers D, Ting A, Robson SC, Moss AC
Inflamm Bowel Dis. 2016;22(9):2182-90 - PMID: 27542133 - PMCID: PMC4995064 - DOI: 10.1097/MIB.0000000000000893

Effect of terminal 3'-hydroxymethyl modification of an RNA primer on nonenzymatic primer extension.

Pal A, Das RS, Zhang W, Lang M, McLaughlin LW, Szostak JW
Chem Commun (Camb). 2016;52(80):11905-11907 - PMID: 27722518 - DOI: 10.1039/c6cc06925h

On the origin of life.

Szostak JW
Medicina (B Aires). 2016;76(4):199-203 - PMID: 27576276

Genomic analysis of the evolution of fluoroquinolone resistance in Mycobacterium tuberculosis prior to tuberculosis diagnosis.

Zhang D, Gomez JE, Chien JY, Haseley N, Desjardins CA, Earl AM, Hsueh PR, Hung DT
Antimicrob Agents Chemother. 2016;60(11):6600-6608 - PMID: 27572408 - PMCID: PMC5075065 - DOI: 10.1128/AAC.00664-16

A highly reactive imidazolium-bridged dinucleotide intermediate in nonenzymatic RNA primer extension.

Walton T, Szostak JW
J Am Chem Soc. 2016;138(36):11996-2002 - PMID: 27552367 - PMCID: PMC6326528 - DOI: 10.1021/jacs.6b07977

Characterization of candidate genes in inflammatory bowel disease-associated risk loci.

Peloquin JM, Goel G, Kong L, Huang H, Haritunians T, Sartor RB, Daly MJ, Newberry RD, McGovern DP, Yajnik V, Lira SA, Xavier RJ
JCI Insight. 2016;1(13):e87899 - PMID: 27668286 - PMCID: PMC5033062 - DOI: 10.1172/jci.insight.87899

Proteasome dysfunction triggers activation of SKN-1A/Nrf1 by the aspartic protease DDI-1.

Lehrbach NJ, Ruvkun G
Elife. 2016;5:ePub - PMID: 27528192 - PMCID: PMC4987142 - DOI: 10.7554/eLife.17721

Prevention of Burn-Induced Inflammatory Responses and Muscle Wasting By GTS-21, A Specific Agonist for ?7 Nicotinic Acetylcholine Receptors.

Kashiwagi S, Khan MA, Yasuhara S, Goto T, Tompkins RG, Kaneki M, Martyn JA
Shock. 2016;47(1):61-69 - PMID: 27529131 - PMCID: PMC5167674 - DOI: 10.1097/SHK.0000000000000729

A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.

Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC, , , MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Fä ...
Nat Commun. 2016;7:12342 - PMID: 27503255 - PMCID: PMC4980482 - DOI: 10.1038/ncomms12342

Understanding human immune function using the resources from the Human Functional Genomics Project.

Netea MG, Joosten LA, Li Y, Kumar V, Oosting M, Smeekens S, Jaeger M, Ter Horst R, Schirmer M, Vlamakis H, Notebaart R, Pavelka N, Aguirre-Gamboa RR, Swertz MA, Tunjungputri RN, van de Heijden W, Franzosa EA, Ng A, Graham D, Lassen K, Schraa K, Netea-Maier R, Smit J, de Mast Q, van de Veerdonk F, Kullberg BJ, Tack C, van de Munckhof I, Rutten J, van der Graaf J, Franke L, Hofker M, Jonkers I, Platteel M, Maatman A, Fu J, Zhernakova A, van der Meer JW, Dinarello CA, van der Ven A, Huttenhouwe ...
Nat Med. 2016;22(8):831-3 - PMID: 27490433 - DOI: 10.1038/nm.4140

A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition.

Li D, Achkar JP, Haritunians T, Jacobs JP, Hui KY, D'Amato M, Brand S, Radford-Smith G, Halfvarson J, Niess JH, Kugathasan S, Büning C, Schumm LP, Klei L, Ananthakrishnan A, Aumais G, Baidoo L, Dubinsky M, Fiocchi C, Glas J, Milgrom R, Proctor DD, Regueiro M, Simms LA, Stempak JM, Targan SR, Törkvist L, Sharma Y, Devlin B, Borneman J, Hakonarson H, Xavier RJ, Daly M, Brant SR, Rioux JD, Silverberg MS, Cho JH, Braun J, McGovern DP, Duerr RH
Gastroenterology. 2016;151(4):724-32 - PMID: 27492617 - PMCID: PMC5037008 - DOI: 10.1053/j.gastro.2016.06.051

Accelerating global innovation to address antibacterial resistance: introducing CARB-X.

Outterson K, Rex JH, Jinks T, Jackson P, Hallinan J, Karp S, Hung DT, Franceschi F, Merkeley T, Houchens C, Dixon DM, Kurilla MG, Aurigemma R, Larsen J
Nat Rev Drug Discov. 2016;15(9):589-590 - PMID: 27469032 - DOI: 10.1038/nrd.2016.155

A highly multiplexed and sensitive RNA-seq protocol for simultaneous analysis of host and pathogen transcriptomes.

Avraham R, Haseley N, Fan A, Bloom-Ackermann Z, Livny J, Hung DT
Nat Protoc. 2016;11(8):1477-91 - PMID: 27442864 - DOI: 10.1038/nprot.2016.090

Dynamic and diverse sugar signaling.

Li L, Sheen J
Curr Opin Plant Biol. 2016;33:116-125 - PMID: 27423125 - PMCID: PMC5050104 - DOI: 10.1016/j.pbi.2016.06.018

Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease.

Shaw KA, Bertha M, Hofmekler T, Chopra P, Vatanen T, Srivatsa A, Prince J, Kumar A, Sauer C, Zwick ME, Satten GA, Kostic AD, Mulle JG, Xavier RJ, Kugathasan S
Genome Med. 2016;8(1):75 - PMID: 27412252 - PMCID: PMC4944441 - DOI: 10.1186/s13073-016-0331-y

Molecular Imaging of Smoke-Induced Changes in Nuclear Factor-Kappa B Expression in Murine Tissues Including the Lung.

Syrkina O, Hales CH, Bonab AA, Hamrahi V, Paul K, Jung WJ, Tompkins RG, Fischman AJ, Carter EA
J Burn Care Res. 2016;37(6):335-342 - PMID: 27437954 - DOI: 10.1097/BCR.0000000000000394

Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi.

Li Y, Oosting M, Deelen P, Ricaño-Ponce I, Smeekens S, Jaeger M, Matzaraki V, Swertz MA, Xavier RJ, Franke L, Wijmenga C, Joosten LA, Kumar V, Netea MG
Nat Med. 2016;22(8):952-960 - PMID: 27376574 - PMCID: PMC5084084 - DOI: 10.1038/nm.4139

Introduction to Gene Editing and Manipulation Using CRISPR/Cas9 Technology.

Newman M, Ausubel FM
Curr Protoc Mol Biol. 2016;115:31.4.1-6 - PMID: 27366890 - PMCID: PMC4963815 - DOI: 10.1002/cpmb.14

A microRNA program in the C. elegans hypodermis couples to intestinal mTORC2/PQM-1 signaling to modulate fat transport.

Dowen RH, Breen PC, Tullius T, Conery AL, Ruvkun G
Genes Dev. 2016;30(13):1515-28 - PMID: 27401555 - PMCID: PMC4949325 - DOI: 10.1101/gad.283895.116

Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62.

DeJesus R, Moretti F, McAllister G, Wang Z, Bergman P, Liu S, Frias E, Alford J, Reece-Hoyes JS, Lindeman A, Kelliher J, Russ C, Knehr J, Carbone W, Beibel M, Roma G, Ng A, Tallarico JA, Porter JA, Xavier RJ, Mickanin C, Murphy LO, Hoffman GR, Nyfeler B
Elife. 2016;5:ePub - PMID: 27351204 - PMCID: PMC4924995 - DOI: 10.7554/eLife.17290

Nonenzymatic copying of RNA templates containing all four letters is catalyzed by activated oligonucleotides.

Prywes N, Blain JC, Del Frate F, Szostak JW
Elife. 2016;5:ePub - PMID: 27351102 - PMCID: PMC4959843 - DOI: 10.7554/eLife.17756

Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells.

Kleinstiver BP, Tsai SQ, Prew MS, Nguyen NT, Welch MM, Lopez JM, McCaw ZR, Aryee MJ, Joung JK
Nat Biotechnol. 2016;34(8):869-874 - PMID: 27347757 - PMCID: PMC4980201 - DOI: 10.1038/nbt.3620

Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication.

Jia TZ, Fahrenbach AC, Kamat NP, Adamala KP, Szostak JW
Nat Chem. 2016;8(10):915-21 - PMID: 27657866 - PMCID: PMC5061144 - DOI: 10.1038/nchem.2551

Microbiota as Therapeutic Targets.

Xavier RJ
Dig Dis. 2016;34(5):558-65 - PMID: 27331403 - DOI: 10.1159/000445263

Caenorhabditis elegans responses to bacteria from its natural habitats.

Samuel BS, Rowedder H, Braendle C, Félix MA, Ruvkun G
Proc Natl Acad Sci U S A. 2016;113(27):E3941-9 - PMID: 27317746 - PMCID: PMC4941482 - DOI: 10.1073/pnas.1607183113

Baeyer-Villiger Monooxygenases EthA and MymA Are Required for Activation of Replicating and Non-replicating Mycobacterium tuberculosis Inhibitors.

Grant SS, Wellington S, Kawate T, Desjardins CA, Silvis MR, Wivagg C, Thompson M, Gordon K, Kazyanskaya E, Nietupski R, Haseley N, Iwase N, Earl AM, Fitzgerald M, Hung DT
Cell Chem Biol. 2016;23(6):666-77 - PMID: 27321573 - PMCID: PMC4920728 - DOI: 10.1016/j.chembiol.2016.05.011

Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks.

Zhou C, Elia AE, Naylor ML, Dephoure N, Ballif BA, Goel G, Xu Q, Ng A, Chou DM, Xavier RJ, Gygi SP, Elledge SJ
Proc Natl Acad Sci U S A. 2016;113(26):E3667-75 - PMID: 27298372 - PMCID: PMC4932963 - DOI: 10.1073/pnas.1602827113

The T300A Crohn's disease risk polymorphism impairs function of the WD40 domain of ATG16L1.

Boada-Romero E, Serramito-Gómez I, Sacristán MP, Boone DL, Xavier RJ, Pimentel-Muiños FX
Nat Commun. 2016;7:11821 - PMID: 27273576 - PMCID: PMC4899871 - DOI: 10.1038/ncomms11821

Genetic Coding Variant in GPR65 Alters Lysosomal pH and Links Lysosomal Dysfunction with Colitis Risk.

Lassen KG, McKenzie CI, Mari M, Murano T, Begun J, Baxt LA, Goel G, Villablanca EJ, Kuo SY, Huang H, Macia L, Bhan AK, Batten M, Daly MJ, Reggiori F, Mackay CR, Xavier RJ
Immunity. 2016;44(6):1392-1405 - PMID: 27287411 - PMCID: PMC4936415 - DOI: 10.1016/j.immuni.2016.05.007

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, , Xavier RJ
Cell. 2016;165(6):1551 - PMID: 27259157 - DOI: 10.1016/j.cell.2016.05.056

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.

Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M, , Xavier RJ
Sci Transl Med. 2016;8(343):343ra81 - PMID: 27306663 - PMCID: PMC5032909 - DOI: 10.1126/scitranslmed.aad0917

Isocitrate dehydrogenase mutations confer dasatinib hypersensitivity and SRC-dependence in intrahepatic cholangiocarcinoma.

Saha SK, Gordan JD, Kleinstiver BP, Vu P, Najem MS, Yeo JC, Shi L, Kato Y, Levin RS, Webber JT, Damon LJ, Egan RK, Greninger P, McDermott U, Garnett MJ, Jenkins RL, Rieger-Christ KM, Sullivan TB, Hezel AF, Liss AS, Mizukami Y, Goyal L, Ferrone CR, Zhu AX, Joung JK, Shokat KM, Benes CH, Bardeesy N
Cancer Discov. 2016;6(7):727-39 - PMID: 27231123 - PMCID: PMC5458737 - DOI: 10.1158/2159-8290.CD-15-1442

Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn's Disease.

Pedamallu CS, Bhatt AS, Bullman S, Fowler S, Freeman SS, Durand J, Jung J, Duke F, Manzo V, Cai D, Ananthakrishnan A, Ojesina AI, Ramachandran A, Gevers D, Xavier RJ, Bhan AK, Meyerson M, Yajnik V
Cell Mol Gastroenterol Hepatol. 2016;2(5):563-566.e5 - PMID: 28174737 - PMCID: PMC5042890 - DOI: 10.1016/j.jcmgh.2016.05.011

Development of Chemical Probes for Investigation of Salt-Inducible Kinase Function In Vivo.

Sundberg TB, Liang Y, Wu H, Choi HG, Kim ND, Sim T, Johannessen L, Petrone A, Khor B, Graham DB, Latorre IJ, Phillips AJ, Schreiber SL, Perez J, Shamji AF, Gray NS, Xavier RJ
ACS Chem Biol. 2016;11(8):2105-11 - PMID: 27224444 - PMCID: PMC4992440 - DOI: 10.1021/acschembio.6b00217

Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.

O'Connell DJ, Kolde R, Sooknah M, Graham DB, Sundberg TB, Latorre IJ, Mikkelsen TS, Xavier RJ
Cell Syst. 2016;2(5):323-334 - PMID: 27211859 - PMCID: PMC5032147 - DOI: 10.1016/j.cels.2016.04.011

Coagulation Biomarkers in Healthy Chinese-Origin Rhesus Macaques (Macaca mulatta).

Frydman GH, Bendapudi PK, Marini RP, Vanderburg CR, Tompkins RG, Fox JG
J Am Assoc Lab Anim Sci. 2016;55(3):252-9 - PMID: 27177557 - PMCID: PMC4865685

Role of Elevated Fibrinogen in Burn-Induced Mitochondrial Dysfunction: Protective Effects of Glycyrrhizin.

Ueki R, Liu L, Kashiwagi S, Kaneki M, Khan M, Hirose M, Tompkins RG, Martyn JA, Yasuhara S
Shock. 2016;46(4):382-9 - PMID: 27172157 - PMCID: PMC5026541 - DOI: 10.1097/SHK.0000000000000602

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands.

Lamas B, Richard ML, Leducq V, Pham HP, Michel ML, Da Costa G, Bridonneau C, Jegou S, Hoffmann TW, Natividad JM, Brot L, Taleb S, Couturier-Maillard A, Nion-Larmurier I, Merabtene F, Seksik P, Bourrier A, Cosnes J, Ryffel B, Beaugerie L, Launay JM, Langella P, Xavier RJ, Sokol H
Nat Med. 2016;22(6):598-605 - PMID: 27158904 - PMCID: PMC5087285 - DOI: 10.1038/nm.4102

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease.

Chu H, Khosravi A, Kusumawardhani IP, Kwon AH, Vasconcelos AC, Cunha LD, Mayer AE, Shen Y, Wu WL, Kambal A, Targan SR, Xavier RJ, Ernst PB, Green DR, McGovern DP, Virgin HW, Mazmanian SK
Science. 2016;352(6289):1116-20 - PMID: 27230380 - PMCID: PMC4996125 - DOI: 10.1126/science.aad9948

Clinical Activity and Quality of Life Indices Are Valid Across Ulcerative Colitis But Not Crohn's Disease Phenotypes.

Taleban S, Stewart KO, Li DK, Singh P, Pardi DS, Sturgeon HC, Yajnik V, Xavier RJ, Ananthakrishnan AN, Khalili H
Dig Dis Sci. 2016;61(9):2627-35 - PMID: 27142671 - PMCID: PMC4982770 - DOI: 10.1007/s10620-016-4180-8

Open-source guideseq software for analysis of GUIDE-seq data.

Tsai SQ, Topkar VV, Joung JK, Aryee MJ
Nat Biotechnol. 2016;34(5):483 - PMID: 27153277 - DOI: 10.1038/nbt.3534

Mechanisms of Pediatric Inflammatory Bowel Disease.

Peloquin JM, Goel G, Villablanca EJ, Xavier RJ
Annu Rev Immunol. 2016;34:31-64 - PMID: 27168239 - DOI: 10.1146/annurev-immunol-032414-112151

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, DIABIMMUNE Study Group, Xavier RJ
Cell. 2016;165(4):842-53 - PMID: 27133167 - PMCID: PMC4950857 - DOI: 10.1016/j.cell.2016.04.007

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, , Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J
Science. 2016;352(6285):565-9 - PMID: 27126040 - PMCID: PMC5240844 - DOI: 10.1126/science.aad3369

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, , Xavier RJ
Cell. 2016;165(4):842-53 - PMID: 27133167 - PMCID: PMC4950857 - DOI: 10.1016/j.cell.2016.04.007

Thiolated uridine substrates and templates improve the rate and fidelity of ribozyme-catalyzed RNA copying.

Prywes N, Michaels YS, Pal A, Oh SS, Szostak JW
Chem Commun (Camb). 2016;52(39):6529-32 - PMID: 27109314 - DOI: 10.1039/c6cc02692c

Trained immunity: A program of innate immune memory in health and disease.

Netea MG, Joosten LA, Latz E, Mills KH, Natoli G, Stunnenberg HG, O'Neill LA, Xavier RJ
Science. 2016;352(6284):aaf1098 - PMID: 27102489 - PMCID: PMC5087274 - DOI: 10.1126/science.aaf1098

Cyclodextrin promotes atherosclerosis regression via macrophage reprogramming.

Zimmer S, Grebe A, Bakke SS, Bode N, Halvorsen B, Ulas T, Skjelland M, De Nardo D, Labzin LI, Kerksiek A, Hempel C, Heneka MT, Hawxhurst V, Fitzgerald ML, Trebicka J, Björkhem I, Gustafsson JÅ, Westerterp M, Tall AR, Wright SD, Espevik T, Schultze JL, Nickenig G, Lütjohann D, Latz E
Sci Transl Med. 2016;8(333):333ra50 - PMID: 27053774 - PMCID: PMC4878149 - DOI: 10.1126/scitranslmed.aad6100

Defining and improving the genome-wide specificities of CRISPR-Cas9 nucleases.

Tsai SQ, Joung JK
Nat Rev Genet. 2016;17(5):300-12 - PMID: 27087594 - DOI: 10.1038/nrg.2016.28

Timothy C. Wang, MD: Our next AGA President.

Abrams JA, Xavier RJ, Rustgi AK
Gastroenterology. 2016;150(5):1231-1236 - PMID: 27018487 - DOI: 10.1053/j.gastro.2016.03.021

Collaboration between primitive cell membranes and soluble catalysts.

Adamala KP, Engelhart AE, Szostak JW
Nat Commun. 2016;7:11041 - PMID: 26996603 - PMCID: PMC4802160 - DOI: 10.1038/ncomms11041

Experimental and computational evidence for a loose transition state in phosphoroimidazolide hydrolysis.

Li L, Lelyveld VS, Prywes N, Szostak JW
J Am Chem Soc. 2016;138(12):3986-9 - PMID: 26974265 - DOI: 10.1021/jacs.6b00784

A simple physical mechanism enables homeostasis in primitive cells.

Engelhart AE, Adamala KP, Szostak JW
Nat Chem. 2016;8(5):448-53 - PMID: 27102678 - PMCID: PMC4929987 - DOI: 10.1038/nchem.2475

?v Integrins combine with LC3 and atg5 to regulate Toll-like receptor signalling in B cells.

Acharya M, Sokolovska A, Tam JM, Conway KL, Stefani C, Raso F, Mukhopadhyay S, Feliu M, Paul E, Savill J, Hynes RO, Xavier RJ, Vyas JM, Stuart LM, Lacy-Hulbert A
Nat Commun. 2016;7:10917 - PMID: 26965188 - PMCID: PMC4792966 - DOI: 10.1038/ncomms10917

Recovery Curves for Pediatric Burn Survivors: Advances in Patient-Oriented Outcomes.

Kazis LE, Lee AF, Rose M, Liang MH, Li NC, Ren XS, Sheridan R, Gilroy-Lewis J, Stoddard F, Hinson M, Warden G, Stubbs K, Blakeney P, Meyer W, McCauley R, Herndon D, Palmieri T, Mooney K, Wood D, Pidcock F, Reilly D, Cullen M, Calvert C, Ryan CM, Schneider JC, Soley-Bori M, Tompkins RG
JAMA Pediatr. 2016;170(6):534-42 - PMID: 26953515 - DOI: 10.1001/jamapediatrics.2015.4722

Impaired antibacterial autophagy links granulomatous intestinal inflammation in Niemann-Pick disease type C1 and XIAP deficiency with NOD2 variants in Crohn's disease.

Schwerd T, Pandey S, Yang HT, Bagola K, Jameson E, Jung J, Lachmann RH, Shah N, Patel SY, Booth C, Runz H, Düker G, Bettels R, Rohrbach M, Kugathasan S, Chapel H, Keshav S, Elkadri A, Platt N, Muise AM, Koletzko S, Xavier RJ, Marquardt T, Powrie F, Wraith JE, Gyrd-Hansen M, Platt FM, Uhlig HH
Gut. 2016;66(6):1060-1073 - PMID: 26953272 - PMCID: PMC5532464 - DOI: 10.1136/gutjnl-2015-310382

Mutation of the Glucosinolate Biosynthesis Enzyme Cytochrome P450 83A1 Monooxygenase Increases Camalexin Accumulation and Powdery Mildew Resistance.

Liu S, Bartnikas LM, Volko SM, Ausubel FM, Tang D
Front Plant Sci. 2016;7:227 - PMID: 26973671 - PMCID: PMC4774424 - DOI: 10.3389/fpls.2016.00227

ABCA7 Deficiency Accelerates Amyloid-? Generation and Alzheimer's Neuronal Pathology.

Sakae N, Liu CC, Shinohara M, Frisch-Daiello J, Ma L, Yamazaki Y, Tachibana M, Younkin L, Kurti A, Carrasquillo MM, Zou F, Sevlever D, Bisceglio G, Gan M, Fol R, Knight P, Wang M, Han X, Fryer JD, Fitzgerald ML, Ohyagi Y, Younkin SG, Bu G, Kanekiyo T
J Neurosci. 2016;36(13):3848-59 - PMID: 27030769 - PMCID: PMC4812140 - DOI: 10.1523/JNEUROSCI.3757-15.2016

New Regulatory Roles of Galectin-3 in the High-affinity IgE Receptor Signaling.

Bambouskova M, Polakovicova I, Halova I, Goel G, Draberova L, Bugajev V, Doan A, Utekal P, Gardet A, Xavier RJ, Draber P
Mol Cell Biol. 2016;36(9):1366-82 - PMID: 26929198 - PMCID: PMC4836217 - DOI: 10.1128/MCB.00064-16

NH125 kills methicillin-resistant Staphylococcus aureus persisters by lipid bilayer disruption.

Kim W, Fricke N, Conery AL, Fuchs BB, Rajamuthiah R, Jayamani E, Vlahovska PM, Ausubel FM, Mylonakis E
Future Med Chem. 2016;8(3):257-69 - PMID: 26910612 - PMCID: PMC4976882 - DOI: 10.4155/fmc.15.189

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.

Yassour M, Lim MY, Yun HS, Tickle TL, Sung J, Song YM, Lee K, Franzosa EA, Morgan XC, Gevers D, Lander ES, Xavier RJ, Birren BW, Ko G, Huttenhower C
Genome Med. 2016;8(1):17 - PMID: 26884067 - PMCID: PMC4756455 - DOI: 10.1186/s13073-016-0271-6

Synthesis of activated 3'-amino-3'-deoxy-2-thio-thymidine, a superior substrate for the nonenzymatic copying of nucleic acid templates.

Izgu EC, Oh SS, Szostak JW
Chem Commun (Camb). 2016;52(18):3684-6 - PMID: 26857159 - DOI: 10.1039/c5cc10317g

Planetary Protection and Mars Special Regions-A Suggestion for Updating the Definition.

Rettberg P, Anesio AM, Baker VR, Baross JA, Cady SL, Detsis E, Foreman CM, Hauber E, Ori GG, Pearce DA, Renno NO, Ruvkun G, Sattler B, Saunders MP, Smith DH, Wagner D, Westall F
Astrobiology. 2016;16(2):119-25 - PMID: 26848950 - DOI: 10.1089/ast.2016.1472

On the Mechanism of Berberine-INF55 (5-Nitro-2-phenylindole) Hybrid Antibacterials.

Dolla NK, Chen C, Larkins-Ford J, Rajamuthiah R, Jagadeesan S, Conery AL, Ausubel FM, Mylonakis E, Bremner JB, Lewis K, Kelso MJ
Aust J Chem. 2016;67:1471-1480 - PMID: 26806960 - PMCID: PMC4720975 - DOI: 10.1071/CH14426

The burn outcome questionnaires: Patient and family reported outcome metrics for children of all ages.

Ryan CM, Cartwright S, Schneider JC, Tompkins RG, Kazis LE
Burns. 2016;42(5):1144-1145 - PMID: 26803370 - DOI: 10.1016/j.burns.2015.10.033

Hold the Pendulum: Rates of Acute Kidney Injury are Increased in Patients Who Receive Resuscitation Volumes Less than Predicted by the Parkland Equation.

Mason SA, Nathens AB, Finnerty CC, Gamelli RL, Gibran NS, Arnoldo BD, Tompkins RG, Herndon DN, Jeschke MG,
Ann Surg. 2016;:ePub - PMID: 26764868

High-fidelity CRISPR-Cas9 nucleases with no detectable genome-wide off-target effects.

Kleinstiver BP, Pattanayak V, Prew MS, Tsai SQ, Nguyen NT, Zheng Z, Joung JK
Nature. 2016;529(7587):490-5 - PMID: 26735016 - PMCID: PMC4851738 - DOI: 10.1038/nature16526

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).

Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, Adachi H, Adams CM, Adams PD, Adeli K, Adhihetty PJ, Adler SG, Agam G, Agarwal R, Aghi MK, Agnello M, Agostinis P, Aguilar PV, Aguirre-Ghiso J, Airoldi EM, Ait-Si-Ali S, Akematsu T, Akporiaye ET, Al-Rubeai M, Albaiceta GM, Albanese C, Albani D, Albert ML, Aldudo J, Algül H, Alirezaei M, Alloza I, Almasan A, Almonte-Beceril M, Alnemri ES, Alonso C, Altan-Bonnet N, Altieri DC, Alvarez S, Alvarez-Erviti L, Alves S, A ...
Autophagy. 2016;12(1):1-222 - PMID: 26799652 - PMCID: PMC4835977 - DOI: 10.1080/15548627.2015.1100356

Mouse embryonic fibroblasts exhibit extensive developmental and phenotypic diversity.

Singhal PK, Sassi S, Lan L, Au P, Halvorsen SC, Fukumura D, Jain RK, Seed B
Proc Natl Acad Sci U S A. 2015;113(1):122-7 - PMID: 26699463 - PMCID: PMC4711836 - DOI: 10.1073/pnas.1522401112

Loss of a Class A Penicillin-Binding Protein Alters ?-Lactam Susceptibilities in Mycobacterium tuberculosis.

Wivagg CN, Wellington S, Gomez JE, Hung DT
ACS Infect Dis. 2015;2(2):104-10 - PMID: 27624961 - DOI: 10.1021/acsinfecdis.5b00119

Proton pump inhibitors affect the gut microbiome.

Imhann F, Bonder MJ, Vich Vila A, Fu J, Mujagic Z, Vork L, Tigchelaar EF, Jankipersadsing SA, Cenit MC, Harmsen HJ, Dijkstra G, Franke L, Xavier RJ, Jonkers D, Wijmenga C, Weersma RK, Zhernakova A
Gut. 2015;65(5):740-8 - PMID: 26657899 - PMCID: PMC4853569 - DOI: 10.1136/gutjnl-2015-310376

In vivo high-resolution magic angle spinning magnetic and electron paramagnetic resonance spectroscopic analysis of mitochondria-targeted peptide in Drosophila melanogaster with trauma-induced thoracic injury.

Constantinou C, Apidianakis Y, Psychogios N, Righi V, Mindrinos MN, Khan N, Swartz HM, Szeto HH, Tompkins RG, Rahme LG, Tzika AA
Int J Mol Med. 2015;37(2):299-308 - PMID: 26648055 - PMCID: PMC4716799 - DOI: 10.3892/ijmm.2015.2426

Quantifying Risk Factors for Long-Term Sleep Problems After Burn Injury in Young Adults.

Lee AF, Ryan CM, Schneider JC, Kazis LE, Li NC, Rose M, Liang MH, Wang C, Palmieri T, Meyer WJ, Pidcock FS, Reilly D, Sheridan RL, Tompkins RG,
J Burn Care Res. 2015;38(2):e510-e520 - PMID: 27003738 - DOI: 10.1097/BCR.0000000000000315

Accelerating research through reagent repositories: the genome editing example.

Joung JK, Voytas DF, Kamens J
Genome Biol. 2015;16(1):255 - PMID: 26585970 - PMCID: PMC4653914 - DOI: 10.1186/s13059-015-0830-y

Pinpointing RNA-protein crosslinks with site-specific stable isotope labeled oligonucleotides.

Lelyveld VS, Bjorkbom A, Ransey E, Sliz P, Szostak JW
J Am Chem Soc. 2015;137(49):15378-15381 - PMID: 26583201 - PMCID: PMC4697197 - DOI: 10.1021/jacs.5b10596

Flow Cytometric Analysis of Mononuclear Phagocytes in Non-diseased Human Lung and Lung-draining Lymph Nodes.

Desch AN, Gibbings SL, Goyal R, Kolde R, Bednarek J, Bruno T, Slansky JE, Jacobelli J, Mason R, Ito Y, Messier E, Randolph GJ, Prabagar M, Atif SM, Segura E, Xavier RJ, Bratton DL, Janssen WJ, Henson PM, Jakubzick CV
Am J Respir Crit Care Med. 2015;193(6):614-626 - PMID: 26551758 - PMCID: PMC4824940 - DOI: 10.1164/rccm.201507-1376OC

Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition.

Kleinstiver BP, Prew MS, Tsai SQ, Nguyen NT, Topkar VV, Zheng Z, Joung JK
Nat Biotechnol. 2015;33(12):1293-1298 - PMID: 26524662 - PMCID: PMC4689141 - DOI: 10.1038/nbt.3404

Early Leukocyte Gene Expression Associated with Age, Burn Size, and Inhalation Injury in Severely Burned Adults.

Sood RF, Gibran NS, Arnoldo BD, Gamelli RL, Herndon DN, Tompkins RG, Inflammation T, Investigators TH
J Trauma Acute Care Surg. 2015;80(2):250-7 - PMID: 26517785 - PMCID: PMC4731271 - DOI: 10.1097/TA.0000000000000905

LXR agonism up-regulates the macrophage ABCA1/syntrophin protein complex which can bind apoA-I and stabilized ABCA1 protein, but complex loss does not inhibit lipid efflux.

Tamehiro N, Park MH, Hawxhurst V, Nagpal K, Adams ME, Zannis VI, Golenbock DT, Fitzgerald ML
Biochemistry. 2015;54(46):6931-41 - PMID: 26506427 - PMCID: PMC4874254 - DOI: 10.1021/acs.biochem.5b00894

Kidney and Liver Injuries After Major Burns in Rats Are Prevented by Resolvin D2.

Inoue Y, Yu YM, Kurihara T, Vasilyev A, Ibrahim A, Oklu R, Zhao G, Nair AV, Brown D, Fischman AJ, Tompkins RG, Irimia D
Crit Care Med. 2015;44(5):e241-52 - PMID: 26509319 - PMCID: PMC4833510 - DOI: 10.1097/CCM.0000000000001397

Bidirectional direct sequencing of non-canonical RNA by two-dimensional analysis of mass chromatograms.

Bjorkbom A, Lelyveld VS, Zhang S, Zhang W, Tam CP, Blain JC, Szostak JW
J Am Chem Soc. 2015;137(45):14430-8 - PMID: 26495937 - DOI: 10.1021/jacs.5b09438

Gene Expression of Proresolving Lipid Mediator Pathways Is Associated With Clinical Outcomes in Trauma Patients.

Orr SK, Butler KL, Hayden D, Tompkins RG, Serhan CN, Irimia D
Crit Care Med. 2015;43(12):2642-2650 - PMID: 26488221 - PMCID: PMC4651815 - DOI: 10.1097/CCM.0000000000001312

Novel links in the plant TOR kinase signaling network.

Xiong Y, Sheen J
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Ubiquitin Ligase TRIM62 Regulates CARD9-Mediated Anti-fungal Immunity and Intestinal Inflammation.

Cao Z, Conway KL, Heath RJ, Rush JS, Leshchiner ES, Ramirez-Ortiz ZG, Nedelsky NB, Huang H, Ng A, Gardet A, Cheng SC, Shamji AF, Rioux JD, Wijmenga C, Netea MG, Means TK, Daly MJ, Xavier RJ
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Genome Editing in Human Cells Using CRISPR/Cas Nucleases.

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Ubiquitin Ligase TRIM62 Regulates CARD9-Mediated Anti-fungal Immunity and Intestinal Inflammation.

Cao Z, Conway KL, Heath RJ, Rush JS, Leshchiner ES, Ramirez-Ortiz ZG, Nedelsky NB, Huang H, Ng A, Gardet A, Cheng SC, Shamji AF, Rioux JD, Wijmenga C, Netea MG, Means TK, Daly MJ, Xavier RJ
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Antibacterial properties of 3-(phenylsulfonyl)-2-pyrazinecarbonitrile.

Rajamuthiah R, Jayamani E, Majed H, Conery AL, Kim W, Kwon B, Fuchs BB, Kelso MJ, Ausubel FM, Mylonakis E
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CAUSEL: an epigenome- and genome-editing pipeline for establishing function of noncoding GWAS variants.

Spisák S, Lawrenson K, Fu Y, Csabai I, Cottman RT, Seo JH, Haiman C, Han Y, Lenci R, Li Q, Tisza V, Szállási Z, Herbert ZT, Chabot M, Pomerantz M, Solymosi N, , Gayther SA, Joung JK, Freedman ML
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Dialogue between E. coli free radical pathways and the mitochondria of C. elegans.

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Patiromer induces rapid and sustained potassium lowering in patients with chronic kidney disease and hyperkalemia.

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The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids.

Fu J, Bonder MJ, Cenit MC, Tigchelaar E, Maatman A, Dekens JA, Brandsma E, Marczynska J, Imhann F, Weersma RK, Franke L, Poon TW, Xavier RJ, Gevers D, Hofker MH, Wijmenga C, Zhernakova A
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A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-?-Activated Human Cells.

Selleck EM, Orchard RC, Lassen KG, Beatty WL, Xavier RJ, Levine B, Virgin HW, Sibley LD
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A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-?-Activated Human Cells.

Selleck EM, Orchard RC, Lassen KG, Beatty WL, Xavier RJ, Levine B, Virgin HW, Sibley LD
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ConStrains identifies microbial strains in metagenomic datasets.

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Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.

Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier RJ, Regev A, Hung DT
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Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier RJ, Regev A, Hung DT
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Lipid signalling couples translational surveillance to systemic detoxification in Caenorhabditis elegans.

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HIV infection induces structural and functional changes in high density lipoproteins.

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Enhancing immunity by engineering DAMPs.

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Is Real-Time Feedback of Burn-Specific Patient-Reported Outcome Measures in Clinical Settings Practical and Useful? A Pilot Study Implementing the Young Adult Burn Outcome Questionnaire.

Ryan CM, Lee AF, Kazis LE, Shapiro GD, Schneider JC, Goverman J, Fagan SP, Wang C, Kim J, Sheridan RL, Tompkins RG
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piRNAs and piRNA-Dependent siRNAs Protect Conserved and Essential C. elegans Genes from Misrouting into the RNAi Pathway.

Phillips CM, Brown KC, Montgomery BE, Ruvkun G, Montgomery TA
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Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization.

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Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases.

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MICROBIOME. Plant microbiome blueprints.

Haney CH, Ausubel FM
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Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples.

Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, Matot E, Jona G, Harmelin A, Cohen N, Sirota-Madi A, Thaiss CA, Pevsner-Fischer M, Sorek R, Xavier R, Elinav E, Segal E
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Kamat NP, Tobé S, Hill IT, Szostak JW
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Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst.

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Pseudomonas syringae enhances herbivory by suppressing the reactive oxygen burst in Arabidopsis.

Groen SC, Humphrey PT, Chevasco D, Ausubel FM, Pierce NE, Whiteman NK
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Small-molecule enhancers of autophagy modulate cellular disease phenotypes suggested by human genetics.

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Body Mass Index, Genetic Susceptibility, and Risk of Complications Among Individuals with Crohn's Disease.

Pringle PL, Stewart KO, Peloquin JM, Sturgeon HC, Nguyen D, Sauk J, Garber JJ, Yajnik V, Ananthakrishnan AN, Chan AT, Xavier RJ, Khalili H
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Role of Autophagy in the Maintenance of Intestinal Homeostasis.

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Unwanted mutations: Standards needed for gene-editing errors.

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Effect of Patiromer on Serum Potassium Level in Patients With Hyperkalemia and Diabetic Kidney Disease: The AMETHYST-DN Randomized Clinical Trial.

Bakris GL, Pitt B, Weir MR, Freeman MW, Mayo MR, Garza D, Stasiv Y, Zawadzki R, Berman L, Bushinsky DA,
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Stimulation of Liver X Receptor Has Potent Anti-HIV Effects in a Humanized Mouse Model.

Ramezani A, Dubrovsky L, Pushkarsky T, Sviridov D, Karandish S, Raj DS, Fitzgerald ML, Bukrinsky M
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Engineered CRISPR-Cas9 nucleases with altered PAM specificities.

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Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy.

Begun J, Lassen KG, Jijon HB, Baxt LA, Goel G, Heath RJ, Ng A, Tam JM, Kuo SY, Villablanca EJ, Fagbami L, Oosting M, Kumar V, Schenone M, Carr SA, Joosten LA, Vyas JM, Daly MJ, Netea MG, Brown GD, Wijmenga C, Xavier RJ
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A Defensin from the Model Beetle Tribolium castaneum Acts Synergistically with Telavancin and Daptomycin against Multidrug Resistant Staphylococcus aureus.

Rajamuthiah R, Jayamani E, Conery AL, Fuchs BB, Kim W, Johnston T, Vilcinskas A, Ausubel FM, Mylonakis E
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Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease.

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Identification of an Antimicrobial Agent Effective against Methicillin-Resistant Staphylococcus aureus Persisters Using a Fluorescence-Based Screening Strategy.

Kim W, Conery AL, Rajamuthiah R, Fuchs BB, Ausubel FM, Mylonakis E
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CARMA3 Is Critical for the Initiation of Allergic Airway Inflammation.

Causton B, Ramadas RA, Cho JL, Jones K, Pardo-Saganta A, Rajagopal J, Xavier RJ, Medoff BD
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Construction of a liposome dialyzer for the preparation of high-value, small-volume liposome formulations.

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Rescue of DNA-PK Signaling and T-Cell Differentiation by Targeted Genome Editing in a prkdc Deficient iPSC Disease Model.

Rahman SH, Kuehle J, Reimann C, Mlambo T, Alzubi J, Maeder ML, Riedel H, Fisch P, Cantz T, Rudolph C, Mussolino C, Joung JK, Schambach A, Cathomen T
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The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells.

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Targeted Mutagenesis in Zebrafish Using CRISPR RNA-Guided Nucleases.

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Associations with rhizosphere bacteria can confer an adaptive advantage to plants.

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Associations with rhizosphere bacteria can confer an adaptive advantage to plants.

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PhyloGene server for identification and visualization of co-evolving proteins using normalized phylogenetic profiles.

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Genome editing technologies: defining a path to clinic.

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An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases.

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Hypoxia drives transient site-specific copy gain and drug-resistant gene expression.

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Jasmonate signalling in Arabidopsis involves SGT1b-HSP70-HSP90 chaperone complexes.

Zhang XC, Millet YA, Cheng Z, Bush J, Ausubel FM
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Do standard burn mortality formulae work on a population of severely burned children and adults?

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Uncovering the Thermodynamics of Monomer Binding for RNA Replication.

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Repurposing Salicylanilide Anthelmintic Drugs to Combat Drug Resistant Staphylococcus aureus.

Rajamuthiah R, Fuchs BB, Conery AL, Kim W, Jayamani E, Kwon B, Ausubel FM, Mylonakis E
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Direct detection and drug-resistance profiling of bacteremias using inertial microfluidics.

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Future Translational Applications From the Contemporary Genomics Era: A Scientific Statement From the American Heart Association.

Fox CS, Hall JL, Arnett DK, Ashley EA, Delles C, Engler MB, Freeman MW, Johnson JA, Lanfear DE, Liggett SB, Lusis AJ, Loscalzo J, MacRae CA, Musunuru K, Newby LK, O'Donnell CJ, Rich SS, Terzic A
Circulation. 2015;131(19):1715-36 - PMID: 25882488 - PMCID: PMC4825323 - DOI: 10.1161/CIR.0000000000000211

Plant immunity triggered by engineered in vivo release of oligogalacturonides, damage-associated molecular patterns.

Benedetti M, Pontiggia D, Raggi S, Cheng Z, Scaloni F, Ferrari S, Ausubel FM, Cervone F, De Lorenzo G
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Discovery of a Small-Molecule Probe for V-ATPase Function.

Aldrich LN, Kuo SY, Castoreno AB, Goel G, Kuballa P, Rees MG, Seashore-Ludlow BA, Cheah JH, Latorre IJ, Schreiber SL, Shamji AF, Xavier RJ
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Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.

Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C
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Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells.

Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A
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Targeted Plant Genome Editing via the CRISPR/Cas9 Technology.

Li JF, Zhang D, Sheen J
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Genomics of injury: The Glue Grant experience.

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Simultaneous generation of many RNA-seq libraries in a single reaction.

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Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.

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Pathogen-secreted proteases activate a novel plant immune pathway.

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A novel role for KLF14 in T regulatory cell differentiation.

Sarmento OF, Svingen PA, Xiong Y, Xavier RJ, McGovern D, Smyrk TC, Papadakis KA, Urrutia RA, Faubion WA
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Chromatin regulation at the frontier of synthetic biology.

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Replacing Uridine with 2-Thio-Uridine Enhances the Rate and Fidelity of Nonenzymatic RNA Primer Extension.

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The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes.

Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Oreši? M, Huttenhower C, Knip M, , Xavier RJ
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Intake of farmed Atlantic salmon fed soybean oil increases hepatic levels of arachidonic acid-derived oxylipins and ceramides in mice.

Midtbø LK, Borkowska AG, Bernhard A, Rønnevik AK, Lock EJ, Fitzgerald ML, Torstensen BE, Liaset B, Brattelid T, Pedersen TL, Newman JW, Kristiansen K, Madsen L
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A new antibiotic with potent activity targets MscL.

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Exome Sequencing in Suspected Monogenic Dyslipidemias.

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A Zebrafish Model of Myelodysplastic Syndrome Produced Through tet2 Genomic Editing.

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Autophagy and checkpoints for intracellular pathogen defense.

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Autophagy Controls BCG-Induced Trained Immunity and the Response to Intravesical BCG Therapy for Bladder Cancer.

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An Image-Based Genetic Assay Identifies Genes in T1D Susceptibility Loci Controlling Cellular Antiviral Immunity in Mouse.

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Transmembrane adaptor protein PAG/CBP is involved in both positive and negative regulation of mast cell signaling.

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Small-molecule control of cytokine function: new opportunities for treating immune disorders.

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Immunochip SNP array identifies novel genetic variants conferring susceptibility to candidaemia.

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Crystal Structure Studies of RNA Duplexes Containing s2U:A and s2U:U Base Pairs.

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Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation.

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Treatment of heterotopic ossification through remote ATP hydrolysis.

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Systematic screening reveals a role for BRCA1 in the response to transcription-associated DNA damage.

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Small-molecule screening identifies inhibition of salt-inducible kinases as a therapeutic strategy to enhance immunoregulatory functions of dendritic cells.

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Apoplastic peroxidases are required for salicylic acid-mediated defense against Pseudomonas syringae.

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Mechanisms of ?-lactam killing and resistance in the context of Mycobacterium tuberculosis.

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Identification of genes in toxicity pathways of trinucleotide-repeat RNA in C. elegans.

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Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.

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What's changed with genome editing?

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SLCO3A1, a Novel Crohn's Disease-Associated Gene, Regulates NF-?B Activity and Associates with Intestinal Perforation.

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Simvastatin Reduces Burn Injury-Induced Splenic Apoptosis via Downregulation of the TNF-?/NF-?B Pathway.

Zhao G, Yu YM, Kaneki M, Bonab AA, Tompkins RG, Fischman AJ
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Prediction of Multiple Infections After Severe Burn Trauma: A Prospective Cohort Study.

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AGROBEST: an efficient Agrobacterium-mediated transient expression method for versatile gene function analyses in Arabidopsis seedlings.

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On the Horizon: Research Priorities in Burns for the Next Decade.

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Detecting differential protein expression in large-scale population proteomics.

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Inflammatory Bowel Disease as a Model for Translating the Microbiome.

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The Evolutionarily Conserved Mediator Subunit MDT-15/MED15 Links Protective Innate Immune Responses and Xenobiotic Detoxification.

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Dectin-1 dependent LC3 recruitment to phagosomes enhances fungicidal activity in macrophages.

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Pseudomonas aeruginosa PA14 Pathogenesis in Caenorhabditis elegans.

Kirienko NV, Cezairliyan BO, Ausubel FM, Powell JR
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Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense.

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Epinecidin-1 has immunomodulatory effects, facilitating its therapeutic use in a mouse model of Pseudomonas aeruginosa sepsis.

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Genetic Polymorphisms in Metabolizing Enzymes Modifying the Association Between Smoking and Inflammatory Bowel Diseases.

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The treatment-naive microbiome in new-onset Crohn's disease.

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Human Genome-Wide RNAi Screen Identifies an Essential Role for Inositol Pyrophosphates in Type-I Interferon Response.

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Identification of Host-Targeted Small Molecules That Restrict Intracellular Mycobacterium tuberculosis Growth.

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Whole Animal Automated Platform for Drug Discovery against Multi-Drug Resistant Staphylococcus aureus.

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IL-1 receptor blockade restores autophagy and reduces inflammation in chronic granulomatous disease in mice and in humans.

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The Microbiome in Inflammatory Bowel Diseases: Current Status and the Future Ahead.

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HDL redox activity is increased in HIV-infected men in association with macrophage activation and noncalcified coronary atherosclerotic plaque.

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Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity.

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An improved predictive recognition model for Cys(2)-His(2) zinc finger proteins.

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Structural insights into the effects of 2'-5' linkages on the RNA duplex.

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The Free Energy Landscape of Pseudorotation in 3'-5' and 2'-5' Linked Nucleic Acids.

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Improving CRISPR-Cas nuclease specificity using truncated guide RNAs.

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SMAD3 gene variant is a risk factor for recurrent surgery in patients with Crohn's disease.

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Differential Effect of Genetic Burden on Disease Phenotypes in Crohn's Disease and Ulcerative Colitis: Analysis of a North American Cohort.

Ananthakrishnan AN, Huang H, Nguyen DD, Sauk J, Yajnik V, Xavier RJ
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Autophagy is essential for cardiac morphogenesis during vertebrate development.

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Membrane potential-dependent uptake of (18)F-triphenylphosphonium-a new voltage sensor as an imaging agent for detecting burn-induced apoptosis.

Zhao G, Yu YM, Shoup TM, Elmaleh DR, Bonab AA, Tompkins RG, Fischman AJ
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Synthesis and Non-Enzymatic Template-Directed Polymerization of 2'-Amino-2'-Deoxythreose Nucleotides.

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Toddler: an embryonic signal that promotes cell movement via Apelin receptors.

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TOR Signaling Networks in Plant Growth and Metabolism.

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Bacterial toxins and small molecules elucidate endosomal trafficking.

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Correction of Crb1rd8 allele and retinal phenotype in C57BL/6N mice via TALEN-mediated homology-directed repair.

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Ancient signals: comparative genomics of green plant CDPKs.

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High-density lipoprotein mediates anti-inflammatory reprogramming of macrophages via the transcriptional regulator ATF3.

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Multiple small RNA pathways regulate the silencing of repeated and foreign genes in C. elegans.

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Interactome maps of mouse gene regulatory domains reveal basic principles of transcriptional regulation.

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Endogenous ?-glucocerebrosidase activity in Abca12-/-epidermis elevates ceramide levels after topical lipid application but does not restore barrier function.

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Pathogen-Triggered Ethylene Signaling Mediates Systemic-Induced Susceptibility to Herbivory in Arabidopsis.

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Autosis is a Na+,K+-ATPase-regulated form of cell death triggered by autophagy-inducing peptides, starvation, and hypoxia-ischemia.

Liu Y, Shoji-Kawata S, Sumpter RM, Wei Y, Ginet V, Zhang L, Posner B, Tran KA, Green DR, Xavier RJ, Shaw SY, Clarke PG, Puyal J, Levine B
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Deletion of the Murine Cytochrome P450 Cyp2j Locus by Fused BAC-Mediated Recombination Identifies a Role for Cyp2j in the Pulmonary Vascular Response to Hypoxia.

Zhou GL, Beloiartsev A, Yu B, Baron DM, Zhou W, Niedra R, Lu N, Tainsh LT, Zapol WM, Seed B, Bloch KD
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High-Resolution Mapping Reveals a Conserved, Widespread, Dynamic mRNA Methylation Program in Yeast Meiosis.

Schwartz S, Agarwala SD, Mumbach MR, Jovanovic M, Mertins P, Shishkin A, Tabach Y, Mikkelsen TS, Satija R, Ruvkun G, Carr SA, Lander ES, Fink GR, Regev A
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Pseudomonas syringae Effector HopF2 Suppresses Arabidopsis Immunity by Targeting BAK1.

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Autophagy is redundant for the host defense against systemic Candida albicans infections.

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Preparation of Fatty Acid micelles.

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Vesicle Extrusion Through Polycarbonate Track-etched Membranes using a Hand-held Mini-extruder.

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Autophagy at the crossroads of metabolism and cellular defense.

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The cytokinin side chain commands shooting.

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Virulence profile: Frederick M Ausubel.

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Long-Lasting Effects of BCG Vaccination on Both Heterologous Th1/Th17 Responses and Innate Trained Immunity.

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Selective Modulation of Autophagy, Innate Immunity, and Adaptive Immunity by Small Molecules.

Shaw SY, Tran K, Castoreno AB, Peloquin JM, Lassen KG, Khor B, Aldrich LN, Tan PH, Graham DB, Kuballa P, Goel G, Daly MJ, Shamji AF, Schreiber SL, Xavier RJ
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Genetic Regulation of Caenorhabditis elegans Lysosome Related Organelle Function.

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mRNA display: from basic principles to macrocycle drug discovery.

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Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins.

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Fast and accurate nonenzymatic copying of an RNA-like synthetic genetic polymer.

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Proc Natl Acad Sci U S A. 2013;110(44):17732-7 - PMID: 24101473 - PMCID: PMC3816440 - DOI: 10.1073/pnas.1312329110

Novel Mechanism of Tumor Suppression by Polarity Gene Discs Large 1 (DLG1) Revealed in a Murine Model of Pediatric B-ALL.

Sandoval GJ, Graham DB, Gmyrek GB, Akilesh HM, Fujikawa K, Sammut B, Bhattacharya D, Srivatsan S, Kim A, Shaw AS, Yang-Iott K, Bassing CH, Duncavage E, Xavier RJ, Swat W
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Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome.

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Human disease locus discovery and mapping to molecular pathways through phylogenetic profiling.

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A Small Volatile Bacterial Molecule Triggers Mitochondrial Dysfunction in Murine Skeletal Muscle.

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Genetic Variants Synthesize to Produce Paneth Cell Phenotypes that Define Subtypes of Crohn's Disease.

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Synthesis and structure-activity relationships of phenyl-substituted coumarins with anti-tubercular activity that target FadD32.

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Dual Regulation of the lin-14 Target mRNA by the lin-4 miRNA.

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Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis.

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Axl mediates acquired resistance of head and neck cancer cells to the epidermal growth factor receptor inhibitor erlotinib.

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Plant immune response to pathogens differs with changing temperatures.

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Tompkins RG, Warren HS, Mindrinos MN, Xiao W, Davis RW
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Targeted Deletion and Inversion of Tandemly Arrayed Genes in Arabidopsis thaliana Using Zinc Finger Nucleases.

Qi Y, Li X, Zhang Y, Starker CG, Baltes NJ, Zhang F, Sander JD, Reyon D, Joung JK, Voytas DF
G3 (Bethesda). 2013;3(10):1707-1715 - PMID: 23979943 - PMCID: PMC3789795 - DOI: 10.1534/g3.113.006270

Out of Context: Clinical Practice Guidelines and Patients With Multiple Chronic Conditions: A Systematic Review.

Wyatt KD, Stuart LM, Brito JP, Carranza Leon B, Domecq JP, Prutsky GJ, Egginton JS, Calvin AD, Shah ND, Murad MH, Montori VM
Med Care. 2013;52 Suppl 3:S92-S100 - PMID: 23969592 - DOI: 10.1097/MLR.0b013e3182a51b3d

Atg16l1 is Required for Autophagy in Intestinal Epithelial Cells and Protection of Mice from Salmonella Infection.

Conway KL, Kuballa P, Song JH, Patel KK, Castoreno AB, Yilmaz OH, Jijon HB, Zhang M, Aldrich LN, Villablanca EJ, Peloquin JM, Goel G, Lee IA, Mizoguchi E, Shi HN, Bhan AK, Shaw SY, Schreiber SL, Virgin HW, Shamji AF, Stappenbeck TS, Reinecker HC, Xavier RJ
Gastroenterology. 2013;145(6):1347-57 - PMID: 23973919 - PMCID: PMC3840157 - DOI: 10.1053/j.gastro.2013.08.035

Differences in Resuscitation in Morbidly Obese Burn Patients May Contribute to High Mortality.

Rae L, Pham TN, Carrougher G, Honari S, Gibran NS, Arnoldo BD, Gamelli RL, Tompkins RG, Herndon DN
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In silico abstraction of zinc finger nuclease cleavage profiles reveals an expanded landscape of off-target sites.

Sander JD, Ramirez CL, Linder SJ, Pattanayak V, Shoresh N, Ku M, Foden JA, Reyon D, Bernstein BE, Liu DR, Joung JK
Nucleic Acids Res. 2013;41(19):e181 - PMID: 23945932 - PMCID: PMC3799455 - DOI: 10.1093/nar/gkt716

Beclin 2 Functions in Autophagy, Degradation of G Protein-Coupled Receptors, and Metabolism.

He C, Wei Y, Sun K, Li B, Dong X, Zou Z, Liu Y, Kinch LN, Khan S, Sinha S, Xavier RJ, Grishin NV, Xiao G, Eskelinen EL, Scherer PE, Whistler JL, Levine B
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Dislodgement of port-A catheters in pediatric oncology patients: 11 years of experience.

Wang SC, Tsai CH, Hou CP, Lee SY, Ko SF, Hsiao CC, Chen YC, Chuang JH, Sheen JM
World J Surg Oncol. 2013;11(1):191 - PMID: 23941644 - PMCID: PMC3765137 - DOI: 10.1186/1477-7819-11-191

Multiplex and homologous recombination-mediated genome editing in Arabidopsis and Nicotiana benthamiana using guide RNA and Cas9.

Li JF, Norville JE, Aach J, McCormack M, Zhang D, Bush J, Church GM, Sheen J
Nat Biotechnol. 2013;31(8):688-91 - PMID: 23929339 - PMCID: PMC4078740 - DOI: 10.1038/nbt.2654

Reply to Cauwels et al.: Of men, not mice, and inflammation.

Warren HS, Tompkins RG, Mindrinos MN, Xiao W, Davis RW
Proc Natl Acad Sci U S A. 2013;110(34):E3151 - PMID: 24137663 - PMCID: PMC3752239 - DOI: 10.1073/pnas.1308943110

Functional profiling of the gut microbiome in disease-associated inflammation.

Börnigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower C
Genome Med. 2013;5(7):65 - PMID: 23906180 - PMCID: PMC3978847 - DOI: 10.1186/gm469

Notch-induced transcription factors are predictive of survival and 5-fluorouracil response in colorectal cancer patients.

Candy PA, Phillips MR, Redfern AD, Colley SM, Davidson JA, Stuart LM, Wood BA, Zeps N, Leedman PJ
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Identification of novel inhibitors of non-replicating M. tuberculosis using a carbon starvation model.

Grant SS, Kawate T, Nag PP, Silvis MR, Gordon K, Stanley SA, Kazyanskaya E, Nietupski R, Golas A, Fitzgerald M, Cho S, Franzblau SG, Hung DT
ACS Chem Biol. 2013;8(10):2224-34 - PMID: 23898841 - PMCID: PMC3864639 - DOI: 10.1021/cb4004817

CRISPR RNA-guided activation of endogenous human genes.

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Mild Obesity Is Protective After Severe Burn Injury.

Jeschke MG, Finnerty CC, Emdad F, Rivero HG, Kraft R, Williams FN, Gamelli RL, Gibran NS, Klein MB, Arnoldo BD, Tompkins RG, Herndon DN
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Genetic risk factors for Clostridium difficile infection in ulcerative colitis.

Ananthakrishnan AN, Oxford EC, Nguyen DD, Sauk J, Yajnik V, Xavier RJ
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Heritable and Precise Zebrafish Genome Editing Using a CRISPR-Cas System.

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Chemical genetics reveals a kinase-independent role for protein kinase R in pyroptosis.

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Competition between model protocells driven by an encapsulated catalyst.

Adamala K, Szostak JW
Nat Chem. 2013;5(7):634 - PMID: 23787756

Engineering Customized TALE Nucleases (TALENs) and TALE Transcription Factors by Fast Ligation-Based Automatable Solid-Phase High-Throughput (FLASH) Assembly.

Reyon D, Maeder ML, Khayter C, Tsai SQ, Foley JE, Sander JD, Joung JK
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Natural selection in a bangladeshi population from the cholera-endemic ganges river delta.

Karlsson EK, Harris JB, Tabrizi S, Rahman A, Shlyakhter I, Patterson N, O'Dushlaine C, Schaffner SF, Gupta S, Chowdhury F, Sheikh A, Shin OS, Ellis C, Becker CE, Stuart LM, Calderwood SB, Ryan ET, Qadri F, Sabeti PC, Larocque RC
Sci Transl Med. 2013;5(192):192ra86 - PMID: 23825302 - PMCID: PMC4367964 - DOI: 10.1126/scitranslmed.3006338

CD36 coordinates NLRP3 inflammasome activation by facilitating intracellular nucleation of soluble ligands into particulate ligands in sterile inflammation.

Sheedy FJ, Grebe A, Rayner KJ, Kalantari P, Ramkhelawon B, Carpenter SB, Becker CE, Ediriweera HN, Mullick AE, Golenbock DT, Stuart LM, Latz E, Fitzgerald KA, Moore KJ
Nat Immunol. 2013;14(8):812-20 - PMID: 23812099 - PMCID: PMC3720827 - DOI: 10.1038/ni.2639

Diarylcoumarins inhibit mycolic acid biosynthesis and kill Mycobacterium tuberculosis by targeting FadD32.

Stanley SA, Kawate T, Iwase N, Shimizu M, Clatworthy AE, Kazyanskaya E, Sacchettini JC, Ioerger TR, Siddiqi NA, Minami S, Aquadro JA, Schmidt Grant S, Rubin EJ, Hung DT
Proc Natl Acad Sci U S A. 2013;110(28):11565-70 - PMID: 23798446 - PMCID: PMC3710825 - DOI: 10.1073/pnas.1302114110

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells.

Fu Y, Foden JA, Khayter C, Maeder ML, Reyon D, Joung JK, Sander JD
Nat Biotechnol. 2013;31(9):822-6 - PMID: 23792628 - PMCID: PMC3773023 - DOI: 10.1038/nbt.2623

Skin Microbiome Imbalance in Patients with STAT1/STAT3 Defects Impairs Innate Host Defense Responses.

Smeekens SP, Huttenhower C, Riza A, van de Veerdonk FL, Zeeuwen PL, Schalkwijk J, van der Meer JW, Xavier RJ, Netea MG, Gevers D
J Innate Immun. 2013;6(3):253-62 - PMID: 23796786 - PMCID: PMC4045018 - DOI: 10.1159/000351912

Moving beyond translation: glucose-TOR signaling in the transcriptional control of cell cycle.

Xiong Y, Sheen J
Cell Cycle. 2013;12(13):1989-90 - PMID: 23759578 - PMCID: PMC3737295 - DOI: 10.4161/cc.25308

Radiation Resistance of Sequencing Chips for in situ Life Detection.

Carr CE, Rowedder H, Lui CS, Zlatkovsky I, Papalias CW, Bolander J, Myers JW, Bustillo J, Rothberg JM, Zuber MT, Ruvkun G
Astrobiology. 2013;13(6):560-9 - PMID: 23734755 - DOI: 10.1089/ast.2012.0923

Card9 Mediates Intestinal Epithelial Cell Restitution, T-helper 17 Responses, and Control of Bacterial Infection in Mice.

Sokol H, Conway KL, Zhang M, Choi M, Morin B, Cao Z, Villablanca EJ, Li C, Wijmenga C, Yun SH, Shi HN, Xavier RJ
Gastroenterology. 2013;145(3):591-601.e3 - PMID: 23732773 - PMCID: PMC3781941 - DOI: 10.1053/j.gastro.2013.05.047

piggyBac transposase tools for genome engineering.

Li X, Burnight ER, Cooney AL, Malani N, Brady T, Sander JD, Staber J, Wheelan SJ, Joung JK, McCray PB, Bushman FD, Sinn PL, Craig NL
Proc Natl Acad Sci U S A. 2013;110(25):E2279-87 - PMID: 23723351 - PMCID: PMC3690869 - DOI: 10.1073/pnas.1305987110

A cytoprotective perspective on longevity regulation.

Shore DE, Ruvkun G
Trends Cell Biol. 2013;23(9):409-20 - PMID: 23726168 - PMCID: PMC4057428 - DOI: 10.1016/j.tcb.2013.04.007

CCT chaperonin complex is required for efficient delivery of anthrax toxin into the cytosol of host cells.

Slater LH, Hett EC, Clatworthy AE, Mark KG, Hung DT
Proc Natl Acad Sci U S A. 2013;110(24):9932-7 - PMID: 23716698 - PMCID: PMC3683768 - DOI: 10.1073/pnas.1302257110

RhoGTPases - NODes for effector-triggered immunity in animals.

Stuart LM, Boyer L
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Competition between model protocells driven by an encapsulated catalyst.

Adamala K, Szostak JW
Nat Chem. 2013;5(6):495-501 - PMID: 23695631 - PMCID: PMC4041014 - DOI: 10.1038/nchem.1650

The hybrid four-CBS-domain KIN?? subunit functions as the canonical ? subunit of the plant energy sensor SnRK1.

Ramon M, Ruelens P, Li Y, Sheen J, Geuten K, Rolland F
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Conformational stability, vibrational spectra, HOMO-LUMO and NBO analysis of 1,3,4-thiadiazolidine-2,5-dithione with experimental (FT-IR and FT-Raman) techniques and scaled quantum mechanical calculations.

Xavier RJ, Dinesh P
Spectrochim Acta A Mol Biomol Spectrosc. 2013;113:171-81 - PMID: 23727670 - DOI: 10.1016/j.saa.2013.04.108

Activation of caspase-1 by the NLRP3 inflammasome regulates the NADPH oxidase NOX2 to control phagosome function.

Sokolovska A, Becker CE, Ip WK, Rathinam VA, Brudner M, Paquette N, Tanne A, Vanaja SK, Moore KJ, Fitzgerald KA, Lacy-Hulbert A, Stuart LM
Nat Immunol. 2013;14(6):543-553 - PMID: 23644505 - PMCID: PMC3708594 - DOI: 10.1038/ni.2595

Comprehensive Protein-Based Artificial MicroRNA Screens for Effective Gene Silencing in Plants.

Li JF, Chung HS, Niu Y, Bush J, McCormack M, Sheen J
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How Does Genotype Influence Disease Phenotype in Inflammatory Bowel Disease?

Ananthakrishnan AN, Xavier RJ
Inflamm Bowel Dis. 2013;19(9):2021-30 - PMID: 23644824 - PMCID: PMC3720704 - DOI: 10.1097/MIB.0b013e318281f5c5

Concomitant BRAF and PI3K/mTOR Blockade Is Required for Effective Treatment of BRAFV600E Colorectal Cancer.

Coffee EM, Faber AC, Roper J, Sinnamon MJ, Goel G, Keung L, Wang WV, Vecchione L, de Vriendt V, Weinstein BJ, Bronson RT, Tejpar S, Xavier RJ, Engelman JA, Martin ES, Hung KE
Clin Cancer Res. 2013;19(10):2688-98 - PMID: 23549875 - PMCID: PMC3815598 - DOI: 10.1158/1078-0432.CCR-12-2556

How antibiotics kill bacteria: new models needed?

Wright GD, Hung DT, Helmann JD
Nat Med. 2013;19(5):544-5 - PMID: 23652106 - DOI: 10.1038/nm.3198

From genetics of inflammatory bowel disease towards mechanistic insights.

Graham DB, Xavier RJ
Trends Immunol. 2013;34(8):371-8 - PMID: 23639549 - PMCID: PMC3735683 - DOI: 10.1016/j.it.2013.04.001

Benchmarks for Multidimensional Recovery After Burn Injury in Young Adults: The Development, Validation, and Testing of the American Burn Association/Shriners Hospitals for Children Young Adult Burn Outcome Questionnaire.

Ryan CM, Schneider JC, Kazis LE, Lee A, Li NC, Hinson M, Bauk H, Peck M, Meyer WJ, Palmieri T, Pidcock FS, Reilly D, Tompkins RG,
J Burn Care Res. 2013;34(3):e121-42 - PMID: 23511284 - DOI: 10.1097/BCR.0b013e31827e7ecf

Genome-wide Analysis of Immune System Genes by Expressed Sequence Tag Profiling.

Giallourakis CC, Benita Y, Molinie B, Cao Z, Despo O, Pratt HE, Zukerberg LR, Daly MJ, Rioux JD, Xavier RJ
J Immunol. 2013;190(11):5578-5587 - PMID: 23616578 - PMCID: PMC3703829 - DOI: 10.4049/jimmunol.1203471

Dectin-1 activation controls maturation of ?-1,3-glucan-containing phagosomes.

Mansour MK, Tam JM, Khan NS, Seward M, Davids PJ, Puranam S, Sokolovska A, Sykes DB, Dagher Z, Becker C, Tanne A, Reedy JL, Stuart LM, Vyas JM
J Biol Chem. 2013;288(22):16043-54 - PMID: 23609446 - PMCID: PMC3668760 - DOI: 10.1074/jbc.M113.473223

Chemical genetics reveals a kinase-independent role for protein kinase R in pyroptosis.

Hett EC, Slater LH, Mark KG, Kawate T, Monks BG, Stutz A, Latz E, Hung DT
Nat Chem Biol. 2013;9(6):398-405 - PMID: 23603659 - PMCID: PMC6615456 - DOI: 10.1038/nchembio.1236

MXL-3 and HLH-30 transcriptionally link lipolysis and autophagy to nutrient availability.

O'Rourke EJ, Ruvkun G
Nat Cell Biol. 2013;15(6):668-676 - PMID: 23604316 - PMCID: PMC3723461 - DOI: 10.1038/ncb2741

DAF-16 employs the chromatin remodeller SWI/SNF to promote stress resistance and longevity.

Riedel CG, Dowen RH, Lourenco GF, Kirienko NV, Heimbucher T, West JA, Bowman SK, Kingston RE, Dillin A, Asara JM, Ruvkun G
Nat Cell Biol. 2013;15(5):491-501 - PMID: 23604319 - PMCID: PMC3748955 - DOI: 10.1038/ncb2720

Trauma-associated Human Neutrophil Alterations Revealed by Comparative Proteomics Profiling.

Zhou JY, Krovvidi RK, Gao Y, Gao H, Petritis BO, De A, Miller-Graziano C, Bankey PE, Petyuk VA, Nicora CD, Clauss TR, Moore RJ, Shi T, Brown JN, Kaushal A, Xiao W, Davis RW, Maier RV, Tompkins RG, Qian WJ, Camp DG, Smith RD,
Proteomics Clin Appl. 2013;7(7-8):571-83 - PMID: 23589343 - PMCID: PMC3737403 - DOI: 10.1002/prca.201200109

Functional RNAs exhibit tolerance for non-heritable 2'-5' versus 3'-5' backbone heterogeneity.

Engelhart AE, Powner MW, Szostak JW
Nat Chem. 2013;5(5):390-4 - PMID: 23609089 - PMCID: PMC4088963 - DOI: 10.1038/nchem.1623

Succinate is an inflammatory signal that induces IL-1β through HIF-1α

Tannahill GM, Curtis AM, Adamik J, Palsson-McDermott EM, McGettrick AF, Goel G, Frezza C, Bernard NJ, Kelly B, Foley NH, Zheng L, Gardet A, Tong Z, Jany SS, Corr SC, Haneklaus M, Caffrey BE, Pierce K, Walmsley S, Beasley FC, Cummins E, Nizet V, Whyte M, Taylor CT, Lin H, Masters SL, Gottlieb E, Kelly VP, Clish C, Auron PE, Xavier RJ, O'Neill LA
Nature. 2013;496(7444):238-42 - PMID: 23535595 - PMCID: PMC4031686 - DOI: 10.1038/nature11986

Persistent bacterial infections, antibiotic tolerance, and the oxidative stress response.

Grant SS, Hung DT
Virulence. 2013;4(4):273-283 - PMID: 23563389 - PMCID: PMC3710330 - DOI: 10.4161/viru.23987

TALEN-based Gene Correction for Epidermolysis Bullosa.

Osborn MJ, Starker CG, McElroy AN, Webber BR, Riddle MJ, Xia L, Defeo AP, Gabriel R, Schmidt M, Von Kalle C, Carlson DF, Maeder ML, Joung JK, Wagner JE, Voytas DF, Blazar BR, Tolar J
Mol Ther. 2013;21(6):1151-1159 - PMID: 23546300 - PMCID: PMC3677309 - DOI: 10.1038/mt.2013.56

Pseudomonas aeruginosa Disrupts Caenorhabditis elegans Iron Homeostasis, Causing a Hypoxic Response and Death.

Kirienko NV, Kirienko DR, Larkins-Ford J, Wählby C, Ruvkun G, Ausubel FM
Cell Host Microbe. 2013;13(4):406-16 - PMID: 23601103 - PMCID: PMC3641844 - DOI: 10.1016/j.chom.2013.03.003

Pseudomonas aeruginosa Disrupts Caenorhabditis elegans Iron Homeostasis, Causing a Hypoxic Response and Death.

Kirienko NV, Kirienko DR, Larkins-Ford J, Wählby C, Ruvkun G, Ausubel FM
Cell Host Microbe. 2013;13(4):406-16 - PMID: 23601103 - PMCID: PMC3641844 - DOI: 10.1016/j.chom.2013.03.003

MicroRNAs Visit the ER.

Montgomery TA, Ruvkun G
Cell. 2013;153(3):511-2 - PMID: 23622236 - DOI: 10.1016/j.cell.2013.04.014

Glucose-TOR signalling reprograms the transcriptome and activates meristems.

Xiong Y, McCormack M, Li L, Hall Q, Xiang C, Sheen J
Nature. 2013;496(7444):181-6 - PMID: 23542588 - PMCID: PMC4140196 - DOI: 10.1038/nature12030

Succinate is an inflammatory signal that induces IL-1? through HIF-1?.

Tannahill GM, Curtis AM, Adamik J, Palsson-McDermott EM, McGettrick AF, Goel G, Frezza C, Bernard NJ, Kelly B, Foley NH, Zheng L, Gardet A, Tong Z, Jany SS, Corr SC, Haneklaus M, Caffrey BE, Pierce K, Walmsley S, Beasley FC, Cummins E, Nizet V, Whyte M, Taylor CT, Lin H, Masters SL, Gottlieb E, Kelly VP, Clish C, Auron PE, Xavier RJ, O'Neill LA
Nature. 2013;496(7444):238-42 - PMID: 23535595 - PMCID: PMC4031686 - DOI: 10.1038/nature11986

Receptor interacting protein kinase 2-mediated mitophagy regulates inflammasome activation during virus infection.

Lupfer C, Thomas PG, Anand PK, Vogel P, Milasta S, Martinez J, Huang G, Green M, Kundu M, Chi H, Xavier RJ, Green DR, Lamkanfi M, Dinarello CA, Doherty PC, Kanneganti TD
Nat Immunol. 2013;14(5):480-8 - PMID: 23525089 - PMCID: PMC3631456 - DOI: 10.1038/ni.2563

Mitochondria-targeted antioxidant promotes recovery of skeletal muscle mitochondrial function after burn trauma assessed by in vivo 31P nuclear magnetic resonance and electron paramagnetic resonance spectroscopy.

Righi V, Constantinou C, Mintzopoulos D, Khan N, Mupparaju SP, Rahme LG, Swartz HM, Szeto HH, Tompkins RG, Tzika AA
FASEB J. 2013;27(6):2521-30 - PMID: 23482635 - PMCID: PMC3659352 - DOI: 10.1096/fj.12-220764

Efficacy of Phosphodiesterase 5 inhibitor on distant burn-induced muscle autophagy, microcirculation and survival rate.

Hosokawa S, Nagashima M, Maeyama Y, Koseki H, Yomogida K, Mehr C, Rutledge M, Greenfeld H, Kaneki M, Tompkins RG, Martyn JJ, Yasuhara SE
Am J Physiol Endocrinol Metab. 2013;304(9):E922-33 - PMID: 23512808 - DOI: 10.1152/ajpendo.00078.2013

Evaluation of Intragastric Vs Intraperitoneal Glucose Tolerance Tests in the Evaluation of Insulin Resistance in a Rodent Model of Burn Injury and Glucagon-Like Polypeptide-1 Treatment.

Watada S, Yu YM, Fischman AJ, Kurihara T, Shen CA, Tompkins RG, Fagan S
J Burn Care Res. 2013;35(1):e66-72 - PMID: 23511296 - PMCID: PMC4053788 - DOI: 10.1097/BCR.0b013e31828a8ede

Determination of Burn Patient Outcome by Large-Scale Quantitative Discovery Proteomics.

Finnerty CC, Jeschke MG, Qian WJ, Kaushal A, Xiao W, Liu T, Gritsenko MA, Moore RJ, Camp DG, Moldawer LL, Elson C, Schoenfeld D, Gamelli R, Gibran N, Klein M, Arnoldo B, Remick D, Smith RD, Davis R, Tompkins RG, Herndon DN,
Crit Care Med. 2013;41(6):1421-1434 - PMID: 23507713 - PMCID: PMC3660437 - DOI: 10.1097/CCM.0b013e31827c072e

Trehalose biosynthesis promotes Pseudomonas aeruginosa pathogenicity in plants.

Djonovi? S, Urbach JM, Drenkard E, Bush J, Feinbaum R, Ausubel JL, Traficante D, Risech M, Kocks C, Fischbach MA, Priebe GP, Ausubel FM
PLoS Pathog. 2013;9(3):e1003217 - PMID: 23505373 - PMCID: PMC3591346 - DOI: 10.1371/journal.ppat.1003217

Polarity gene discs large homolog 1 regulates the generation of memory T cells.

Gmyrek GB, Graham DB, Sandoval G, Blaufuss GS, Akilesh HM, Fujikawa K, Xavier RJ, Swat W
Eur J Immunol. 2013;43(5):1185-94 - PMID: 23436244 - PMCID: PMC3894631 - DOI: 10.1002/eji.201142362

Resolvin D2 restores neutrophil directionality and improves survival after burns.

Kurihara T, Jones CN, Yu YM, Fischman AJ, Watada S, Tompkins RG, Fagan SP, Irimia D
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Cutting Edge: cell-autonomous control of IL-7 response revealed in a novel stage of precursor B cells.

Sandoval GJ, Graham DB, Bhattacharya D, Sleckman BP, Xavier RJ, Swat W
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Effector-triggered versus pattern-triggered immunity: how animals sense pathogens.

Stuart LM, Paquette N, Boyer L
Nat Rev Immunol. 2013;13(3):199-206 - PMID: 23411798 - PMCID: PMC4121468 - DOI: 10.1038/nri3398

Development of a Colon Cancer GEMM-Derived Orthotopic Transplant Model for Drug Discovery and Validation.

Martin ES, Belmont PJ, Sinnamon MJ, Georgeon Richard L, Yuan J, Coffee EM, Roper J, Lee L, Heidari P, Lunt SY, Goel G, Ji C, Xie J, Xie T, Lamb J, Weinrich S, Vanarsdale TL, Bronson RT, Xavier RJ, Vander Heiden M, Kan JL, Mahmood U, Hung KE
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Genomic responses in mouse models poorly mimic human inflammatory diseases.

Seok J, Warren HS, Cuenca AG, Mindrinos MN, Baker HV, Xu W, Richards DR, McDonald-Smith GP, Gao H, Hennessy L, Finnerty CC, López CM, Honari S, Moore EE, Minei JP, Cuschieri J, Bankey PE, Johnson JL, Sperry J, Nathens AB, Billiar TR, West MA, Jeschke MG, Klein MB, Gamelli RL, Gibran NS, Brownstein BH, Miller-Graziano C, Calvano SE, Mason PH, Cobb JP, Rahme LG, Lowry SF, Maier RV, Moldawer LL, Herndon DN, Davis RW, Xiao W, Tompkins RG,
Proc Natl Acad Sci U S A. 2013;110(9):3507-12 - PMID: 23401516 - PMCID: PMC3587220 - DOI: 10.1073/pnas.1222878110

Robust, synergistic regulation of human gene expression using TALE activators.

Maeder ML, Linder SJ, Reyon D, Angstman JF, Fu Y, Sander JD, Joung JK
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Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing.

Kirby A, Gnirke A, Jaffe DB, Barešová V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, Defelice M, H?lková H, Sovová J, Vylet'al P, Antignac C, Guttman M, Handsaker RE, Perrin D, Steelman S, Sigurdsson S, Scheinman SJ, Sougnez C, Cibulskis K, Parkin M, Green T, Rossin E, Zody MC, Xavier RJ, Pollak MR, Alper SL, Lindblad-Toh K, Gabriel S, Hart PS, Regev A, Nusbaum C, Kmoch S, Bleyer AJ, Lander ES, Daly MJ
Nat Genet. 2013;45(3):299-303 - PMID: 23396133 - PMCID: PMC3901305 - DOI: 10.1038/ng.2543

Phosphorylation of D-allose by hexokinase involved in regulation of OsABF1 expression for growth inhibition in Oryza sativa L.

Fukumoto T, Kano A, Ohtani K, Inoue M, Yoshihara A, Izumori K, Tajima S, Shigematsu Y, Tanaka K, Ohkouchi T, Ishida Y, Nishizawa Y, Tada Y, Ichimura K, Gomi K, Yoo SD, Sheen J, Akimitsu K
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?-6 Polyunsaturated fatty acids extend life span through the activation of autophagy.

O'Rourke EJ, Kuballa P, Xavier R, Ruvkun G
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Autophagy modulates Borrelia burgdorferi-induced production of interleukin-1? (IL-1?).

Buffen K, Oosting M, Mennens S, Anand PK, Plantinga TS, Sturm P, van de Veerdonk FL, van der Meer JW, Xavier RJ, Kannegati TD, Netea MG, Joosten LA
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Development of a Genomic Metric That Can Be Rapidly Used to Predict Clinical Outcome in Severely Injured Trauma Patients.

Cuenca AG, Gentile LF, Lopez MC, Ungaro R, Liu H, Xiao W, Seok J, Mindrinos MN, Ang D, Ozrazgat Baslanti T, Bihorac A, Efron PA, Cuschieri J, Warren HS, Tompkins RG, Maier RV, Baker HV, Moldawer LL,
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Translating the Genomics Revolution: The Need for an International Gene Therapy Consortium for Monogenic Diseases.

Tremblay JP, Xiao X, Aartsma-Rus A, Barbas C, Blau HM, Bogdanove AJ, Boycott K, Braun S, Breakefield XO, Bueren JA, Buschmann M, Byrne BJ, Calos M, Cathomen T, Chamberlain J, Chuah M, Cornetta K, Davies KE, Dickson JG, Duchateau P, Flotte TR, Gaudet D, Gersbach CA, Gilbert R, Glorioso J, Herzog RW, High KA, Huang W, Huard J, Joung JK, Liu D, Liu D, Lochmüller H, Lustig L, Martens J, Massie B, Mavilio F, Mendell JR, Nathwani A, Ponder K, Porteus M, Puymirat J, Samulski J, Takeda S, Thrasher A ...
Mol Ther. 2013;21(2):266-268 - PMID: 23369965 - PMCID: PMC3594019 - DOI: 10.1038/mt.2013.4

Bifurcation of Arabidopsis NLR Immune Signaling via Ca(2+)-Dependent Protein Kinases.

Gao X, Chen X, Lin W, Chen S, Lu D, Niu Y, Li L, Cheng C, McCormack M, Sheen J, Shan L, He P
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Identification of a candidate therapeutic autophagy-inducing peptide.

Shoji-Kawata S, Sumpter R, Leveno M, Campbell GR, Zou Z, Kinch L, Wilkins AD, Sun Q, Pallauf K, MacDuff D, Huerta C, Virgin HW, Helms JB, Eerland R, Tooze SA, Xavier R, Lenschow DJ, Yamamoto A, King D, Lichtarge O, Grishin NV, Spector SA, Kaloyanova DV, Levine B
Nature. 2013;494(7436):201-6 - PMID: 23364696 - PMCID: PMC3788641 - DOI: 10.1038/nature11866

High-throughput sequencing reveals extraordinary fluidity of miRNA, piRNA, and siRNA pathways in nematodes.

Shi Z, Montgomery TA, Qi Y, Ruvkun G
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Efficient genome editing in zebrafish using a CRISPR-Cas system.

Hwang WY, Fu Y, Reyon D, Maeder ML, Tsai SQ, Sander JD, Peterson RT, Yeh JR, Joung JK
Nat Biotechnol. 2013;31(3):227-9 - PMID: 23360964 - PMCID: PMC3686313 - DOI: 10.1038/nbt.2501

Burn injury-induced IRS-1 degradation in mouse skeletal muscle.

Lu XM, Tompkins R, Fischman A
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Identification of Novel Host-Targeted Compounds That Protect From Anthrax Lethal Toxin-Induced Cell Death.

Slater LH, Hett EC, Mark K, Chumbler NM, Patel D, Lacy DB, Collier RJ, Hung DT
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ATG5 regulates plasma cell differentiation.

Conway KL, Kuballa P, Khor B, Zhang M, Shi HN, Virgin HW, Xavier RJ
Autophagy. 2013;9(4):528-37 - PMID: 23327930 - PMCID: PMC3627668 - DOI: 10.4161/auto.23484

Angiotensin II Drives the Production of Tumor-Promoting Macrophages.

Cortez-Retamozo V, Etzrodt M, Newton A, Ryan R, Pucci F, Sio SW, Kuswanto W, Rauch PJ, Chudnovskiy A, Iwamoto Y, Kohler R, Marinelli B, Gorbatov R, Wojtkiewicz G, Panizzi P, Mino-Kenudson M, Forghani R, Figueiredo JL, Chen JW, Xavier R, Swirski FK, Nahrendorf M, Weissleder R, Pittet MJ
Immunity. 2013;38(2):296-308 - PMID: 23333075 - PMCID: PMC3582771 - DOI: 10.1016/j.immuni.2012.10.015

Nitric oxide activates intradomain disulfide bond formation in the kinase loop of Akt1/PKB? after burn injury.

Lu XM, Tompkins RG, Fischman AJ
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Synthesis of N3'-P5'-linked phosphoramidate DNA by nonenzymatic template-directed primer extension.

Zhang S, Zhang N, Blain JC, Szostak JW
J Am Chem Soc. 2013;135(2):924-32 - PMID: 23252395 - PMCID: PMC3548433 - DOI: 10.1021/ja311164j

Identification of Pseudomonas aeruginosa Phenazines that Kill Caenorhabditis elegans.

Cezairliyan B, Vinayavekhin N, Grenfell-Lee D, Yuen GJ, Saghatelian A, Ausubel FM
PLoS Pathog. 2013;9(1):e1003101 - PMID: 23300454 - PMCID: PMC3536714 - DOI: 10.1371/journal.ppat.1003101

Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans.

Smeekens SP, Ng A, Kumar V, Johnson MD, Plantinga TS, van Diemen C, Arts P, Verwiel ET, Gresnigt MS, Fransen K, van Sommeren S, Oosting M, Cheng SC, Joosten LA, Hoischen A, Kullberg BJ, Scott WK, Perfect JR, van der Meer JW, Wijmenga C, Netea MG, Xavier RJ
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Radiation resistance of biological reagents for in situ life detection.

Carr CE, Rowedder H, Vafadari C, Lui CS, Cascio E, Zuber MT, Ruvkun G
Astrobiology. 2013;13(1):68-78 - PMID: 23330963 - DOI: 10.1089/ast.2012.0869

Simvastatin Protects Hepatocytes From Apoptosis by Suppressing the TNF-?/Caspase-3 Signaling Pathway in Mice With Burn Injury.

Zhao G, Yu YM, Kaneki M, Tompkins RG, Fischman AJ
Ann Surg. 2012;257(6):1129-36 - PMID: 23275311 - PMCID: PMC4102342 - DOI: 10.1097/SLA.0b013e318273fdca

Identification of small RNA pathway genes using patterns of phylogenetic conservation and divergence.

Tabach Y, Billi AC, Hayes GD, Newman MA, Zuk O, Gabel H, Kamath R, Yacoby K, Chapman B, Garcia SM, Borowsky M, Kim JK, Ruvkun G
Nature. 2012;493(7434):694-8 - PMID: 23364702 - PMCID: PMC3762460 - DOI: 10.1038/nature11779

Synthesis of N3´-P5´-Phosphoramidate DNA by Non-enzymatic Template-directed Primer Extension.

Zhang S, Zhang N, Blain JC, Szostak JW
J Am Chem Soc. 2012;135(2):924-32 - PMID: 23252395 - PMCID: PMC3548433 - DOI: 10.1021/ja311164j

Concentration-driven growth of model protocell membranes.

Budin I, Debnath A, Szostak JW
J Am Chem Soc. 2012;134(51):20812-9 - PMID: 23198690 - PMCID: PMC3530389 - DOI: 10.1021/ja310382d

Reply to Guy et al.: Support for a bottleneck in the 2011 Escherichia coli O104:H4 outbreak in Germany.

Grad YH, Lipsitch M, Griggs AD, Haas BJ, Shea TP, McCowan C, Montmayeur A, FitzGerald M, Wortman JR, Krogfelt KA, Bingen E, Weill FX, Tietze E, Flieger A, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP
Proc Natl Acad Sci U S A. 2012;109(52):E3629-30 - PMID: 23479789 - PMCID: PMC3535640 - DOI: 10.1073/pnas.1209419110

The LRR and RING Domain Protein LRSAM1 Is an E3 Ligase Crucial for Ubiquitin-Dependent Autophagy of Intracellular Salmonella Typhimurium.

Huett A, Heath RJ, Begun J, Sassi SO, Baxt LA, Vyas JM, Goldberg MB, Xavier RJ
Cell Host Microbe. 2012;12(6):778-90 - PMID: 23245322 - PMCID: PMC3785244 - DOI: 10.1016/j.chom.2012.10.019

Concentration-driven growth of model protocell membranes.

Budin I, Debnath A, Szostak JW
J Am Chem Soc. 2012;134(51):20812-9 - PMID: 23198690 - PMCID: PMC3530389 - DOI: 10.1021/ja310382d

TALENs: a widely applicable technology for targeted genome editing.

Joung JK, Sander JD
Nat Rev Mol Cell Biol. 2012;14(1):49-55 - PMID: 23169466 - PMCID: PMC3547402 - DOI: 10.1038/nrm3486

Stem Cell Signaling in Immunity and Development.

Lee H, Chah OK, Plotnikov J, Sheen J
Cold Spring Harb Symp Quant Biol. 2012;77:75-81 - PMID: 23174766 - DOI: 10.1101/sqb.2012.77.014837

Brown Adipose Tissue and Its Modulation by a Mitochondria-targeted Peptide in Rat Burn Injury Induced Hypermetabolism.

Yo K, Yu YM, Zhao G, Bonab AA, Aikawa N, Tompkins RG, Fischman AJ
Am J Physiol Endocrinol Metab. 2012;304(4):E331-41 - PMID: 23169784 - PMCID: PMC3566510 - DOI: 10.1152/ajpendo.00098.2012

Measurement of Phagocytosis, Phagosome Acidification, and Intracellular Killing of Staphylococcus aureus.

Sokolovska A, Becker CE, Stuart LM
Curr Protoc Immunol. 2012;Chapter 14:Unit14.30 - PMID: 23129153 - DOI: 10.1002/0471142735.im1430s99

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.

Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA, Essers J, Mitrovic M, Ning K, Cleynen I, Theatre E, Spain SL, Raychaudhuri S, Goyette P, Wei Z, Abraham C, Achkar JP, Ahmad T, Amininejad L, Ananthakrishnan AN, Andersen V, Andrews JM, Baidoo L, Balschun T, Bampton PA, Bitton A, Boucher G, Brand S, Büning C, Cohain A, Cichon S, D'Amato M, De Jong D, Devaney KL, Dubinsky M, Edwards C, Ellinghaus D, Ferguson LR, Franchimont D, Fransen K, Ge ...
Nature. 2012;491(7422):119-24 - PMID: 23128233 - PMCID: PMC3491803 - DOI: 10.1038/nature11582

Combination of Radiation and Burn Injury Alters [18F] 2-Fluoro-2-Deoxy-D-Glucose Uptake in Mice.

Carter EA, Winter D, Tolman C, Paul K, Hamrahi V, Tompkins RG, Fischman AJ
J Burn Care Res. 2012;33(6):723-30 - PMID: 23143615 - PMCID: PMC3673011 - DOI: 10.1097/BCR.0b013e31825d678f

A high-content imaging workflow to study Grb2 signaling complexes by expression cloning.

Freeman J, Kriston-Vizi J, Seed B, Ketteler R
J Vis Exp. 2012;(68):ePub - PMID: 23150065 - PMCID: PMC3499067 - DOI: 10.3791/4382

A High-content Imaging Workflow to Study Grb2 Signaling Complexes by Expression Cloning.

Freeman J, Kriston-Vizi J, Seed B, Ketteler R
J Vis Exp. 2012;(68):ePub - PMID: 23150065 - PMCID: PMC3499067 - DOI: 10.3791/4382

Prediction of C. elegans Longevity Genes by Human and Worm Longevity Networks.

Tacutu R, Shore DE, Budovsky A, de Magalhães JP, Ruvkun G, Fraifeld VE, Curran SP
PLoS One. 2012;7(10):e48282 - PMID: 23144747 - PMCID: PMC3483217 - DOI: 10.1371/journal.pone.0048282

Common alleles that influence autophagy and the risk for inflammatory bowel disease.

Gardet A, Xavier RJ
Curr Opin Immunol. 2012;24(5):522-9 - PMID: 23041451 - DOI: 10.1016/j.coi.2012.08.001

Imaging C-Fos Gene Expression in Burns Using Lipid Coated Spion Nanoparticles.

Papagiannaros A, Righi V, Day GG, Rahme LG, Liu PK, Fischman AJ, Tompkins RG, Tzika AA
Adv J Mol Imaging. 2012;2(4):31-37 - PMID: 24995147 - PMCID: PMC4076698 - DOI: 10.4236/ami.2012.24005

Engineering Designer Transcription Activator--Like Effector Nucleases (TALENs) by REAL or REAL-Fast Assembly.

Reyon D, Khayter C, Regan MR, Joung JK, Sander JD
Curr Protoc Mol Biol. 2012;Chapter 12:Unit12.15 - PMID: 23026907 - PMCID: PMC3753116 - DOI: 10.1002/0471142727.mb1215s100

The Two-Component Sensor KinB Acts as a Phosphatase to Regulate Pseudomonas aeruginosa Virulence.

Chand NS, Clatworthy AE, Hung DT
J Bacteriol. 2012;194(23):6537-47 - PMID: 23024348 - PMCID: PMC3497526 - DOI: 10.1128/JB.01168-12

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.

Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, Leleiko N, Snapper SB, Bousvaros A, Korzenik J, Sands BE, Xavier RJ, Huttenhower C
Genome Biol. 2012;13(9):R79 - PMID: 23013615 - PMCID: PMC3506950 - DOI: 10.1186/gb-2012-13-9-r79

Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes.

Kleinnijenhuis J, Quintin J, Preijers F, Joosten LA, Ifrim DC, Saeed S, Jacobs C, van Loenhout J, de Jong D, Stunnenberg HG, Xavier RJ, van der Meer JW, van Crevel R, Netea MG
Proc Natl Acad Sci U S A. 2012;109(43):17537-42 - PMID: 22988082 - PMCID: PMC3491454 - DOI: 10.1073/pnas.1202870109

Essential cell autonomous role for interferon regulatory factor 1 in interferon-?-mediated inhibition of norovirus replication in macrophages.

Maloney NS, Thackray LB, Goel G, Hwang S, Duan E, Vachharajani P, Xavier R, Virgin HW
J Virol. 2012;86(23):12655-64 - PMID: 22973039 - PMCID: PMC3497668 - DOI: 10.1128/JVI.01564-12

CDPKs in immune and stress signaling.

Boudsocq M, Sheen J
Trends Plant Sci. 2012;18(1):30-40 - PMID: 22974587 - PMCID: PMC3534830 - DOI: 10.1016/j.tplants.2012.08.008

Evaluation of OPEN Zinc Finger Nucleases for Direct Gene Targeting of the ROSA26 Locus in Mouse Embryos.

Hermann M, Maeder ML, Rector K, Ruiz J, Becher B, Bürki K, Khayter C, Aguzzi A, Joung JK, Buch T, Pelczar P
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Measuring the cost of care for children with acute burn injury.

Carey K, Kazis LE, Lee AF, Liang MH, Li NC, Hinson MI, Lydon MK, Bauk H, Shapiro GD, Tompkins RG,
J Trauma Acute Care Surg. 2012;73(3 Suppl 2):S229-33 - PMID: 22929551 - DOI: 10.1097/TA.0b013e318265c88a

Impact of hand burns on health-related quality of life in children younger than 5 years.

Palmieri TL, Nelson-Mooney K, Kagan RJ, Stubbs TK, Meyer WJ, Herndon DN, Hinson MI, Lee AF, Li NC, Kazis LE, Tompkins RG,
J Trauma Acute Care Surg. 2012;73(3 Suppl 2):S197-204 - PMID: 22929547 - DOI: 10.1097/TA.0b013e318265c7ff

The American Burn Association/Shriners Hospitals for Children Burn Outcomes Program: A progress report at 15 years.

Tompkins RG, Liang MH, Lee AF, Kazis LE,
J Trauma Acute Care Surg. 2012;73(3 Suppl 2):S173-8 - PMID: 22929544 - DOI: 10.1097/TA.0b013e318265c53e

Previous burn injury predisposes mice to lipopolysaccharide-induced changes in glucose metabolism.

Carter EA, Paul KW, Barrow SA, Fischman AJ, Tompkins RG
J Burn Care Res. 2012;33(5):683-9 - PMID: 22961012 - PMCID: PMC3441057 - DOI: 10.1097/BCR.0b013e31825d6a86

Safety and dosing of bevacizumab (avastin) for the treatment of recurrent respiratory papillomatosis.

Best SR, Friedman AD, Landau-Zemer T, Barbu AM, Burns JA, Freeman MW, Halvorsen YD, Hillman RE, Zeitels SM
Ann Otol Rhinol Laryngol. 2012;121(9):587-93 - PMID: 23012897 - DOI: 10.1177/000348941212100905

Complexity in Differential Peptide-Receptor Signaling: Response to Segonzac et al. and Mueller et al. Commentaries.

Lee H, Khatri A, Plotnikov JM, Zhang XC, Sheen J
Plant Cell. 2012;24(8):3177-85 - PMID: 22923676 - PMCID: PMC3462623 - DOI: 10.1105/tpc.112.099259

FLS2-Mediated Responses to Ax21-Derived Peptides: Response to the Mueller et al. Commentary.

Danna CH, Zhang XC, Khatri A, Bent AF, Ronald PC, Ausubel FM
Plant Cell. 2012;24(8):3174-6 - PMID: 22923675 - PMCID: PMC3462622 - DOI: 10.1105/tpc.112.099275

p40phox Expression Regulates Neutrophil Recruitment and Function during the Resolution Phase of Intestinal Inflammation.

Conway KL, Goel G, Sokol H, Manocha M, Mizoguchi E, Terhorst C, Bhan AK, Gardet A, Xavier RJ
J Immunol. 2012;189(7):3631-40 - PMID: 22914050 - PMCID: PMC3780969 - DOI: 10.4049/jimmunol.1103746

Multicomponent assembly of proposed DNA precursors in water.

Powner MW, Zheng SL, Szostak JW
J Am Chem Soc. 2012;134(33):13889-95 - PMID: 22839703 - PMCID: PMC3424849 - DOI: 10.1021/ja306176n

Enhanced Tim3 Activity Improves Survival after Influenza Infection.

Cho JL, Roche MI, Sandall B, Brass AL, Seed B, Xavier RJ, Medoff BD
J Immunol. 2012;189(6):2879-89 - PMID: 22875804 - PMCID: PMC3436990 - DOI: 10.4049/jimmunol.1102483

Enhanced Tim3 activity improves survival after influenza infection.

Cho JL, Roche MI, Sandall B, Brass AL, Seed B, Xavier RJ, Medoff BD
J Immunol. 2012;189(6):2879-89 - PMID: 22875804 - PMCID: PMC3436990 - DOI: 10.4049/jimmunol.1102483

Candida albicans Infection Affords Protection against Reinfection via Functional Reprogramming of Monocytes.

Quintin J, Saeed S, Martens JH, Giamarellos-Bourboulis EJ, Ifrim DC, Logie C, Jacobs L, Jansen T, Kullberg BJ, Wijmenga C, Joosten LA, Xavier RJ, van der Meer JW, Stunnenberg HG, Netea MG
Cell Host Microbe. 2012;12(2):223-32 - PMID: 22901542 - PMCID: PMC3864037 - DOI: 10.1016/j.chom.2012.06.006

New insights into siRNA amplification and RNAi.

Zhang C, Ruvkun G
RNA Biol. 2012;9(8):1045-9 - PMID: 22858672 - PMCID: PMC3551858 - DOI: 10.4161/rna.21246

A synthetic biology framework for programming eukaryotic transcription functions.

Khalil AS, Lu TK, Bashor CJ, Ramirez CL, Pyenson NC, Joung JK, Collins JJ
Cell. 2012;150(3):647-58 - PMID: 22863014 - PMCID: PMC3653585 - DOI: 10.1016/j.cell.2012.05.045

Multicomponent assembly of proposed DNA precursors in water.

Powner MW, Zheng SL, Szostak JW
J Am Chem Soc. 2012;134(33):13889-95 - PMID: 22839703 - PMCID: PMC3424849 - DOI: 10.1021/ja306176n

Gram-Negative Bacterial Infection in Thigh Abscess Can Migrate to Distant Burn Depending on Burn Depth.

Hamrahi V, Hamblin MR, Jung W, Benjamin JB, Paul KW, Fischman AJ, Tompkins RG, Carter EA
Interdiscip Perspect Infect Dis. 2012;2012:567140 - PMID: 22899912 - PMCID: PMC3412104 - DOI: 10.1155/2012/567140

Genome-Wide Identification of Pseudomonas aeruginosa Virulence-Related Genes Using a Caenorhabditis elegans Infection Model.

Feinbaum RL, Urbach JM, Liberati NT, Djonovic S, Adonizio A, Carvunis AR, Ausubel FM
PLoS Pathog. 2012;8(7):e1002813 - PMID: 22911607 - PMCID: PMC3406104 - DOI: 10.1371/journal.ppat.1002813

Genes Involved in the Evolution of Herbivory By A Leaf-Mining, Drosophilid Fly.

Whiteman NK, Gloss AD, Sackton TB, Groen SC, Humphrey PT, Lapoint RT, Sønderby IE, Halkier BA, Kocks C, Ausubel FM, Pierce NE
Genome Biol Evol. 2012;4(9):900-16 - PMID: 22813779 - PMCID: PMC3516228 - DOI: 10.1093/gbe/evs063

TRIF Licenses Caspase-11-Dependent NLRP3 Inflammasome Activation by Gram-Negative Bacteria.

Rathinam VA, Vanaja SK, Waggoner L, Sokolovska A, Becker C, Stuart LM, Leong JM, Fitzgerald KA
Cell. 2012;150(3):606-19 - PMID: 22819539 - PMCID: PMC3660860 - DOI: 10.1016/j.cell.2012.07.007

Induction of cytoprotective pathways is central to the extension of lifespan conferred by multiple longevity pathways.

Shore DE, Carr CE, Ruvkun G
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Eradication of bacterial persisters with antibiotic-generated hydroxyl radicals.

Schmidt Grant S, Kaufmann BB, Chand NS, Haseley N, Hung DT
Proc Natl Acad Sci U S A. 2012;109(30):12147-52 - PMID: 22778419 - PMCID: PMC3409745 - DOI: 10.1073/pnas.1203735109

EGL-9 Controls C. elegans Host Defense Specificity through Prolyl Hydroxylation-Dependent and -Independent HIF-1 Pathways.

Luhachack LG, Visvikis O, Wollenberg AC, Lacy-Hulbert A, Stuart LM, Irazoqui JE
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Perception of volatiles produced by UVC-irradiated plants alters the response to viral infection in naïve neighboring plants.

Yao Y, Danna CH, Ausubel FM, Kovalchuk I
Plant Signal Behav. 2012;7(7):741-5 - PMID: 22751319 - PMCID: PMC3583953 - DOI: 10.4161/psb.20406

Case 23-2012.

Xavier RJ, Gala MK, Bronzo BK, Kelly PJ
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Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease.

Papa E, Docktor M, Smillie C, Weber S, Preheim SP, Gevers D, Giannoukos G, Ciulla D, Tabbaa D, Ingram J, Schauer DB, Ward DV, Korzenik JR, Xavier RJ, Bousvaros A, Alm EJ
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Helminth Infection Impairs Autophagy-Mediated Killing of Bacterial Enteropathogens by Macrophages.

Su CW, Cao Y, Zhang M, Kaplan J, Su L, Fu Y, Walker WA, Xavier R, Cherayil BJ, Shi HN
J Immunol. 2012;189(3):1459-66 - PMID: 22732589 - PMCID: PMC3423331 - DOI: 10.4049/jimmunol.1200484

MUT-16 promotes formation of perinuclear Mutator foci required for RNA silencing in the C. elegans germline.

Phillips CM, Montgomery TA, Breen PC, Ruvkun G
Genes Dev. 2012;26(13):1433-44 - PMID: 22713602 - PMCID: PMC3403012 - DOI: 10.1101/gad.193904.112

Stimulation of Host Immune Defenses by a Small Molecule Protects C. elegans from Bacterial Infection.

Pukkila-Worley R, Feinbaum R, Kirienko NV, Larkins-Ford J, Conery AL, Ausubel FM
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Highly efficient generation of heritable zebrafish gene mutations using homo- and heterodimeric TALENs.

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Clinical review. Comparative effectiveness of drug treatments to prevent fragility fractures: a systematic review and network meta-analysis.

Murad MH, Drake MT, Mullan RJ, Mauck KF, Stuart LM, Lane MA, Abu Elnour NO, Erwin PJ, Hazem A, Puhan MA, Li T, Montori VM
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Cytokinin signaling networks

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Improved Somatic Mutagenesis in Zebrafish Using Transcription Activator-Like Effector Nucleases (TALENs).

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Identification of novel inhibitors of M. tuberculosis growth using whole cell based high-throughput screening.

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Penetration Resistance: PKR's Other Talent.

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In vivo molecular imaging of murine embryonic stem cells delivered to a burn wound surface via Integra® scaffolding.

Hamrahi VF, Goverman J, Jung W, Wu JC, Fischman AJ, Tompkins RG, Yu YY, Fagan SP, Carter EA
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The Caenorhabditis elegans RDE-10/RDE-11 Complex Regulates RNAi by Promoting Secondary siRNA Amplification.

Zhang C, Montgomery TA, Fischer SE, Garcia SM, Riedel CG, Fahlgren N, Sullivan CM, Carrington JC, Ruvkun G
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An image analysis toolbox for high-throughput C. elegans assays.

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PIWI Associated siRNAs and piRNAs Specifically Require the Caenorhabditis elegans HEN1 Ortholog henn-1.

Montgomery TA, Rim YS, Zhang C, Dowen RH, Phillips CM, Fischer SE, Ruvkun G
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Establishment and characterization of a novel chordoma cell line: CH22.

Liu X, Nielsen GP, Rosenberg AE, Waterman PR, Yang W, Choy E, Sassi S, Yang S, Harmon DC, Yang C, Schwab JH, Kobayashi E, Mankin HJ, Xavier R, Weissleder R, Duan Z, Hornicek FJ
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FLASH assembly of TALENs for high-throughput genome editing.

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Nat Biotechnol. 2012;30(5):460-5 - PMID: 22484455 - PMCID: PMC3558947 - DOI: 10.1038/nbt.2170

Regulation of monocyte functional heterogeneity by miR-146a and Relb.

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RNA signatures allow rapid identification of pathogens and antibiotic susceptibilities.

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Proc Natl Acad Sci U S A. 2012;109(16):6217-22 - PMID: 22474362 - PMCID: PMC3341018 - DOI: 10.1073/pnas.1119540109

Patterns of Care at End of Life in Children With Advanced Heart Disease.

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Arch Pediatr Adolesc Med. 2012;166(8):745-8 - PMID: 22473887 - PMCID: PMC4119813

Inactivation of Conserved C. elegans Genes Engages Pathogen- and Xenobiotic-Associated Defenses.

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Host Translational Inhibition by Pseudomonas aeruginosa Exotoxin A Triggers an Immune Response in Caenorhabditis elegans.

McEwan DL, Kirienko NV, Ausubel FM
Cell Host Microbe. 2012;11(4):364-74 - PMID: 22520464 - PMCID: PMC3334877 - DOI: 10.1016/j.chom.2012.02.007

Autophagy and the immune system.

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Annu Rev Immunol. 2012;30:611-46 - PMID: 22449030 - DOI: 10.1146/annurev-immunol-020711-074948

The changing pattern and implications of multiple organ failure after blunt injury with hemorrhagic shock*

Minei JP, Cuschieri J, Sperry J, Moore EE, West MA, Harbrecht BG, O'Keefe GE, Cohen MJ, Moldawer LL, Tompkins RG, Maier RV
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Nondegradative Role of Atg5-Atg12/ Atg16L1 Autophagy Protein Complex in Antiviral Activity of Interferon Gamma.

Hwang S, Maloney NS, Bruinsma MW, Goel G, Duan E, Zhang L, Shrestha B, Diamond MS, Dani A, Sosnovtsev SV, Green KY, Lopez-Otin C, Xavier RJ, Thackray LB, Virgin HW
Cell Host Microbe. 2012;11(4):397-409 - PMID: 22520467 - PMCID: PMC3348177 - DOI: 10.1016/j.chom.2012.03.002

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Autophagy. 2012;8(4):445-544 - PMID: 22966490 - PMCID: PMC3404883 - DOI: 10.4161/auto.19496

Targeted parallel sequencing of large genetically-defined genomic regions for identifying mutations in Arabidopsis.

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Plant Methods. 2012;8(1):12 - PMID: 22462410 - PMCID: PMC3348062 - DOI: 10.1186/1746-4811-8-12

Benchmarking Outcomes in the Critically Injured Trauma Patient and the Effect of Implementing Standard Operating Procedures.

Cuschieri J, Johnson JL, Sperry J, West MA, Moore EE, Minei JP, Bankey PE, Nathens AB, Cuenca AG, Efron PA, Hennessy L, Xiao W, Mindrinos MN, McDonald-Smith GP, Mason PH, Billiar TR, Schoenfeld DA, Warren HS, Cobb JP, Moldawer LL, Davis RW, Maier RV, Tompkins RG,
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Clinical review. Risk factors for low bone mass-related fractures in men: a systematic review and meta-analysis.

Drake MT, Murad MH, Mauck KF, Lane MA, Undavalli C, Elraiyah T, Stuart LM, Prasad C, Shahrour A, Mullan RJ, Hazem A, Erwin PJ, Montori VM
J Clin Endocrinol Metab. 2012;97(6):1861-70 - PMID: 22466344 - DOI: 10.1210/jc.2011-3058

In Vitro Selection of Highly Modified Cyclic Peptides That Act as Tight Binding Inhibitors.

Guillen Schlippe YV, Hartman MC, Josephson K, Szostak JW
J Am Chem Soc. 2012;134(25):10469-77 - PMID: 22428867 - PMCID: PMC3384292 - DOI: 10.1021/ja301017y

Apoptotic cells can deliver chemotherapeutics to engulfing macrophages and suppress inflammatory cytokine production.

Perez B, Paquette N, Païdassi H, Zhai B, White K, Skvirsky R, Lacy-Hulbert A, Stuart LM
J Biol Chem. 2012;287(19):16029-36 - PMID: 22433861 - PMCID: PMC3346138 - DOI: 10.1074/jbc.M112.340489

Integration of architectural and cytologic driven image algorithms for prostate adenocarcinoma identification.

Hipp J, Monaco J, Kunju LP, Cheng J, Yagi Y, Rodriguez-Canales J, Emmert-Buck MR, Hewitt S, Feldman MD, Tomaszewski JE, Toner M, Tompkins RG, Flotte T, Lucas D, Gilbertson JR, Madabhushi A, Balis U
Anal Cell Pathol (Amst). 2012;35(4):251-65 - PMID: 22425661 - PMCID: PMC4605585 - DOI: 10.3233/ACP-2012-0054

DNA purification from multiple sources in plant research with homemade silica resins.

Li JF, Sheen J
Methods Mol Biol. 2012;862:53-9 - PMID: 22419488 - DOI: 10.1007/978-1-61779-609-8_5

Glucose metabolism during the early after burn injury.

Xu H, Yu YM, Ma H, Carter EA, Fagan S, Tompkins RG, Fischman AJ
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Repression of Germline RNAi Pathways in Somatic Cells by Retinoblastoma Pathway Chromatin Complexes.

Wu X, Shi Z, Cui M, Han M, Ruvkun G
PLoS Genet. 2012;8(3):e1002542 - PMID: 22412383 - PMCID: PMC3297578 - DOI: 10.1371/journal.pgen.1002542

The mevalonate pathway regulates microRNA activity in Caenorhabditis elegans.

Shi Z, Ruvkun G
Proc Natl Acad Sci U S A. 2012;109(12):4568-73 - PMID: 22396595 - PMCID: PMC3311396 - DOI: 10.1073/pnas.1202421109

In Vivo Molecular Imaging of Murine Embryonic Stem Cells Delivered to a Burn Wound Surface via Integra® Scaffolding.

Hamrahi VF, Goverman J, Jung W, Wu JC, Fischman AJ, Tompkins RG, Yu YY, Fagan SP, Carter EA
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ONCOGENIC KRAS REGULATES BMP4 EXPRESSION IN COLON CANCER CELL LINES.

Duerr EM, Mizukami Y, Moriichi K, Gala M, Jo WS, Kikuchi H, Xavier RJ, Chung DC
Am J Physiol Gastrointest Liver Physiol. 2012;302(10):G1223-30 - PMID: 22383492 - PMCID: PMC3362092 - DOI: 10.1152/ajpgi.00047.2011

Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects.

Ramirez CL, Certo MT, Mussolino C, Goodwin MJ, Cradick TJ, McCaffrey AP, Cathomen T, Scharenberg AM, Joung JK
Nucleic Acids Res. 2012;40(12):5560-8 - PMID: 22373919 - PMCID: PMC3384306 - DOI: 10.1093/nar/gks179

A Peroxidase-Dependent Apoplastic Oxidative Burst in Cultured Arabidopsis Cells Functions in MAMP-Elicited Defense.

O'Brien JA, Daudi A, Finch P, Butt VS, Whitelegge JP, Souda P, Ausubel FM, Bolwell GP
Plant Physiol. 2012;158(4):2013-27 - PMID: 22319074 - PMCID: PMC3320203 - DOI: 10.1104/pp.111.190140

Genomic epidemiology of the Escherichia coli O104:H4 outbreaks in Europe, 2011.

Grad YH, Lipsitch M, Feldgarden M, Arachchi HM, Cerqueira GC, Fitzgerald M, Godfrey P, Haas BJ, Murphy CI, Russ C, Sykes S, Walker BJ, Wortman JR, Young S, Zeng Q, Abouelleil A, Bochicchio J, Chauvin S, Desmet T, Gujja S, McCowan C, Montmayeur A, Steelman S, Frimodt-Møller J, Petersen AM, Struve C, Krogfelt KA, Bingen E, Weill FX, Lander ES, Nusbaum C, Birren BW, Hung DT, Hanage WP
Proc Natl Acad Sci U S A. 2012;109(8):3065-70 - PMID: 22315421 - PMCID: PMC3286951 - DOI: 10.1073/pnas.1121491109

Activated ribonucleotides undergo a sugar pucker switch upon binding to a single-stranded RNA template.

Zhang N, Zhang S, Szostak JW
J Am Chem Soc. 2012;134(8):3691-4 - PMID: 22296305 - PMCID: PMC3448298 - DOI: 10.1021/ja212027q

Severe injury is associated with insulin resistance, endoplasmic reticulum stress response, and unfolded protein response.

Jeschke MG, Finnerty CC, Herndon DN, Song J, Boehning D, Tompkins RG, Baker HV, Gauglitz GG
Ann Surg. 2012;255(2):370-8 - PMID: 22241293 - PMCID: PMC3395076 - DOI: 10.1097/SLA.0b013e31823e76e7

Attempts to define life do not help to understand the origin of life.

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J Biomol Struct Dyn. 2012;29(4):599-600 - PMID: 22208251 - PMCID: PMC4208307 - DOI: 10.1080/073911012010524998

Survival of children with burn injuries.

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Lancet. 2012;379(9820):983-4 - PMID: 22296811 - PMCID: PMC4019221 - DOI: 10.1016/S0140-6736(11)61626-7

Thermal Injury Activates eEF2k-Dependent eEF2 Pathway in Pediatric Patients.

Song J, Finnerty CC, Herndon DN, Kraft R, Boehning D, Brooks NC, Tompkins RG, Jeschke MG
JPEN J Parenter Enteral Nutr. 2012;36(5):596-602 - PMID: 22269896 - PMCID: PMC3580832 - DOI: 10.1177/0148607111422234

Tribbles 2 (Trib2) is a novel regulator of toll-like receptor 5 signaling.

Wei SC, Rosenberg IM, Cao Z, Huett AS, Xavier RJ, Podolsky DK
Inflamm Bowel Dis. 2012;18(5):877-88 - PMID: 22271508 - PMCID: PMC3881418 - DOI: 10.1002/ibd.22883

HIV-1 Nef mobilizes lipid rafts in macrophages through a pathway that competes with ABCA1-dependent cholesterol efflux.

Cui HL, Grant A, Mukhamedova N, Pushkarsky T, Jennelle L, Dubrovsky L, Gaus K, Fitzgerald ML, Sviridov D, Bukrinsky M
J Lipid Res. 2012;53(4):696-708 - PMID: 22262807 - PMCID: PMC3307646 - DOI: 10.1194/jlr.M023119

Genome-wide siRNA screen for mediators of NF-?B activation.

Gewurz BE, Towfic F, Mar JC, Shinners NP, Takasaki K, Zhao B, Cahir-McFarland ED, Quackenbush J, Xavier RJ, Kieff E
Proc Natl Acad Sci U S A. 2012;109(7):2467-72 - PMID: 22308454 - PMCID: PMC3289371 - DOI: 10.1073/pnas.1120542109

The apoplastic oxidative burst peroxidase in Arabidopsis is a major component of pattern-triggered immunity.

Daudi A, Cheng Z, O'Brien JA, Mammarella N, Khan S, Ausubel FM, Bolwell GP
Plant Cell. 2012;24(1):275-87 - PMID: 22247251 - PMCID: PMC3289579 - DOI: 10.1105/tpc.111.093039

Immune defense mechanisms in the Caenorhabditis elegans intestinal epithelium.

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Curr Opin Immunol. 2012;24(1):3-9 - PMID: 22236697 - PMCID: PMC3660727 - DOI: 10.1016/j.coi.2011.10.004

The neuroimmune guidance cue netrin-1 promotes atherosclerosis by inhibiting the emigration of macrophages from plaques.

van Gils JM, Derby MC, Fernandes LR, Ramkhelawon B, Ray TD, Rayner KJ, Parathath S, Distel E, Feig JL, Alvarez-Leite JI, Rayner AJ, McDonald TO, O'Brien KD, Stuart LM, Fisher EA, Lacy-Hulbert A, Moore KJ
Nat Immunol. 2012;13(2):136-43 - PMID: 22231519 - PMCID: PMC3262880 - DOI: 10.1038/ni.2205

Incidence of Catheter-Associated Bloodstream Infection After Introduction of Minocycline and Rifampin Antimicrobial-Coated Catheters in a Pediatric Burn Population.

Weber JM, Sheridan RL, Fagan S, Ryan CM, Pasternack MS, Tompkins RG
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STAT6 phosphorylation inhibitors block eotaxin-3 secretion in bronchial epithelial cells.

Zhou L, Kawate T, Liu X, Kim YB, Zhao Y, Feng G, Banerji J, Nash H, Whitehurst C, Jindal S, Siddiqui A, Seed B, Wolfe JL
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SILAM for quantitative proteomics of liver Akt1/PKB? after burn injury.

Lu XM, Tompkins RG, Fischman AJ
Int J Mol Med. 2011;29(3):461-71 - PMID: 22179310 - PMCID: PMC3981641 - DOI: 10.3892/ijmm.2011.861

Autophagy suppresses interleukin-1? (IL-1?) signaling by activation of p62 degradation via lysosomal and proteasomal pathways.

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Resuscitation-promoting factors are required for ?-lactam tolerance and the permeability barrier in Mycobacterium tuberculosis.

Wivagg CN, Hung DT
Antimicrob Agents Chemother. 2011;56(3):1591-4 - PMID: 22155826 - PMCID: PMC3294900 - DOI: 10.1128/AAC.06027-11

Rapamycin and glucose-target of rapamycin (TOR) protein signaling in plants.

Xiong Y, Sheen J
J Biol Chem. 2011;287(4):2836-42 - PMID: 22134914 - PMCID: PMC3268441 - DOI: 10.1074/jbc.M111.300749

Image-based genome-wide siRNA screen identifies selective autophagy factors.

Orvedahl A, Sumpter R, Xiao G, Ng A, Zou Z, Tang Y, Narimatsu M, Gilpin C, Sun Q, Roth M, Forst CV, Wrana JL, Zhang YE, Luby-Phelps K, Xavier RJ, Xie Y, Levine B
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Novel mitochondria-targeted antioxidant peptide ameliorates burn-induced apoptosis and endoplasmic reticulum stress in the skeletal muscle of mice.

Lee HY, Kaneki M, Andreas J, Tompkins RG, Martyn JA
Shock. 2011;36(6):580-5 - PMID: 21937949 - PMCID: PMC3230221 - DOI: 10.1097/SHK.0b013e3182366872

Acetylcholine ?7 nicotinic and dopamine D(2) receptors are targeted to many of the same postsynaptic dendrites and astrocytes in the rodent prefrontal cortex.

Duffy AM, Fitzgerald ML, Chan J, Robinson DC, Milner TA, Mackie K, Pickel VM
Synapse. 2011;65(12):1350-67 - PMID: 21858872 - PMCID: PMC3356922 - DOI: 10.1002/syn.20977

Bacterial effectors: learning on the fly.

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Adv Exp Med Biol. 2011;710:29-36 - PMID: 22127883 - PMCID: PMC3427734 - DOI: 10.1007/978-1-4419-5638-5_4

The C. elegans DAF-2 Insulin-Like Receptor is Abundantly Expressed in the Nervous System and Regulated by Nutritional Status.

Kimura KD, Riddle DL, Ruvkun G
Cold Spring Harb Symp Quant Biol. 2011;76:113-20 - PMID: 22123849 - DOI: 10.1101/sqb.2011.76.010660

The Creating an Optimal Warfarin Nomogram (CROWN) Study.

Perlstein TS, Goldhaber SZ, Nelson K, Joshi V, Morgan TV, Lesko LJ, Lee JY, Gobburu J, Schoenfeld D, Kucherlapati R, Freeman MW, Creager MA
Thromb Haemost. 2011;107(1):59-68 - PMID: 22116191 - PMCID: PMC4133142 - DOI: 10.1160/TH11-08-0568

A genomic storm in critically injured humans.

Xiao W, Mindrinos MN, Seok J, Cuschieri J, Cuenca AG, Gao H, Hayden DL, Hennessy L, Moore EE, Minei JP, Bankey PE, Johnson JL, Sperry J, Nathens AB, Billiar TR, West MA, Brownstein BH, Mason PH, Baker HV, Finnerty CC, Jeschke MG, López MC, Klein MB, Gamelli RL, Gibran NS, Arnoldo B, Xu W, Zhang Y, Calvano SE, McDonald-Smith GP, Schoenfeld DA, Storey JD, Cobb JP, Warren HS, Moldawer LL, Herndon DN, Lowry SF, Maier RV, Davis RW, Tompkins RG,
J Exp Med. 2011;208(13):2581-90 - PMID: 22110166 - PMCID: PMC3244029 - DOI: 10.1084/jem.20111354

Wild type and Tangier disease ABCA1 mutants modulate cellular amyloid-? production independent of cholesterol efflux activity.

Kim WS, Hill AF, Fitzgerald ML, Freeman MW, Evin G, Garner B
J Alzheimers Dis. 2011;27(2):441-52 - PMID: 21860089 - DOI: 10.3233/JAD-2011-110521

Systematics-guided bioprospecting for bioactive microbial natural products.

Liu X, Bolla K, Ashforth EJ, Zhuo Y, Gao H, Huang P, Stanley SA, Hung DT, Zhang L
Antonie Van Leeuwenhoek. 2011;101(1):55-66 - PMID: 22086462 - DOI: 10.1007/s10482-011-9671-1

PrimerBank: a PCR primer database for quantitative gene expression analysis, 2012 update.

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The ERI-6/7 helicase acts at the first stage of an siRNA amplification pathway that targets recent gene duplications.

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CARMA1 is necessary for optimal T cell responses in a murine model of allergic asthma.

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The two-component sensor kinase KinB acts as a non-canonical switch between acute and chronic infection.

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Virulence. 2011;2(6):553-8 - PMID: 21971182 - DOI: 10.4161/viru.2.6.17987

In situ genetic correction of the sickle cell anemia mutation in human induced pluripotent stem cells using engineered zinc finger nucleases.

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Caspase 8 inhibits programmed necrosis by processing CYLD.

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Down-regulation of glutatione S-transferase ? 4 (hGSTA4) in the muscle of thermally injured patients is indicative of susceptibility to bacterial infection.

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UV-C-irradiated Arabidopsis and tobacco emit volatiles that trigger genomic instability in neighboring plants.

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Simvastatin treatment improves survival in a murine model of burn sepsis: Role of interleukin 6.

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Burns. 2010;37(2):222-6 - PMID: 21145172 - PMCID: PMC4085785 - DOI: 10.1016/j.burns.2010.10.010

Cancer. Germ cell genes and cancer.

Wu X, Ruvkun G
Science. 2010;330(6012):1761-2 - PMID: 21205660 - DOI: 10.1126/science.1200772

Failure and exploitation of autophagy in human pathologies-cellular integrity between inflammation, infection, and cell survival.

Kuballa P, Xavier RJ
Semin Immunopathol. 2010;32(4):319-22 - PMID: 21107575 - DOI: 10.1007/s00281-010-0229-5

The contribution of muscle to whole-body protein turnover throughout the course of burn injury in children.

Prelack K, Yu YM, Dylewski M, Lydon M, Sheridan RL, Tompkins RG
J Burn Care Res. 2010;31(6):942-8 - PMID: 21105320 - PMCID: PMC4084779 - DOI: 10.1097/BCR.0b013e3181f938e1

av Integrin expression by DCs is required for Th17 cell differentiation and development of experimental autoimmune encephalomyelitis in mice.

Acharya M, Mukhopadhyay S, Païdassi H, Jamil T, Chow C, Kissler S, Stuart LM, Hynes RO, Lacy-Hulbert A
J Clin Invest. 2010;120(12):4445-52 - PMID: 21099114 - PMCID: PMC2993596 - DOI: 10.1172/JCI43796

Mining the plant-herbivore interface with a leafmining Drosophila of Arabidopsis.

Whiteman NK, Groen SC, Chevasco D, Bear A, Beckwith N, Gregory TR, Denoux C, Mammarella N, Ausubel FM, Pierce NE
Mol Ecol. 2010;20(5):995-1014 - PMID: 21073583 - PMCID: PMC3062943 - DOI: 10.1111/j.1365-294X.2010.04901.x

Stem cells and burns: review and therapeutic implications.

Butler KL, Goverman J, Ma H, Fischman A, Yu YM, Bilodeau M, Rad AM, Bonab AA, Tompkins RG, Fagan SP
J Burn Care Res. 2010;31(6):874-81 - PMID: 20859216 - DOI: 10.1097/BCR.0b013e3181f9353a

Predicting success of oligomerized pool engineering (OPEN) for zinc finger target site sequences.

Sander JD, Reyon D, Maeder ML, Foley JE, Thibodeau-Beganny S, Li X, Regan MR, Dahlborg EJ, Goodwin MJ, Fu F, Voytas DF, Joung JK, Dobbs D
BMC Bioinformatics. 2010;11:543 - PMID: 21044337 - PMCID: PMC3098093 - DOI: 10.1186/1471-2105-11-543

Chemoselective multicomponent one-pot assembly of purine precursors in water.

Powner MW, Sutherland JD, Szostak JW
J Am Chem Soc. 2010;132(46):16677-88 - PMID: 21043502 - PMCID: PMC2984373 - DOI: 10.1021/ja108197s

Ubiquitin accumulation in autophagy-deficient mice is dependent on the Nrf2-mediated stress response pathway: a potential role for protein aggregation in autophagic substrate selection.

Riley BE, Kaiser SE, Shaler TA, Ng AC, Hara T, Hipp MS, Lage K, Xavier RJ, Ryu KY, Taguchi K, Yamamoto M, Tanaka K, Mizushima N, Komatsu M, Kopito RR
J Cell Biol. 2010;191(3):537-52 - PMID: 21041446 - PMCID: PMC3003313 - DOI: 10.1083/jcb.201005012

LRRK2 is involved in the IFN-gamma response and host response to pathogens.

Gardet A, Benita Y, Li C, Sands BE, Ballester I, Stevens C, Korzenik JR, Rioux JD, Daly MJ, Xavier RJ, Podolsky DK
J Immunol. 2010;185(9):5577-85 - PMID: 20921534 - PMCID: PMC3156100 - DOI: 10.4049/jimmunol.1000548

DNA ends: just the beginning (Nobel lecture).

Szostak JW
Angew Chem Int Ed Engl. 2010;49(41):7386-404 - PMID: 20818632 - DOI: 10.1002/anie.201000635

Discover and connect cellular signaling.

Sheen J
Plant Physiol. 2010;154(2):562-6 - PMID: 20921185 - PMCID: PMC2949017 - DOI: 10.1104/pp.110.161364

Morphology-guided graph search for untangling objects: C. elegans analysis.

Raviv TR, Ljosa V, Conery AL, Ausubel FM, Carpenter AE, Golland P, Wählby C
Med Image Comput Comput Assist Interv. 2010;13(Pt 3):634-41 - PMID: 20879454 - PMCID: PMC3050593

NLRP3 inflammasome plays a key role in the regulation of intestinal homeostasis.

Hirota SA, Ng J, Lueng A, Khajah M, Parhar K, Li Y, Lam V, Potentier MS, Ng K, Bawa M, McCafferty DM, Rioux KP, Ghosh S, Xavier RJ, Colgan SP, Tschopp J, Muruve D, MacDonald JA, Beck PL
Inflamm Bowel Dis. 2010;17(6):1359-72 - PMID: 20872834 - PMCID: PMC3026862 - DOI: 10.1002/ibd.21478

Mutation of the ATP cassette binding transporter A1 (ABCA1) C-terminus disrupts HIV-1 Nef binding but does not block the Nef enhancement of ABCA1 protein degradation.

Mujawar Z, Tamehiro N, Grant A, Sviridov D, Bukrinsky M, Fitzgerald ML
Biochemistry. 2010;49(38):8338-49 - PMID: 20731376 - PMCID: PMC2943568 - DOI: 10.1021/bi100466q

Plasma proteome response to severe burn injury revealed by 18O-labeled "universal" reference-based quantitative proteomics.

Qian WJ, Petritis BO, Kaushal A, Finnerty CC, Jeschke MG, Monroe ME, Moore RJ, Schepmoes AA, Xiao W, Moldawer LL, Davis RW, Tompkins RG, Herndon DN, Camp DG, Smith RD,
J Proteome Res. 2010;9(9):4779-89 - PMID: 20698492 - PMCID: PMC2945297 - DOI: 10.1021/pr1005026

Effect of simvastatin on burn-induced alterations in tissue specific glucose metabolism: implications for burn associated insulin resistance.

Bonab AA, Carter EA, Paul K, Kaneki M, Yu YM, Tompkins RG, Fischman AJ
Int J Mol Med. 2010;26(3):311-6 - PMID: 20664945 - PMCID: PMC4090513

Clinical microfluidics for neutrophil genomics and proteomics.

Kotz KT, Xiao W, Miller-Graziano C, Qian WJ, Russom A, Warner EA, Moldawer LL, De A, Bankey PE, Petritis BO, Camp DG, Rosenbach AE, Goverman J, Fagan SP, Brownstein BH, Irimia D, Xu W, Wilhelmy J, Mindrinos MN, Smith RD, Davis RW, Tompkins RG, Toner M,
Nat Med. 2010;16(9):1042-7 - PMID: 20802500 - PMCID: PMC3136804 - DOI: 10.1038/nm.2205

Human IRGM gene "to be or not to be".

Bekpen C, Xavier RJ, Eichler EE
Semin Immunopathol. 2010;32(4):437-44 - PMID: 20737271 - DOI: 10.1007/s00281-010-0224-x

Autonomous zinc-finger nuclease pairs for targeted chromosomal deletion.

Söllü C, Pars K, Cornu TI, Thibodeau-Beganny S, Maeder ML, Joung JK, Heilbronn R, Cathomen T
Nucleic Acids Res. 2010;38(22):8269-76 - PMID: 20716517 - PMCID: PMC3001086 - DOI: 10.1093/nar/gkq720

Engineering single Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system.

Thibodeau-Beganny S, Maeder ML, Joung JK
Methods Mol Biol. 2010;649:31-50 - PMID: 20680826 - DOI: 10.1007/978-1-60761-753-2_2

Single-molecule binding experiments on long time scales.

Elenko MP, Szostak JW, van Oijen AM
Rev Sci Instrum. 2010;81(8):083705 - PMID: 20815611 - DOI: 10.1063/1.3473936

Circulating Nef induces dyslipidemia in simian immunodeficiency virus-infected macaques by suppressing cholesterol efflux.

Asztalos BF, Mujawar Z, Morrow MP, Grant A, Pushkarsky T, Wanke C, Shannon R, Geyer M, Kirchhoff F, Sviridov D, Fitzgerald ML, Bukrinsky M, Mansfield KG
J Infect Dis. 2010;202(4):614-23 - PMID: 20617930 - PMCID: PMC2932757 - DOI: 10.1086/654817

Burn injury reduces neutrophil directional migration speed in microfluidic devices.

Butler KL, Ambravaneswaran V, Agrawal N, Bilodeau M, Toner M, Tompkins RG, Fagan S, Irimia D
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Reactive bone marrow stromal cells attenuate systemic inflammation via sTNFR1.

Yagi H, Soto-Gutierrez A, Navarro-Alvarez N, Nahmias Y, Goldwasser Y, Kitagawa Y, Tilles AW, Tompkins RG, Parekkadan B, Yarmush ML
Mol Ther. 2010;18(10):1857-64 - PMID: 20664529 - PMCID: PMC2951565 - DOI: 10.1038/mt.2010.155

Genome-wide analysis reveals mechanisms modulating autophagy in normal brain aging and in Alzheimer's disease.

Lipinski MM, Zheng B, Lu T, Yan Z, Py BF, Ng A, Xavier RJ, Li C, Yankner BA, Scherzer CR, Yuan J
Proc Natl Acad Sci U S A. 2010;107(32):14164-9 - PMID: 20660724 - PMCID: PMC2922576 - DOI: 10.1073/pnas.1009485107

Wnt signaling regulates mitochondrial physiology and insulin sensitivity.

Yoon JC, Ng A, Kim BH, Bianco A, Xavier RJ, Elledge SJ
Genes Dev. 2010;24(14):1507-18 - PMID: 20634317 - PMCID: PMC2904941 - DOI: 10.1101/gad.1924910

Distinct pathogenesis and host responses during infection of C. elegans by P. aeruginosa and S. aureus.

Irazoqui JE, Troemel ER, Feinbaum RL, Luhachack LG, Cezairliyan BO, Ausubel FM
PLoS Pathog. 2010;6:e1000982 - PMID: 20617181 - PMCID: PMC2895663 - DOI: 10.1371/journal.ppat.1000982

A systems biology viewpoint on autophagy in health and disease.

Huett A, Goel G, Xavier RJ
Curr Opin Gastroenterol. 2010;26(4):302-9 - PMID: 20571384 - DOI: 10.1097/MOG.0b013e32833ae2ed

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity.

Ng AC, Eisenberg JM, Heath RJ, Huett A, Robinson CM, Nau GJ, Xavier RJ
Proc Natl Acad Sci U S A. 2010;108 Suppl 1:4631-8 - PMID: 20616063 - PMCID: PMC3063585 - DOI: 10.1073/pnas.1000093107

The transcription factor MafB antagonizes antiviral responses by blocking recruitment of coactivators to the transcription factor IRF3.

Kim H, Seed B
Nat Immunol. 2010;11(8):743-50 - PMID: 20581830 - PMCID: PMC3050627 - DOI: 10.1038/ni.1897

Bone marrow mesenchymal stromal cells attenuate organ injury induced by LPS and burn.

Yagi H, Soto-Gutierrez A, Kitagawa Y, Tilles AW, Tompkins RG, Yarmush ML
Cell Transplant. 2010;19(6):823-30 - PMID: 20573305 - PMCID: PMC2957544 - DOI: 10.3727/096368910X508942

Mice lacking Dok-1, Dok-2, and Dok-3 succumb to aggressive histiocytic sarcoma.

Mashima R, Honda K, Yang Y, Morita Y, Inoue A, Arimura S, Nishina H, Ema H, Nakauchi H, Seed B, Oda H, Yamanashi Y
Lab Invest. 2010;90(9):1357-64 - PMID: 20548287 - DOI: 10.1038/labinvest.2010.121

Mesenchymal stem cells: Mechanisms of immunomodulation and homing.

Yagi H, Soto-Gutierrez A, Parekkadan B, Kitagawa Y, Tompkins RG, Kobayashi N, Yarmush ML
Cell Transplant. 2010;19(6):667-79 - PMID: 20525442 - PMCID: PMC2957533 - DOI: 10.3727/096368910X508762

Conformationally constrained spiro C-arylglucosides as potent and selective renal sodium-dependent glucose co-transporter 2 (SGLT2) inhibitors.

Lv B, Feng Y, Dong J, Xu M, Xu B, Zhang W, Sheng Z, Welihinda A, Seed B, Chen Y
ChemMedChem. 2010;5(6):827-31 - PMID: 20414917 - DOI: 10.1002/cmdc.201000051

A genome-wide siRNA screen reveals multiple mTORC1 independent signaling pathways regulating autophagy under normal nutritional conditions.

Lipinski MM, Hoffman G, Ng A, Zhou W, Py BF, Hsu E, Liu X, Eisenberg J, Liu J, Blenis J, Xavier RJ, Yuan J
Dev Cell. 2010;18(6):1041-52 - PMID: 20627085 - PMCID: PMC2935848 - DOI: 10.1016/j.devcel.2010.05.005

Characterization and analysis of human chordoma cell lines.

Yang C, Hornicek FJ, Wood KB, Schwab JH, Choy E, Iafrate J, Rosenberg A, Nielsen GP, Xavier RJ, Mankin H, Duan Z
Spine (Phila Pa 1976). 2010;35(13):1257-64 - PMID: 20461036 - PMCID: PMC3769690 - DOI: 10.1097/BRS.0b013e3181c2a8b0

Expanding roles for diverse physical phenomena during the origin of life.

Budin I, Szostak JW
Annu Rev Biophys. 2010;39:245-63 - PMID: 20192779 - PMCID: PMC4992673 - DOI: 10.1146/annurev.biophys.050708.133753

Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine.

Cadwell K, Patel KK, Maloney NS, Liu TC, Ng AC, Storer CE, Head RD, Xavier R, Stappenbeck TS, Virgin HW
Cell. 2010;141(7):1135-45 - PMID: 20602997 - PMCID: PMC2908380 - DOI: 10.1016/j.cell.2010.05.009

Differential expression of microRNA (miRNA) in chordoma reveals a role for miRNA-1 in Met expression.

Duan Z, Choy E, Nielsen GP, Rosenberg A, Iafrate J, Yang C, Schwab J, Mankin H, Xavier R, Hornicek FJ
J Orthop Res. 2010;28(6):746-52 - PMID: 20041488 - DOI: 10.1002/jor.21055

RESOLVING CLUSTERED WORMS VIA PROBABILISTIC SHAPE MODELS.

Wählby C, Riklin-Raviv T, Ljosa V, Conery AL, Golland P, Ausubel FM, Carpenter AE
Proc IEEE Int Symp Biomed Imaging. 2010;2010(14-17 April 2010):552-555 - PMID: 21383863 - PMCID: PMC3048333 - DOI: 10.1109/ISBI.2010.5490286

Activating WASP mutations associated with X-linked neutropenia result in enhanced actin polymerization, altered cytoskeletal responses, and genomic instability in lymphocytes.

Westerberg LS, Meelu P, Baptista M, Eston MA, Adamovich DA, Cotta-de-Almeida V, Seed B, Rosen MK, Vandenberghe P, Thrasher AJ, Klein C, Alt FW, Snapper SB
J Exp Med. 2010;207(6):1145-52 - PMID: 20513746 - PMCID: PMC2882832 - DOI: 10.1084/jem.20091245

High frequency targeted mutagenesis in Arabidopsis thaliana using zinc finger nucleases.

Zhang F, Maeder ML, Unger-Wallace E, Hoshaw JP, Reyon D, Christian M, Li X, Pierick CJ, Dobbs D, Peterson T, Joung JK, Voytas DF
Proc Natl Acad Sci U S A. 2010;107(26):12028-33 - PMID: 20508152 - PMCID: PMC2900673 - DOI: 10.1073/pnas.0914991107

Berberine-INF55 (5-nitro-2-phenylindole) hybrid antimicrobials: effects of varying the relative orientation of the berberine and INF55 components.

Tomkiewicz D, Casadei G, Larkins-Ford J, Moy TI, Garner J, Bremner JB, Ausubel FM, Lewis K, Kelso MJ
Antimicrob Agents Chemother. 2010;54(8):3219-24 - PMID: 20498327 - PMCID: PMC2916310 - DOI: 10.1128/AAC.01715-09

Helical apolipoproteins of high-density lipoprotein enhance phagocytosis by stabilizing ATP-binding cassette transporter A7.

Tanaka N, Abe-Dohmae S, Iwamoto N, Fitzgerald ML, Yokoyama S
J Lipid Res. 2010;51(9):2591-9 - PMID: 20495215 - PMCID: PMC2918442 - DOI: 10.1194/jlr.M006049

The origins of cellular life.

Schrum JP, Zhu TF, Szostak JW
Cold Spring Harb Perspect Biol. 2010;2(9):a002212 - PMID: 20484387 - PMCID: PMC2926753 - DOI: 10.1101/cshperspect.a002212

Phagocytosis and phagosome acidification are required for pathogen processing and MyD88-dependent responses to Staphylococcus aureus.

Ip WK, Sokolovska A, Charriere GM, Boyer L, Dejardin S, Cappillino MP, Yantosca LM, Takahashi K, Moore KJ, Lacy-Hulbert A, Stuart LM
J Immunol. 2010;184(12):7071-81 - PMID: 20483752 - PMCID: PMC2935932 - DOI: 10.4049/jimmunol.1000110

MiR-33 contributes to the regulation of cholesterol homeostasis.

Rayner KJ, Suárez Y, Dávalos A, Parathath S, Fitzgerald ML, Tamehiro N, Fisher EA, Moore KJ, Fernández-Hernando C
Science. 2010;328(5985):1570-3 - PMID: 20466885 - PMCID: PMC3114628 - DOI: 10.1126/science.1189862

ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool.

Sander JD, Maeder ML, Reyon D, Voytas DF, Joung JK, Dobbs D
Nucleic Acids Res. 2010;38(Web Server issue):W462-8 - PMID: 20435679 - PMCID: PMC2896148 - DOI: 10.1093/nar/gkq319

ortho-Substituted C-aryl glucosides as highly potent and selective renal sodium-dependent glucose co-transporter 2 (SGLT2) inhibitors.

Xu B, Feng Y, Lv B, Xu G, Zhang L, Du J, Peng K, Xu M, Dong J, Zhang W, Zhang T, Zhu L, Ding H, Sheng Z, Welihinda A, Seed B, Chen Y
Bioorg Med Chem. 2010;18(12):4422-32 - PMID: 20576578 - DOI: 10.1016/j.bmc.2010.04.088

Host-encoded reporters for the detection and purification of multiple enveloped viruses.

Ketteler R, Tomov V, Neunkirchner A, Xie Q, Pickl WF, Seed B
J Virol Methods. 2010;167(2):178-85 - PMID: 20399809 - PMCID: PMC2916077 - DOI: 10.1016/j.jviromet.2010.04.002

Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor.

Benita Y, Cao Z, Giallourakis C, Li C, Gardet A, Xavier RJ
Blood. 2010;115(26):5376-84 - PMID: 20410506 - PMCID: PMC2902135 - DOI: 10.1182/blood-2010-01-263855

Identification of Drosophila Yin and PEPT2 as evolutionarily conserved phagosome-associated muramyl dipeptide transporters.

Charrière GM, Ip WE, Dejardin S, Boyer L, Sokolovska A, Cappillino MP, Cherayil BJ, Podolsky DK, Kobayashi KS, Silverman N, Lacy-Hulbert A, Stuart LM
J Biol Chem. 2010;285(26):20147-54 - PMID: 20406817 - PMCID: PMC2888427 - DOI: 10.1074/jbc.M110.115584

99th Dahlem conference on infection, inflammation and chronic inflammatory disorders: Caenorhabditis elegans as a model to study tissues involved in host immunity and microbial pathogenesis.

Irazoqui JE, Ausubel FM
Clin Exp Immunol. 2010;160(1):48-57 - PMID: 20415851 - PMCID: PMC2841835 - DOI: 10.1111/j.1365-2249.2010.04122.x

Effect of stalling after mismatches on the error catastrophe in nonenzymatic nucleic acid replication.

Rajamani S, Ichida JK, Antal T, Treco DA, Leu K, Nowak MA, Szostak JW, Chen IA
J Am Chem Soc. 2010;132(16):5880-5 - PMID: 20359213 - PMCID: PMC2857888 - DOI: 10.1021/ja100780p

Innate immune responses activated in Arabidopsis roots by microbe-associated molecular patterns.

Millet YA, Danna CH, Clay NK, Songnuan W, Simon MD, Werck-Reichhart D, Ausubel FM
Plant Cell. 2010;22(3):973-90 - PMID: 20348432 - PMCID: PMC2861455 - DOI: 10.1105/tpc.109.069658

Binding of PDZ-RhoGEF to ATP-binding cassette transporter A1 (ABCA1) induces cholesterol efflux through RhoA activation and prevention of transporter degradation.

Okuhira K, Fitzgerald ML, Tamehiro N, Ohoka N, Suzuki K, Sawada J, Naito M, Nishimaki-Mogami T
J Biol Chem. 2010;285(21):16369-77 - PMID: 20348106 - PMCID: PMC2871504 - DOI: 10.1074/jbc.M109.061424

MLT-10 defines a family of DUF644 and proline-rich repeat proteins involved in the molting cycle of Caenorhabditis elegans.

Meli VS, Osuna B, Ruvkun G, Frand AR
Mol Biol Cell. 2010;21(10):1648-61 - PMID: 20335506 - PMCID: PMC2869372 - DOI: 10.1091/mbc.E08-07-0708

Exploring the interplay of barrier function and leukocyte recruitment in intestinal inflammation by targeting fucosyltransferase VII and trefoil factor 3.

Beck PL, Ihara E, Hirota SA, MacDonald JA, Meng D, Nanthakumar NN, Podolsky DK, Xavier RJ
Am J Physiol Gastrointest Liver Physiol. 2010;299(1):G43-53 - PMID: 20299601 - PMCID: PMC2904110 - DOI: 10.1152/ajpgi.00228.2009

Genome-wide association identifies multiple ulcerative colitis susceptibility loci.

McGovern DP, Gardet A, Törkvist L, Goyette P, Essers J, Taylor KD, Neale BM, Ong RT, Lagacé C, Li C, Green T, Stevens CR, Beauchamp C, Fleshner PR, Carlson M, D'Amato M, Halfvarson J, Hibberd ML, Lördal M, Padyukov L, Andriulli A, Colombo E, Latiano A, Palmieri O, Bernard EJ, Deslandres C, Hommes DW, de Jong DJ, Stokkers PC, Weersma RK, , Sharma Y, Silverberg MS, Cho JH, Wu J, Roeder K, Brant SR, Schumm LP, Duerr RH, Dubinsky MC, Glazer NL, Haritunians T, Ippoliti A, Melmed GY, Siscovick DS ...
Nat Genet. 2010;42(4):332-7 - PMID: 20228799 - PMCID: PMC3087600 - DOI: 10.1038/ng.549

Isolation and characterization of circulating tumor cells from patients with localized and metastatic prostate cancer.

Stott SL, Lee RJ, Nagrath S, Yu M, Miyamoto DT, Ulkus L, Inserra EJ, Ulman M, Springer S, Nakamura Z, Moore AL, Tsukrov DI, Kempner ME, Dahl DM, Wu CL, Iafrate AJ, Smith MR, Tompkins RG, Sequist LV, Toner M, Haber DA, Maheswaran S
Sci Transl Med. 2010;2(25):25ra23 - PMID: 20424012 - PMCID: PMC3141292 - DOI: 10.1126/scitranslmed.3000403

Differential innate immune signalling via Ca(2+) sensor protein kinases.

Boudsocq M, Willmann MR, McCormack M, Lee H, Shan L, He P, Bush J, Cheng SH, Sheen J
Nature. 2010;464(7287):418-22 - PMID: 20164835 - PMCID: PMC2841715 - DOI: 10.1038/nature08794

Analysis of high-throughput sequencing and annotation strategies for phage genomes.

Henn MR, Sullivan MB, Stange-Thomann N, Osburne MS, Berlin AM, Kelly L, Yandava C, Kodira C, Zeng Q, Weiand M, Sparrow T, Saif S, Giannoukos G, Young SK, Nusbaum C, Birren BW, Chisholm SW
PLoS One. 2010;5(2):e9083 - PMID: 20140207 - PMCID: PMC2816706 - DOI: 10.1371/journal.pone.0009083

The fast track to multidrug resistance.

Kaufmann BB, Hung DT
Mol Cell. 2010;37(3):297-8 - PMID: 20159549 - DOI: 10.1016/j.molcel.2010.01.027

ABC transporters, atherosclerosis and inflammation.

Fitzgerald ML, Mujawar Z, Tamehiro N
Atherosclerosis. 2010;211(2):361-70 - PMID: 20138281 - PMCID: PMC2888932 - DOI: 10.1016/j.atherosclerosis.2010.01.011

bZIP transcription factor zip-2 mediates an early response to Pseudomonas aeruginosa infection in Caenorhabditis elegans.

Estes KA, Dunbar TL, Powell JR, Ausubel FM, Troemel ER
Proc Natl Acad Sci U S A. 2010;107(5):2153-8 - PMID: 20133860 - PMCID: PMC2836710 - DOI: 10.1073/pnas.0914643107

Protocol: a rapid and economical procedure for purification of plasmid or plant DNA with diverse applications in plant biology.

Li JF, Li L, Sheen J
Plant Methods. 2010;6(1):1 - PMID: 20180960 - PMCID: PMC2829548 - DOI: 10.1186/1746-4811-6-1

Early acute kidney injury predicts progressive renal dysfunction and higher mortality in severely burned adults.

Mosier MJ, Pham TN, Klein MB, Gibran NS, Arnoldo BD, Gamelli RL, Tompkins RG, Herndon DN
J Burn Care Res. 2010;31(1):83-92 - PMID: 20061841 - PMCID: PMC3045668 - DOI: 10.1097/BCR.0b013e3181cb8c87

Fluorosomes: a convenient new reagent to detect and block multivalent and complex receptor-ligand interactions.

Kueng HJ, Manta C, Haiderer D, Leb VM, Schmetterer KG, Neunkirchner A, Byrne RA, Scheinecker C, Steinberger P, Seed B, Pickl WF
FASEB J. 2010;24(5):1572-82 - PMID: 20056716 - PMCID: PMC2879947 - DOI: 10.1096/fj.09-137281

Evolution of host innate defence: insights from Caenorhabditis elegans and primitive invertebrates.

Irazoqui JE, Urbach JM, Ausubel FM
Nat Rev Immunol. 2010;10(1):47-58 - PMID: 20029447 - PMCID: PMC2965059 - DOI: 10.1038/nri2689

Autophagy at the gut interface: mucosal responses to stress and the consequences for inflammatory bowel diseases.

Huett A, Xavier RJ
Inflamm Bowel Dis. 2010;16(1):152-74 - PMID: 19575363 - PMCID: PMC3954538 - DOI: 10.1002/ibd.20991

CD36 ligands promote sterile inflammation through assembly of a Toll-like receptor 4 and 6 heterodimer.

Stewart CR, Stuart LM, Wilkinson K, van Gils JM, Deng J, Halle A, Rayner KJ, Boyer L, Zhong R, Frazier WA, Lacy-Hulbert A, El Khoury J, Golenbock DT, Moore KJ
Nat Immunol. 2009;11(2):155-61 - PMID: 20037584 - PMCID: PMC2809046 - DOI: 10.1038/ni.1836

Low glucose uncouples hexokinase1-dependent sugar signaling from stress and defense hormone abscisic acid and C2H4 responses in Arabidopsis.

Cho YH, Sheen J, Yoo SD
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Targeted mutagenesis in zebrafish using customized zinc-finger nucleases.

Foley JE, Maeder ML, Pearlberg J, Joung JK, Peterson RT, Yeh JR
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Yagi H, Parekkadan B, Suganuma K, Soto-Gutierrez A, Tompkins RG, Tilles AW, Yarmush ML
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Cold Spring Harb Symp Quant Biol. 2009;74:47-54 - PMID: 19734203 - DOI: 10.1101/sqb.2009.74.014

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J Allergy Clin Immunol. 2009;124(1):121-8 - PMID: 19500826 - DOI: 10.1016/j.jaci.2009.04.008

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia.

Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung DC, Xavier RJ
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Proc Natl Acad Sci U S A. 2009;106(17):7263 - PMID: 19380733 - PMCID: PMC2678432 - DOI: 10.1073/pnas.0903110106

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Exp Cell Res. 2009;315(12):2001-11 - PMID: 19371741 - PMCID: PMC2693461 - DOI: 10.1016/j.yexcr.2009.04.003

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Neuroscience. 2009;160(2):530-9 - PMID: 19285117 - PMCID: PMC2673023 - DOI: 10.1016/j.neuroscience.2009.02.073

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Adams JC, Seed B, Lu N, Landry A, Xavier RJ
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A functional genomic screen identifies cellular cofactors of hepatitis C virus replication.

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Cell Host Microbe. 2009;5(3):298-307 - PMID: 19286138 - PMCID: PMC2756022 - DOI: 10.1016/j.chom.2009.02.001

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Foley JE, Yeh JR, Maeder ML, Reyon D, Sander JD, Peterson RT, Joung JK
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The G protein-coupled receptor FSHR-1 is required for the Caenorhabditis elegans innate immune response.

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Proc Natl Acad Sci U S A. 2009;106(8):2782-7 - PMID: 19196974 - PMCID: PMC2650343 - DOI: 10.1073/pnas.0813048106

Enhancing the performance of a point-of-care CD4+ T-cell counting microchip through monocyte depletion for HIV/AIDS diagnostics.

Cheng X, Gupta A, Chen C, Tompkins RG, Rodriguez W, Toner M
Lab Chip. 2009;9(10):1357-64 - PMID: 19417901 - PMCID: PMC4064257 - DOI: 10.1039/b818813k

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Temporal global expression data reveal known and novel salicylate-impacted processes and regulators mediating powdery mildew growth and reproduction on Arabidopsis.

Chandran D, Tai YC, Hather G, Dewdney J, Denoux C, Burgess DG, Ausubel FM, Speed TP, Wildermuth MC
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Proc Natl Acad Sci U S A. 2009;106(6):1875-9 - PMID: 19174521 - PMCID: PMC2631283 - DOI: 10.1073/pnas.0810338106

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Are topical antimicrobials effective against bacteria that are highly resistant to systemic antibiotics?

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Eur J Immunol. 2009;39(1):78-84 - PMID: 19130560 - PMCID: PMC2747028 - DOI: 10.1002/eji.200838734

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Genome-wide SNP genotyping highlights the role of natural selection in Plasmodium falciparum population divergence.

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A metasystem of framework model organisms to study emergence of new host-microbe adaptations.

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PLoS One. 2008;3(12):e3891 - PMID: 19066631 - PMCID: PMC2588659 - DOI: 10.1371/journal.pone.0003891

An affinity-based scoring scheme for predicting DNA-binding activities of modularly assembled zinc-finger proteins.

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Microsporidia are natural intracellular parasites of the nematode Caenorhabditis elegans.

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Deficiency of mannose-binding lectin greatly increases antibody response in a mouse model of vaccination.

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Role for beta-catenin and HOX transcription factors in Caenorhabditis elegans and mammalian host epithelial-pathogen interactions.

Irazoqui JE, Ng A, Xavier RJ, Ausubel FM
Proc Natl Acad Sci U S A. 2008;105(45):17469-74 - PMID: 18981407 - PMCID: PMC2582251 - DOI: 10.1073/pnas.0809527105

Fat metabolism links germline stem cells and longevity in C. elegans.

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Loss of SR-A and CD36 activity reduces atherosclerotic lesion complexity without abrogating foam cell formation in hyperlipidemic mice.

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The most conserved genome segments for life detection on Earth and other planets.

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Impaired autophagy of an intracellular pathogen induced by a Crohn's disease associated ATG16L1 variant.

Kuballa P, Huett A, Rioux JD, Daly MJ, Xavier RJ
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A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells.

Cadwell K, Liu JY, Brown SL, Miyoshi H, Loh J, Lennerz JK, Kishi C, Kc W, Carrero JA, Hunt S, Stone CD, Brunt EM, Xavier RJ, Sleckman BP, Li E, Mizushima N, Stappenbeck TS, Virgin HW
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The perfect storm of tiny RNAs.

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A microfluidics approach for the isolation of nucleated red blood cells (NRBCs) from the peripheral blood of pregnant women.

Huang R, Barber TA, Schmidt MA, Tompkins RG, Toner M, Bianchi DW, Kapur R, Flejter WL
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Selection of cyclic peptide aptamers to HCV IRES RNA using mRNA display.

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Proc Natl Acad Sci U S A. 2008;105(40):15293-8 - PMID: 18824687 - PMCID: PMC2556359 - DOI: 10.1073/pnas.0805837105

Temporal cytokine profiles in severely burned patients: a comparison of adults and children.

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The AtrbohD-mediated oxidative burst elicited by oligogalacturonides in Arabidopsis is dispensable for the activation of defense responses effective against Botrytis cinerea.

Galletti R, Denoux C, Gambetta S, Dewdney J, Ausubel FM, De Lorenzo G, Ferrari S
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Myelinated, synapsing cultures of murine spinal cord--validation as an in vitro model of the central nervous system.

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Trans-splicing in C. elegans generates the negative RNAi regulator ERI-6/7.

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Thermostability of model protocell membranes.

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Proc Natl Acad Sci U S A. 2008;105(36):13351-5 - PMID: 18768808 - PMCID: PMC2528865 - DOI: 10.1073/pnas.0805086105

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease.

McCarroll SA, Huett A, Kuballa P, Chilewski SD, Landry A, Goyette P, Zody MC, Hall JL, Brant SR, Cho JH, Duerr RH, Silverberg MS, Taylor KD, Rioux JD, Altshuler D, Daly MJ, Xavier RJ
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Targeting innate immunity for CV benefit

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Drug Discovery Today: Therapeutic Strategies. 2008;5:15-23

RNA interference screen for human genes associated with West Nile virus infection.

Krishnan MN, Ng A, Sukumaran B, Gilfoy FD, Uchil PD, Sultana H, Brass AL, Adametz R, Tsui M, Qian F, Montgomery RR, Lev S, Mason PW, Koski RA, Elledge SJ, Xavier RJ, Agaisse H, Fikrig E
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CARMA3 mediates lysophosphatidic acid-stimulated cytokine secretion by bronchial epithelial cells.

Medoff BD, Landry AL, Wittbold KA, Sandall BP, Derby MC, Cao Z, Adams JC, Xavier RJ
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Convergent energy and stress signaling.

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Trends Plant Sci. 2008;13(9):474-82 - PMID: 18701338 - PMCID: PMC3075853 - DOI: 10.1016/j.tplants.2008.06.006

Genome-wide association studies: a new window into immune-mediated diseases.

Xavier RJ, Rioux JD
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Genome-wide association studies: a new window into immune-mediated diseases.

Xavier RJ, Rioux JD
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MAST3: a novel IBD risk factor that modulates TLR4 signaling.

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Hoxc6 is overexpressed in gastrointestinal carcinoids and interacts with JunD to regulate tumor growth.

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Molecular association between beta-catenin degradation complex and Rac guanine exchange factor DOCK4 is essential for Wnt/beta-catenin signaling.

Upadhyay G, Goessling W, North TE, Xavier R, Zon LI, Yajnik V
Oncogene. 2008;27(44):5845-55 - PMID: 18641688 - PMCID: PMC4774646 - DOI: 10.1038/onc.2008.202

The tumour suppressor CYLD is a negative regulator of RIG-I-mediated antiviral response.

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Detection of mutations in EGFR in circulating lung-cancer cells.

Maheswaran S, Sequist LV, Nagrath S, Ulkus L, Brannigan B, Collura CV, Inserra E, Diederichs S, Iafrate AJ, Bell DW, Digumarthy S, Muzikansky A, Irimia D, Settleman J, Tompkins RG, Lynch TJ, Toner M, Haber DA
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Attenuation of Pseudomonas aeruginosa virulence by medicinal plants in a Caenorhabditis elegans model system.

Adonizio A, Leal SM, Ausubel FM, Mathee K
J Med Microbiol. 2008;57(Pt 7):809-13 - PMID: 18566137 - DOI: 10.1099/jmm.0.47802-0

Bacterial effectors target the common signaling partner BAK1 to disrupt multiple MAMP receptor-signaling complexes and impede plant immunity.

Shan L, He P, Li J, Heese A, Peck SC, Nürnberger T, Martin GB, Sheen J
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Rapid open-source engineering of customized zinc-finger nucleases for highly efficient gene modification.

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Mol Cell. 2008;31(2):294-301 - PMID: 18657511 - PMCID: PMC2535758 - DOI: 10.1016/j.molcel.2008.06.016

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.

Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, , Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E, , , Cardon LR, Anderson CA, Drummond H, Nimm ...
Nat Genet. 2008;40(8):955-62 - PMID: 18587394 - PMCID: PMC2574810 - DOI: 10.1038/ng.175

Early supplemental parenteral nutrition is associated with increased infectious complications in critically ill trauma patients.

Sena MJ, Utter GH, Cuschieri J, Maier RV, Tompkins RG, Harbrecht BG, Moore EE, O'Keefe GE
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Tiny RNA: Where do we come from? What are we? Where are we going?

Ruvkun G
Trends Plant Sci. 2008;13(7):313-6 - PMID: 18562240 - DOI: 10.1016/j.tplants.2008.05.005

Zinc-finger nucleases: the next generation emerges.

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Mol Ther. 2008;16(7):1200-7 - PMID: 18545224 - DOI: 10.1038/mt.2008.114

Animal models for host-pathogen interactions.

Lemaitre B, Ausubel FM
Curr Opin Microbiol. 2008;11(3):249-50 - PMID: 18539076 - DOI: 10.1016/j.mib.2008.05.002

Template-directed synthesis of a genetic polymer in a model protocell.

Mansy SS, Schrum JP, Krishnamurthy M, Tobé S, Treco DA, Szostak JW
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Identification of Caenorhabditis elegans genes regulating longevity using enhanced RNAi-sensitive strains.

Samuelson AV, Klimczak RR, Thompson DB, Carr CE, Ruvkun G
Cold Spring Harb Symp Quant Biol. 2008;72:489-97 - PMID: 18419309 - DOI: 10.1101/sqb.2007.72.068

Quantitation of autophagy by luciferase release assay.

Ketteler R, Seed B
Autophagy. 2008;4(6):801-6 - PMID: 18641457 - PMCID: PMC2910585 - DOI: 10.4161/auto.6401

Murine intramyocellular lipids quantified by NMR act as metabolic biomarkers in burn trauma.

Tzika AA, Astrakas LG, Cao H, Mintzopoulos D, Zhang Q, Padfield K, Yu H, Mindrinos MN, Rahme LG, Tompkins RG
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cDNA sequences for transcription factors and signaling proteins of the hemichordate Saccoglossus kowalevskii: efficacy of the expressed sequence tag (EST) approach for evolutionary and developmental studies of a new organism.

Freeman RM, Wu M, Cordonnier-Pratt MM, Pratt LH, Gruber CE, Smith M, Lander ES, Stange-Thomann N, Lowe CJ, Gerhart J, Kirschner M
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Activation of defense response pathways by OGs and Flg22 elicitors in Arabidopsis seedlings.

Denoux C, Galletti R, Mammarella N, Gopalan S, Werck D, De Lorenzo G, Ferrari S, Ausubel FM, Dewdney J
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Genetic identification of HSD-1, a conserved steroidogenic enzyme that directs larval development in Caenorhabditis elegans.

Patel DS, Fang LL, Svy DK, Ruvkun G, Li W
Development. 2008;135(13):2239-49 - PMID: 18495818 - DOI: 10.1242/dev.016972

SPTLC1 binds ABCA1 to negatively regulate trafficking and cholesterol efflux activity of the transporter.

Tamehiro N, Zhou S, Okuhira K, Benita Y, Brown CE, Zhuang DZ, Latz E, Hornemann T, von Eckardstein A, Xavier RJ, Freeman MW, Fitzgerald ML
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Neither hide nor hair: the difficulty of identifying useful disease biomarkers.

Huett A, Xavier RJ
Gastroenterology. 2008;134(7):2164-8 - PMID: 18486617 - DOI: 10.1053/j.gastro.2008.04.013

Expression and evolutionary features of the hexokinase gene family in Arabidopsis.

Karve A, Rauh BL, Xia X, Kandasamy M, Meagher RB, Sheen J, Moore BD
Planta. 2008;228(3):411-25 - PMID: 18481082 - PMCID: PMC2953952 - DOI: 10.1007/s00425-008-0746-9

Cytokinin and auxin interaction in root stem-cell specification during early embryogenesis.

Müller B, Sheen J
Nature. 2008;453(7198):1094-7 - PMID: 18463635 - PMCID: PMC2601652 - DOI: 10.1038/nature06943

The microRNA miR-1 regulates a MEF-2-dependent retrograde signal at neuromuscular junctions.

Simon DJ, Madison JM, Conery AL, Thompson-Peer KL, Soskis M, Ruvkun GB, Kaplan JM, Kim JK
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Unexpected failure rates for modular assembly of engineered zinc fingers.

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Estimating glutathione synthesis with deuterated water: a model for peptide biosynthesis.

Cabral CB, Bullock KH, Bischoff DJ, Tompkins RG, Yu YM, Kelleher JK
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The exonuclease ERI-1 has a conserved dual role in 5.8S rRNA processing and RNAi.

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Spinophilin and the immune synapse.

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Ribosomal synthesis of N-methyl peptides.

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Comparing insertion libraries in two Pseudomonas aeruginosa strains to assess gene essentiality.

Liberati NT, Urbach JM, Thurber TK, Wu G, Ausubel FM
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Increased uncoupling protein 1 mRNA expression in mice brown adipose tissue after burn injury.

Zhang Q, Ma B, Fischman AJ, Tompkins RG, Carter EA
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Burn-related metabolic and signaling changes in rat brain.

Zhang Q, Carter EA, Ma B, Fischman AJ, Tompkins RG
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A pathway sensor for genome-wide screens of intracellular proteolytic cleavage.

Ketteler R, Sun Z, Kovacs KF, He WW, Seed B
Genome Biol. 2008;9(4):R64 - PMID: 18387192 - PMCID: PMC2643935 - DOI: 10.1186/gb-2008-9-4-r64

Microfluidic leukocyte isolation for gene expression analysis in critically ill hospitalized patients.

Russom A, Sethu P, Irimia D, Mindrinos MN, Calvano SE, Garcia I, Finnerty C, Tannahill C, Abouhamze A, Wilhelmy J, López MC, Baker HV, Herndon DN, Lowry SF, Maier RV, Davis RW, Moldawer LL, Tompkins RG, Toner M,
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Models of Caenorhabditis elegans infection by bacterial and fungal pathogens.

Powell JR, Ausubel FM
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A novel sorting nexin modulates endocytic trafficking and alpha-secretase cleavage of the amyloid precursor protein.

Schöbel S, Neumann S, Hertweck M, Dislich B, Kuhn PH, Kremmer E, Seed B, Baumeister R, Haass C, Lichtenthaler SF
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Comparison of zinc finger nucleases for use in gene targeting in mammalian cells.

Pruett-Miller SM, Connelly JP, Maeder ML, Joung JK, Porteus MH
Mol Ther. 2008;16(4):707-17 - PMID: 18334988 - DOI: 10.1038/mt.2008.20

Engineering Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system.

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Defining molecular classifications and targets in gastroenteropancreatic neuroendocrine tumors through DNA microarray analysis.

Duerr EM, Mizukami Y, Ng A, Xavier RJ, Kikuchi H, Deshpande V, Warshaw AL, Glickman J, Kulke MH, Chung DC
Endocr Relat Cancer. 2008;15(1):243-56 - PMID: 18310291 - DOI: 10.1677/ERC-07-0194

Improvement of bone disease by imiglucerase (Cerezyme) therapy in patients with skeletal manifestations of type 1 Gaucher disease: results of a 48-month longitudinal cohort study.

Sims KB, Pastores GM, Weinreb NJ, Barranger J, Rosenbloom BE, Packman S, Kaplan P, Mankin H, Xavier R, Angell J, Fitzpatrick MA, Rosenthal D
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Equilibrium separation and filtration of particles using differential inertial focusing.

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Autophagy as an important process in gut homeostasis and Crohn's disease pathogenesis.

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Gut. 2008;57(6):717-20 - PMID: 18272545 - PMCID: PMC2735854 - DOI: 10.1136/gut.2007.134254

Metal-ion catalyzed polymerization in the eutectic phase in water-ice: a possible approach to template-directed RNA polymerization.

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DAF-16-dependent suppression of immunity during reproduction in Caenorhabditis elegans.

Miyata S, Begun J, Troemel ER, Ausubel FM
Genetics. 2008;178(2):903-18 - PMID: 18245330 - PMCID: PMC2248360 - DOI: 10.1534/genetics.107.083923

Invention, innovation, entrepreneurship in academic medical centers.

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Surgery. 2008;143(2):168-71 - PMID: 18242329 - PMCID: PMC2408552 - DOI: 10.1016/j.surg.2007.11.004

Phagocytosis and comparative innate immunity: learning on the fly.

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Reduced rate of adenosine triphosphate synthesis by in vivo 31P nuclear magnetic resonance spectroscopy and downregulation of PGC-1beta in distal skeletal muscle following burn.

Tzika AA, Mintzopoulos D, Padfield K, Wilhelmy J, Mindrinos MN, Yu H, Cao H, Zhang Q, Astrakas LG, Zhang J, Yu YM, Rahme LG, Tompkins RG
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IL-22 ameliorates intestinal inflammation in a mouse model of ulcerative colitis.

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Dual control of nuclear EIN3 by bifurcate MAPK cascades in C2H4 signalling.

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Influence of age on the association of retinol-binding protein 4 with metabolic syndrome.

Gavi S, Qurashi S, Stuart LM, Lau R, Melendez MM, Mynarcik DC, McNurlan MA, Gelato MC
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Large-scale screens for cDNAs with in vivo activity.

Ting A, Lichtenthaler S, Xavier R, Na SY, Rabizadeh S, Holmes T, Seed B
Novartis Found Symp. 2005;267:219-29; discussion 229-30 - PMID: 15999809

Somatic misexpression of germline P granules and enhanced RNA interference in retinoblastoma pathway mutants.

Wang D, Kennedy S, Conte D, Kim JK, Gabel HW, Kamath RS, Mello CC, Ruvkun G
Nature. 2005;436(7050):593-7 - PMID: 16049496 - DOI: 10.1038/nature04010

Systematic analysis of genes required for synapse structure and function.

Sieburth D, Ch'ng Q, Dybbs M, Tavazoie M, Kennedy S, Wang D, Dupuy D, Rual JF, Hill DE, Vidal M, Ruvkun G, Kaplan JM
Nature. 2005;436(7050):510-7 - PMID: 16049479 - DOI: 10.1038/nature03809

A systematic RNAi screen for longevity genes in C. elegans.

Hamilton B, Dong Y, Shindo M, Liu W, Odell I, Ruvkun G, Lee SS
Genes Dev. 2005;19(13):1544-55 - PMID: 15998808 - PMCID: PMC1172061 - DOI: 10.1101/gad.1308205

Inhibition of atherogenesis in BLT1-deficient mice reveals a role for LTB4 and BLT1 in smooth muscle cell recruitment.

Heller EA, Liu E, Tager AM, Sinha S, Roberts JD, Koehn SL, Libby P, Aikawa ER, Chen JQ, Huang P, Freeman MW, Moore KJ, Luster AD, Gerszten RE
Circulation. 2005;112(4):578-86 - PMID: 16043658 - DOI: 10.1161/CIRCULATIONAHA.105.545616

Galleria mellonella as a model system to study Cryptococcus neoformans pathogenesis.

Mylonakis E, Moreno R, El Khoury JB, Idnurm A, Heitman J, Calderwood SB, Ausubel FM, Diener A
Infect Immun. 2005;73(7):3842-50 - PMID: 15972469 - PMCID: PMC1168598 - DOI: 10.1128/IAI.73.7.3842-3850.2005

Membrane recruitment of NOD2 in intestinal epithelial cells is essential for nuclear factor-{kappa}B activation in muramyl dipeptide recognition.

Barnich N, Aguirre JE, Reinecker HC, Xavier R, Podolsky DK
J Cell Biol. 2005;170(1):21-6 - PMID: 15998797 - PMCID: PMC2171381 - DOI: 10.1083/jcb.200502153

The tiny RNA world.

Ruvkun GB
Harvey Lect. 2005;99:1-21 - PMID: 15984549

Molecular mechanism(s) of burn-induced insulin resistance in murine skeletal muscle: role of IRS phosphorylation.

Zhang Q, Carter EA, Ma BY, White M, Fischman AJ, Tompkins RG
Life Sci. 2005;77(24):3068-77 - PMID: 15982669 - DOI: 10.1016/j.lfs.2005.02.034

RESISTANCE TO FUSARIUM OXYSPORUM 1, a dominant Arabidopsis disease-resistance gene, is not race specific.

Diener AC, Ausubel FM
Genetics. 2005;171(1):305-21 - PMID: 15965251 - PMCID: PMC1456520 - DOI: 10.1534/genetics.105.042218

Identification of eosinophil lineage-committed progenitors in the murine bone marrow.

Iwasaki H, Mizuno S, Mayfield R, Shigematsu H, Arinobu Y, Seed B, Gurish MF, Takatsu K, Akashi K
J Exp Med. 2005;201(12):1891-7 - PMID: 15955840 - PMCID: PMC2212039 - DOI: 10.1084/jem.20050548

PDZ domains and the politics of polarity in lymphocytes.

Xavier R, Seed B
Immunity. 2005;22(6):655-6 - PMID: 15963778 - DOI: 10.1016/j.immuni.2005.06.003

A new approach for sequencing human IRS1 phosphotyrosine-containing peptides using CapLC-Q-TOF(micro).

Lu XM, Lu MY, Fischman AJ, Tompkins RG
J Mass Spectrom. 2005;40(5):599-607 - PMID: 15739155 - DOI: 10.1002/jms.826

Phagocytosis: elegant complexity.

Stuart LM, Ezekowitz RA
Immunity. 2005;22(5):539-50 - PMID: 15894272 - DOI: 10.1016/j.immuni.2005.05.002

Kinetic analysis of an efficient DNA-dependent TNA polymerase.

Horhota A, Zou K, Ichida JK, Yu B, McLaughlin LW, Szostak JW, Chaput JC
J Am Chem Soc. 2005;127(20):7427-34 - PMID: 15898792 - PMCID: PMC5042361 - DOI: 10.1021/ja0428255

Scanning the human proteome for calmodulin-binding proteins.

Shen X, Valencia CA, Szostak JW, Szostak J, Dong B, Liu R
Proc Natl Acad Sci U S A. 2005;102(17):5969-74 - PMID: 15840729 - PMCID: PMC1087907 - DOI: 10.1073/pnas.0407928102

Semipermeable lipid bilayers exhibit diastereoselectivity favoring ribose.

Sacerdote MG, Szostak JW
Proc Natl Acad Sci U S A. 2005;102(17):6004-8 - PMID: 15831588 - PMCID: PMC556129 - DOI: 10.1073/pnas.0408440102

Burn injury causes mitochondrial dysfunction in skeletal muscle.

Padfield KE, Astrakas LG, Zhang Q, Gopalan S, Dai G, Mindrinos MN, Tompkins RG, Rahme LG, Tzika AA
Proc Natl Acad Sci U S A. 2005;102(15):5368-73 - PMID: 15809440 - PMCID: PMC556259 - DOI: 10.1073/pnas.0501211102

Analysis of xbx genes in C. elegans.

Efimenko E, Bubb K, Mak HY, Holzman T, Leroux MR, Ruvkun G, Thomas JH, Swoboda P
Development. 2005;132(8):1923-34 - PMID: 15790967 - DOI: 10.1242/dev.01775

Commensal flora: wolf in sheep's clothing.

Xavier R, Podolsky DK
Gastroenterology. 2005;128(4):1122-6 - PMID: 15825094 - DOI: 10.1053/j.gastro.2005.02.053

Synthesis of alpha-L-threofuranosyl nucleoside triphosphates (tNTPs).

Zou K, Horhota A, Yu B, Szostak JW, McLaughlin LW
Org Lett. 2005;7(8):1485-7 - PMID: 15816733 - PMCID: PMC5022784 - DOI: 10.1021/ol050081+

Functional genomic analysis of RNA interference in C. elegans.

Kim JK, Gabel HW, Kamath RS, Tewari M, Pasquinelli A, Rual JF, Kennedy S, Dybbs M, Bertin N, Kaplan JM, Vidal M, Ruvkun G
Science. 2005;308(5725):1164-7 - PMID: 15790806 - DOI: 10.1126/science.1109267

Application of genome-wide expression analysis to human health and disease.

Cobb JP, Mindrinos MN, Miller-Graziano C, Calvano SE, Baker HV, Xiao W, Laudanski K, Brownstein BH, Elson CM, Hayden DL, Herndon DN, Lowry SF, Maier RV, Schoenfeld DA, Moldawer LL, Davis RW, Tompkins RG, Baker HV, Bankey P, Billiar T, Brownstein BH, Calvano SE, Camp D, Chaudry I, Cobb JP, Davis RW, Elson CM, Freeman B, Gamelli R, Gibran N, Harbrecht B, Hayden DL, Heagy W, Heimbach D, Herndon DN, Horton J, Hunt J, Laudanski K, Lederer J, Lowry SF, Maier RV, Mannick J, McKinley B, Miller-Grazi ...
Proc Natl Acad Sci U S A. 2005;102(13):4801-6 - PMID: 15781863 - PMCID: PMC555033 - DOI: 10.1073/pnas.0409768102

Efficacy and safety of the coadministration of ezetimibe with fenofibrate in patients with mixed hyperlipidaemia.

Farnier M, Freeman MW, Macdonell G, Perevozskaya I, Davies MJ, Mitchel YB, Gumbiner B,
Eur Heart J. 2005;26(9):897-905 - PMID: 15781429 - DOI: 10.1093/eurheartj/ehi231

A combined yeast/bacteria two-hybrid system: development and evaluation.

Serebriiskii IG, Fang R, Latypova E, Hopkins R, Vinson C, Joung JK, Golemis EA
Mol Cell Proteomics. 2005;4(6):819-26 - PMID: 15781424 - PMCID: PMC2670611 - DOI: 10.1074/mcp.T500005-MCP200

GRIM-19 interacts with nucleotide oligomerization domain 2 and serves as downstream effector of anti-bacterial function in intestinal epithelial cells.

Barnich N, Hisamatsu T, Aguirre JE, Xavier R, Reinecker HC, Podolsky DK
J Biol Chem. 2005;280(19):19021-6 - PMID: 15753091 - DOI: 10.1074/jbc.M413776200

Quantitative proteome analysis of human plasma following in vivo lipopolysaccharide administration using 16O/18O labeling and the accurate mass and time tag approach.

Qian WJ, Monroe ME, Liu T, Jacobs JM, Anderson GA, Shen Y, Moore RJ, Anderson DJ, Zhang R, Calvano SE, Lowry SF, Xiao W, Moldawer LL, Davis RW, Tompkins RG, Camp DG, Smith RD,
Mol Cell Proteomics. 2005;4(5):700-9 - PMID: 15753121 - PMCID: PMC1829297 - DOI: 10.1074/mcp.M500045-MCP200

Mannose-binding lectin-deficient mice display defective apoptotic cell clearance but no autoimmune phenotype.

Stuart LM, Takahashi K, Shi L, Savill J, Ezekowitz RA
J Immunol. 2005;174(6):3220-6 - PMID: 15749852 - DOI: 10.4049/jimmunol.174.6.3220

Mediation of pathogen resistance by exudation of antimicrobials from roots.

Bais HP, Prithiviraj B, Jha AK, Ausubel FM, Vivanco JM
Nature. 2005;434(7030):217-21 - PMID: 15759001 - DOI: 10.1038/nature03356

Distinct roles of pattern recognition receptors CD14 and Toll-like receptor 4 in acute lung injury.

Jeyaseelan S, Chu HW, Young SK, Freeman MW, Worthen GS
Infect Immun. 2005;73(3):1754-63 - PMID: 15731076 - PMCID: PMC1064978 - DOI: 10.1128/IAI.73.3.1754-1763.2005

Evolution of intrahepatic carbon, nitrogen, and energy metabolism in a D-galactosamine-induced rat liver failure model.

Yokoyama T, Banta S, Berthiaume F, Nagrath D, Tompkins RG, Yarmush ML
Metab Eng. 2005;7(2):88-103 - PMID: 15781418 - DOI: 10.1016/j.ymben.2004.09.003

The worm has turned--microbial virulence modeled in Caenorhabditis elegans.

Sifri CD, Begun J, Ausubel FM
Trends Microbiol. 2005;13(3):119-27 - PMID: 15737730 - DOI: 10.1016/j.tim.2005.01.003

An in vitro selection system for TNA.

Ichida JK, Zou K, Horhota A, Yu B, McLaughlin LW, Szostak JW
J Am Chem Soc. 2005;127(9):2802-3 - PMID: 15740086 - PMCID: PMC5072288 - DOI: 10.1021/ja045364w

A high-throughput, near-saturating screen for type III effector genes from Pseudomonas syringae.

Chang JH, Urbach JM, Law TF, Arnold LW, Hu A, Gombar S, Grant SR, Ausubel FM, Dangl JL
Proc Natl Acad Sci U S A. 2005;102(7):2549-54 - PMID: 15701698 - PMCID: PMC549004 - DOI: 10.1073/pnas.0409660102

Bile acids induce cholera toxin expression in Vibrio cholerae in a ToxT-independent manner.

Hung DT, Mekalanos JJ
Proc Natl Acad Sci U S A. 2005;102(8):3028-33 - PMID: 15699331 - PMCID: PMC549475 - DOI: 10.1073/pnas.0409559102

Staphylococcus aureus virulence factors identified by using a high-throughput Caenorhabditis elegans-killing model.

Begun J, Sifri CD, Goldman S, Calderwood SB, Ausubel FM
Infect Immun. 2005;73(2):872-7 - PMID: 15664928 - PMCID: PMC547013 - DOI: 10.1128/IAI.73.2.872-877.2005

Sugar sensing and signalling networks in plants.

Rolland F, Sheen J
Biochem Soc Trans. 2005;33(Pt 1):269-71 - PMID: 15667323 - DOI: 10.1042/BST0330269

Evolutionary perspectives on innate immunity from the study of Caenorhabditis elegans.

Kim DH, Ausubel FM
Curr Opin Immunol. 2005;17(1):4-10 - PMID: 15653303 - DOI: 10.1016/j.coi.2004.11.007

Comparative proteome analyses of human plasma following in vivo lipopolysaccharide administration using multidimensional separations coupled with tandem mass spectrometry.

Qian WJ, Jacobs JM, Camp DG, Monroe ME, Moore RJ, Gritsenko MA, Calvano SE, Lowry SF, Xiao W, Moldawer LL, Davis RW, Tompkins RG, Smith RD
Proteomics. 2005;5(2):572-84 - PMID: 15627965 - PMCID: PMC1781926 - DOI: 10.1002/pmic.200400942

Generalized rank tests for replicated microarray data.

Lee ML, Gray RJ, Björkbacka H, Freeman MW
Stat Appl Genet Mol Biol. 2005;4:Article3 - PMID: 16646848 - DOI: 10.2202/1544-6115.1093

Pseudomonas syringae manipulates systemic plant defenses against pathogens and herbivores.

Cui J, Bahrami AK, Pringle EG, Hernandez-Guzman G, Bender CL, Pierce NE, Ausubel FM
Proc Natl Acad Sci U S A. 2005;102(5):1791-6 - PMID: 15657122 - PMCID: PMC547856 - DOI: 10.1073/pnas.0409450102

Bioluminescence resonance energy transfer identify scaffold protein CNK1 interactions in intact cells.

Lopez-Ilasaca MA, Bernabe-Ortiz JC, Na SY, Dzau VJ, Xavier RJ
FEBS Lett. 2005;579(3):648-54 - PMID: 15670823 - DOI: 10.1016/j.febslet.2004.12.039

Cryopreservation of isolated primary rat hepatocytes: enhanced survival and long-term hepatospecific function.

Sosef MN, Baust JM, Sugimachi K, Fowler A, Tompkins RG, Toner M
Ann Surg. 2005;241(1):125-33 - PMID: 15622000 - PMCID: PMC1356855 - DOI: 10.1097/01.sla.0000149303.48692.0f

Effect of flow and surface conditions on human lymphocyte isolation using microfluidic chambers.

Murthy SK, Sin A, Tompkins RG, Toner M
Langmuir. 2004;20(26):11649-55 - PMID: 15595794 - DOI: 10.1021/la048047b

Wave2 activates serum response element via its VCA region and functions downstream of Rac.

Ishiguro K, Cao Z, Ilasca ML, Ando T, Xavier R
Exp Cell Res. 2004;301(2):331-7 - PMID: 15530867 - DOI: 10.1016/j.yexcr.2004.09.003

Replicating vesicles as models of primitive cell growth and division.

Hanczyc MM, Szostak JW
Curr Opin Chem Biol. 2004;8(6):660-4 - PMID: 15556412 - DOI: 10.1016/j.cbpa.2004.10.002

Abca7 null mice retain normal macrophage phosphatidylcholine and cholesterol efflux activity despite alterations in adipose mass and serum cholesterol levels.

Kim WS, Fitzgerald ML, Kang K, Okuhira K, Bell SA, Manning JJ, Koehn SL, Lu N, Moore KJ, Freeman MW
J Biol Chem. 2004;280(5):3989-95 - PMID: 15550377 - DOI: 10.1074/jbc.M412602200

Continuous flow microfluidic device for rapid erythrocyte lysis.

Sethu P, Anahtar M, Moldawer LL, Tompkins RG, Toner M
Anal Chem. 2004;76(21):6247-53 - PMID: 15516115 - DOI: 10.1021/ac049429p

Whole blood and leukocyte RNA isolation for gene expression analyses.

Feezor RJ, Baker HV, Mindrinos M, Hayden D, Tannahill CL, Brownstein BH, Fay A, MacMillan S, Laramie J, Xiao W, Moldawer LL, Cobb JP, Laudanski K, Miller-Graziano CL, Maier RV, Schoenfeld D, Davis RW, Tompkins RG,
Physiol Genomics. 2004;19(3):247-54 - PMID: 15548831 - DOI: 10.1152/physiolgenomics.00020.2004

Construction of an Enterococcus faecalis Tn917-mediated-gene-disruption library offers insight into Tn917 insertion patterns.

Garsin DA, Urbach J, Huguet-Tapia JC, Peters JE, Ausubel FM
J Bacteriol. 2004;186(21):7280-9 - PMID: 15489440 - PMCID: PMC523214 - DOI: 10.1128/JB.186.21.7280-7289.2004

Requirement of JNK2 for scavenger receptor A-mediated foam cell formation in atherogenesis.

Ricci R, Sumara G, Sumara I, Rozenberg I, Kurrer M, Akhmedov A, Hersberger M, Eriksson U, Eberli FR, Becher B, Borén J, Chen M, Cybulsky MI, Moore KJ, Freeman MW, Wagner EF, Matter CM, Lüscher TF
Science. 2004;306(5701):1558-61 - PMID: 15567863 - DOI: 10.1126/science.1101909

VPEgamma exhibits a caspase-like activity that contributes to defense against pathogens.

Rojo E, Martín R, Carter C, Zouhar J, Pan S, Plotnikova J, Jin H, Paneque M, Sánchez-Serrano JJ, Baker B, Ausubel FM, Raikhel NV
Curr Biol. 2004;14(21):1897-906 - PMID: 15530390 - DOI: 10.1016/j.cub.2004.09.056

Development of a microfabricated cytometry platform for characterization and sorting of individual leukocytes.

Revzin A, Sekine K, Sin A, Tompkins RG, Toner M
Lab Chip. 2004;5(1):30-7 - PMID: 15616737 - DOI: 10.1039/b405557h

Single-cell chemical lysis in picoliter-scale closed volumes using a microfabricated device.

Irimia D, Tompkins RG, Toner M
Anal Chem. 2004;76(20):6137-43 - PMID: 15481964 - DOI: 10.1021/ac0497508

Cryptococcus neoformans Kin1 protein kinase homologue, identified through a Caenorhabditis elegans screen, promotes virulence in mammals.

Mylonakis E, Idnurm A, Moreno R, El Khoury J, Rottman JB, Ausubel FM, Heitman J, Calderwood SB
Mol Microbiol. 2004;54(2):407-19 - PMID: 15469513 - DOI: 10.1111/j.1365-2958.2004.04310.x

Insulin resistance in thermally-injured rats is associated with post-receptor alterations in skeletal muscle, liver and adipose tissue.

Carter EA, Burks D, Fischman AJ, White M, Tompkins RG
Int J Mol Med. 2004;14(4):653-8 - PMID: 15375597

Genome duplication in the teleost fish Tetraodon nigroviridis reveals the early vertebrate proto-karyotype.

Jaillon O, Aury JM, Brunet F, Petit JL, Stange-Thomann N, Mauceli E, Bouneau L, Fischer C, Ozouf-Costaz C, Bernot A, Nicaud S, Jaffe D, Fisher S, Lutfalla G, Dossat C, Segurens B, Dasilva C, Salanoubat M, Levy M, Boudet N, Castellano S, Anthouard V, Jubin C, Castelli V, Katinka M, Vacherie B, Biémont C, Skalli Z, Cattolico L, Poulain J, De Berardinis V, Cruaud C, Duprat S, Brottier P, Coutanceau JP, Gouzy J, Parra G, Lardier G, Chapple C, McKernan KJ, McEwan P, Bosak S, Kellis M, Volff JN, G ...
Nature. 2004;431(7011):946-57 - PMID: 15496914 - DOI: 10.1038/nature03025

The induction of macrophage gene expression by LPS predominantly utilizes Myd88-independent signaling cascades.

Björkbacka H, Fitzgerald KA, Huet F, Li X, Gregory JA, Lee MA, Ordija CM, Dowley NE, Golenbock DT, Freeman MW
Physiol Genomics. 2004;19(3):319-30 - PMID: 15367722 - DOI: 10.1152/physiolgenomics.00128.2004

MicroRNA-responsive 'sensor' transgenes uncover Hox-like and other developmentally regulated patterns of vertebrate microRNA expression.

Mansfield JH, Harfe BD, Nissen R, Obenauer J, Srineel J, Chaudhuri A, Farzan-Kashani R, Zuker M, Pasquinelli AE, Ruvkun G, Sharp PA, Tabin CJ, McManus MT
Nat Genet. 2004;36(10):1079-83 - PMID: 15361871 - DOI: 10.1038/ng1421

ATP-binding cassette transporter A1 contains a novel C-terminal VFVNFA motif that is required for its cholesterol efflux and ApoA-I binding activities.

Fitzgerald ML, Okuhira K, Short GF, Manning JJ, Bell SA, Freeman MW
J Biol Chem. 2004;279(46):48477-85 - PMID: 15347662 - DOI: 10.1074/jbc.M409848200

Differential transplantability of tumor-associated stromal cells.

Duda DG, Fukumura D, Munn LL, Booth MF, Brown EB, Huang P, Seed B, Jain RK
Cancer Res. 2004;64(17):5920-4 - PMID: 15342367 - DOI: 10.1158/0008-5472.CAN-04-1268

The knockout mouse project.

Austin CP, Battey JF, Bradley A, Bucan M, Capecchi M, Collins FS, Dove WF, Duyk G, Dymecki S, Eppig JT, Grieder FB, Heintz N, Hicks G, Insel TR, Joyner A, Koller BH, Lloyd KC, Magnuson T, Moore MW, Nagy A, Pollock JD, Roses AD, Sands AT, Seed B, Skarnes WC, Snoddy J, Soriano P, Stewart DJ, Stewart F, Stillman B, Varmus H, Varticovski L, Verma IM, Vogt TF, von Melchner H, Witkowski J, Woychik RP, Wurst W, Yancopoulos GD, Young SG, Zambrowicz B
Nat Genet. 2004;36(9):921-4 - PMID: 15340423 - PMCID: PMC2716027 - DOI: 10.1038/ng0904-921

The emergence of competition between model protocells.

Chen IA, Roberts RW, Szostak JW
Science. 2004;305(5689):1474-6 - PMID: 15353806 - PMCID: PMC4484590 - DOI: 10.1126/science.1100757

The complete genome and proteome of Mycoplasma mobile.

Jaffe JD, Stange-Thomann N, Smith C, DeCaprio D, Fisher S, Butler J, Calvo S, Elkins T, FitzGerald MG, Hafez N, Kodira CD, Major J, Wang S, Wilkinson J, Nicol R, Nusbaum C, Birren B, Berg HC, Church GM
Genome Res. 2004;14(8):1447-61 - PMID: 15289470 - PMCID: PMC509254 - DOI: 10.1101/gr.2674004

Cytotoxicity of hydrogen peroxide produced by Enterococcus faecium.

Moy TI, Mylonakis E, Calderwood SB, Ausubel FM
Infect Immun. 2004;72(8):4512-20 - PMID: 15271910 - PMCID: PMC470665 - DOI: 10.1128/IAI.72.8.4512-4520.2004

A kinetic study of the growth of fatty acid vesicles.

Chen IA, Szostak JW
Biophys J. 2004;87(2):988-98 - PMID: 15298905 - PMCID: PMC1304506 - DOI: 10.1529/biophysj.104.039875

Integration of Caenorhabditis elegans MAPK pathways mediating immunity and stress resistance by MEK-1 MAPK kinase and VHP-1 MAPK phosphatase.

Kim DH, Liberati NT, Mizuno T, Inoue H, Hisamoto N, Matsumoto K, Ausubel FM
Proc Natl Acad Sci U S A. 2004;101(30):10990-4 - PMID: 15256594 - PMCID: PMC503731 - DOI: 10.1073/pnas.0403546101

Discs large (Dlg1) complexes in lymphocyte activation.

Xavier R, Rabizadeh S, Ishiguro K, Andre N, Ortiz JB, Wachtel H, Morris DG, Lopez-Ilasaca M, Shaw AC, Swat W, Seed B
J Cell Biol. 2004;166(2):173-8 - PMID: 15263016 - PMCID: PMC2172307 - DOI: 10.1083/jcb.200309044

A small aptamer with strong and specific recognition of the triphosphate of ATP.

Sazani PL, Larralde R, Szostak JW
J Am Chem Soc. 2004;126(27):8370-1 - PMID: 15237981 - PMCID: PMC4983724 - DOI: 10.1021/ja049171k

Support of the metabolic response to burn injury.

Herndon DN, Tompkins RG
Lancet. 2004;363(9424):1895-902 - PMID: 15183630 - DOI: 10.1016/S0140-6736(04)16360-5

Caenorhabditis elegans-based screen identifies Salmonella virulence factors required for conserved host-pathogen interactions.

Tenor JL, McCormick BA, Ausubel FM, Aballay A
Curr Biol. 2004;14(11):1018-24 - PMID: 15182677 - DOI: 10.1016/j.cub.2004.05.050

Contribution of gelatinase, serine protease, and fsr to the pathogenesis of Enterococcus faecalis endophthalmitis.

Engelbert M, Mylonakis E, Ausubel FM, Calderwood SB, Gilmore MS
Infect Immun. 2004;72(6):3628-33 - PMID: 15155673 - PMCID: PMC415677 - DOI: 10.1128/IAI.72.6.3628-3633.2004

Short-term enteral glutamine does not enhance protein accretion in burned children: a stable isotope study.

Sheridan RL, Prelack K, Yu YM, Lydon M, Petras L, Young VR, Tompkins RG
Surgery. 2004;135(6):671-8 - PMID: 15179374 - DOI: 10.1016/j.surg.2003.11.014

Evolutionary optimization of a nonbiological ATP binding protein for improved folding stability.

Chaput JC, Szostak JW
Chem Biol. 2004;11(6):865-74 - PMID: 15217619 - DOI: 10.1016/j.chembiol.2004.04.006

Membrane growth can generate a transmembrane pH gradient in fatty acid vesicles.

Chen IA, Szostak JW
Proc Natl Acad Sci U S A. 2004;101(21):7965-70 - PMID: 15148394 - PMCID: PMC419540 - DOI: 10.1073/pnas.0308045101

Long-term function of cryopreserved rat hepatocytes in a coculture system.

Sugimachi K, Sosef MN, Baust JM, Fowler A, Tompkins RG, Toner M
Cell Transplant. 2004;13(2):187-95 - PMID: 15129765 - DOI: 10.3727/000000004773301799

The Caenorhabditis elegans MAPK phosphatase VHP-1 mediates a novel JNK-like signaling pathway in stress response.

Mizuno T, Hisamoto N, Terada T, Kondo T, Adachi M, Nishida E, Kim DH, Ausubel FM, Matsumoto K
EMBO J. 2004;23(11):2226-34 - PMID: 15116070 - PMCID: PMC419906 - DOI: 10.1038/sj.emboj.7600226

The scaffold protein CNK1 interacts with the tumor suppressor RASSF1A and augments RASSF1A-induced cell death.

Rabizadeh S, Xavier RJ, Ishiguro K, Bernabeortiz J, Lopez-Ilasaca M, Khokhlatchev A, Mollahan P, Pfeifer GP, Avruch J, Seed B
J Biol Chem. 2004;279(28):29247-54 - PMID: 15075335 - DOI: 10.1074/jbc.M401699200

Allosteric inhibition of zinc-finger binding in the major groove of DNA by minor-groove binding ligands.

Nguyen-Hackley DH, Ramm E, Taylor CM, Joung JK, Dervan PB, Pabo CO
Biochemistry. 2004;43(13):3880-90 - PMID: 15049695 - DOI: 10.1021/bi030223c

Challenge of Drosophila melanogaster with Cryptococcus neoformans and role of the innate immune response.

Apidianakis Y, Rahme LG, Heitman J, Ausubel FM, Calderwood SB, Mylonakis E
Eukaryot Cell. 2004;3(2):413-9 - PMID: 15075271 - PMCID: PMC387633 - DOI: 10.1128/ec.3.2.413-419.2004

Requirement for a conserved Toll/interleukin-1 resistance domain protein in the Caenorhabditis elegans immune response.

Liberati NT, Fitzgerald KA, Kim DH, Feinbaum R, Golenbock DT, Ausubel FM
Proc Natl Acad Sci U S A. 2004;101(17):6593-8 - PMID: 15123841 - PMCID: PMC404090 - DOI: 10.1073/pnas.0308625101

Informational complexity and functional activity of RNA structures.

Carothers JM, Oestreich SC, Davis JH, Szostak JW
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Cross-linking and lipid efflux properties of apoA-I mutants suggest direct association between apoA-I helices and ABCA1.

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Ultra-high-efficiency strong cation exchange LC/RPLC/MS/MS for high dynamic range characterization of the human plasma proteome.

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Analysis of Pseudomonas aeruginosa 4-hydroxy-2-alkylquinolines (HAQs) reveals a role for 4-hydroxy-2-heptylquinoline in cell-to-cell communication.

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Epstein-Barr virus latent infection membrane protein 1 TRAF-binding site induces NIK/IKK alpha-dependent noncanonical NF-kappaB activation.

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Identification of many microRNAs that copurify with polyribosomes in mammalian neurons.

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An improved strategy for constructing "designer" Cys2His2 zinc finger proteins.

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ABCA1 and amphipathic apolipoproteins form high-affinity molecular complexes required for cholesterol efflux.

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Experimental models of primitive cellular compartments: encapsulation, growth, and division.

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Central role of interleukin-6 in burn induced stimulation of hepatic amino acid transport.

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Differential regulation of EIN3 stability by glucose and ethylene signalling in plants.

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Activation of signaling pathways by putative scavenger receptor class A (SR-A) ligands requires CD14 but not SR-A.

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The cell adhesion protein P-selectin glycoprotein ligand-1 is a substrate for the aspartyl protease BACE1.

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Functional tests of enhancer conservation between distantly related species.

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The Caenorhabditis elegans ems class homeobox gene ceh-2 is required for M3 pharynx motoneuron function.

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Comparative genomic analysis reveals independent expansion of a lineage-specific gene family in vertebrates: the class II cytokine receptors and their ligands in mammals and fish.

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Coordinate regulation of small temporal RNAs at the onset of Drosophila metamorphosis.

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The Drosophila melanogaster toll pathway participates in resistance to infection by the gram-negative human pathogen Pseudomonas aeruginosa.

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Colonic epithelial functional phenotype varies with type and phase of experimental colitis.

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Arabidopsis local resistance to Botrytis cinerea involves salicylic acid and camalexin and requires EDS4 and PAD2, but not SID2, EDS5 or PAD4.

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A novel, modification-dependent ATP-binding aptamer selected from an RNA library incorporating a cationic functionality.

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CD36 mediates the innate host response to beta-amyloid.

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Long-lived C. elegans daf-2 mutants are resistant to bacterial pathogens.

Garsin DA, Villanueva JM, Begun J, Kim DH, Sifri CD, Calderwood SB, Ruvkun G, Ausubel FM
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Anteroposterior patterning in hemichordates and the origins of the chordate nervous system.

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The art of serendipity: killing of Caenorhabditis elegans by human pathogens as a model of bacterial and fungal pathogenesis.

Mylonakis E, Ausubel FM, Tang RJ, Calderwood SB
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Long-lived C. elegans daf-2 mutants are resistant to bacterial pathogens.

Garsin DA, Villanueva JM, Begun J, Kim DH, Sifri CD, Calderwood SB, Ruvkun G, Ausubel FM
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Functional information: Molecular messages.

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Dynamic imaging of collagen and its modulation in tumors in vivo using second-harmonic generation.

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Selection of oligonucleotide probes for protein coding sequences.

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Efficacy of an extracorporeal flat-plate bioartificial liver in treating fulminant hepatic failure.

Shito M, Tilles AW, Tompkins RG, Yarmush ML, Toner M
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Computational and experimental identification of C. elegans microRNAs.

Grad Y, Aach J, Hayes GD, Reinhart BJ, Church GM, Ruvkun G, Kim J
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Use of the Galleria mellonella caterpillar as a model host to study the role of the type III secretion system in Pseudomonas aeruginosa pathogenesis.

Miyata S, Casey M, Frank DW, Ausubel FM, Drenkard E
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DAF-16 target genes that control C. elegans life-span and metabolism.

Lee SS, Kennedy S, Tolonen AC, Ruvkun G
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Selective labeling and detection of specific RNAs in an RNA mixture.

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The genome sequence of the filamentous fungus Neurospora crassa.

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Role of the Arabidopsis glucose sensor HXK1 in nutrient, light, and hormonal signaling.

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Caenorhabditis elegans as a model host for Staphylococcus aureus pathogenesis.

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Infect Immun. 2003;71(4):2208-17 - PMID: 12654843 - PMCID: PMC152095 - DOI: 10.1128/iai.71.4.2208-2217.2003

Bioengineering of liver assist devices.

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daf-28 encodes a C. elegans insulin superfamily member that is regulated by environmental cues and acts in the DAF-2 signaling pathway.

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Site-specific gene targeting in mouse embryonic stem cells with intact bacterial artificial chromosomes.

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A uniform system for microRNA annotation.

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Sugar and hormone connections.

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Trends Plant Sci. 2003;8(3):110-6 - PMID: 12663220 - DOI: 10.1016/S1360-1385(03)00011-6

Five components of the ethylene-response pathway identified in a screen for weak ethylene-insensitive mutants in Arabidopsis.

Alonso JM, Stepanova AN, Solano R, Wisman E, Ferrari S, Ausubel FM, Ecker JR
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Hypersusceptibility of cystic fibrosis mice to chronic Pseudomonas aeruginosa oropharyngeal colonization and lung infection.

Coleman FT, Mueschenborn S, Meluleni G, Ray C, Carey VJ, Vargas SO, Cannon CL, Ausubel FM, Pier GB
Proc Natl Acad Sci U S A. 2003;100(4):1949-54 - PMID: 12578988 - PMCID: PMC149939 - DOI: 10.1073/pnas.0437901100

Efficient and stable retroviral transfection of ovine endothelial cells with green fluorescent protein for cardiovascular tissue engineering.

Afting M, Stock UA, Nasseri B, Pomerantseva I, Seed B, Vacanti JP
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eLiXiRs for restraining inflammation.

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Essential role for Vav1 in activation, but not development, of gammadelta T cells.

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Transforming growth factor-beta mediates intestinal healing and susceptibility to injury in vitro and in vivo through epithelial cells.

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Genome-wide RNAi analysis of Caenorhabditis elegans fat regulatory genes.

Ashrafi K, Chang FY, Watts JL, Fraser AG, Kamath RS, Ahringer J, Ruvkun G
Nature. 2003;421(6920):268-72 - PMID: 12529643 - DOI: 10.1038/nature01279

Tandemly duplicated Arabidopsis genes that encode polygalacturonase-inhibiting proteins are regulated coordinately by different signal transduction pathways in response to fungal infection.

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Caenorhabditis elegans innate immune response triggered by Salmonella enterica requires intact LPS and is mediated by a MAPK signaling pathway.

Aballay A, Drenkard E, Hilbun LR, Ausubel FM
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DNA polymerase-mediated DNA synthesis on a TNA template.

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Initial sequencing and comparative analysis of the mouse genome.

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A systematic RNAi screen identifies a critical role for mitochondria in C. elegans longevity.

Lee SS, Lee RY, Fraser AG, Kamath RS, Ahringer J, Ruvkun G
Nat Genet. 2002;33(1):40-8 - PMID: 12447374 - DOI: 10.1038/ng1056

Killing of Caenorhabditis elegans by Cryptococcus neoformans as a model of yeast pathogenesis.

Mylonakis E, Ausubel FM, Perfect JR, Heitman J, Calderwood SB
Proc Natl Acad Sci U S A. 2002;99(24):15675-80 - PMID: 12438649 - PMCID: PMC137775 - DOI: 10.1073/pnas.232568599

A unique short-chain dehydrogenase/reductase in Arabidopsis glucose signaling and abscisic acid biosynthesis and functions.

Cheng WH, Endo A, Zhou L, Penney J, Chen HC, Arroyo A, Leon P, Nambara E, Asami T, Seo M, Koshiba T, Sheen J
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Insulin receptor substrate and p55 orthologous adaptor proteins function in the Caenorhabditis elegans daf-2/insulin-like signaling pathway.

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Scavenger receptors class A-I/II and CD36 are the principal receptors responsible for the uptake of modified low density lipoprotein leading to lipid loading in macrophages.

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Virulence effect of Enterococcus faecalis protease genes and the quorum-sensing locus fsr in Caenorhabditis elegans and mice.

Sifri CD, Mylonakis E, Singh KV, Qin X, Garsin DA, Murray BE, Ausubel FM, Calderwood SB
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Neutrophil influx in response to a peritoneal infection with Salmonella is delayed in lipopolysaccharide-binding protein or CD14-deficient mice.

Yang KK, Dorner BG, Merkel U, Ryffel B, Schütt C, Golenbock D, Freeman MW, Jack RS
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Cellular activation, phagocytosis, and bactericidal activity against group B streptococcus involve parallel myeloid differentiation factor 88-dependent and independent signaling pathways.

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Molecular biology: RNA gets a grip on translation.

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Use of Integra artificial skin is associated with decreased length of stay for severely injured adult burn survivors.

Ryan CM, Schoenfeld DA, Malloy M, Schulz JT, Sheridan RL, Tompkins RG
J Burn Care Rehabil. 2002;23(5):311-7 - PMID: 12352131 - DOI: 10.1097/01.BCR.0000028566.85892.54

In vivo rabbit hindquarter model for assessment of regional burn hypermetabolism.

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A CD36-initiated signaling cascade mediates inflammatory effects of beta-amyloid.

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Effectiveness of bacteria-controlled nursing units in preventing cross-colonization with resistant bacteria in severely burned children.

Weber JM, Sheridan RL, Schulz JT, Tompkins RG, Ryan CM
Infect Control Hosp Epidemiol. 2002;23(9):549-51 - PMID: 12269456 - DOI: 10.1086/502106

The Treatment of Dyslipidemia: LDL Reduction and Beyond

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Identification of epitope-like consensus motifs using mRNA display.

Baggio R, Burgstaller P, Hale SP, Putney AR, Lane M, Lipovsek D, Wright MC, Roberts RW, Liu R, Szostak JW, Wagner RW
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Isolation of high-affinity GTP aptamers from partially structured RNA libraries.

Davis JH, Szostak JW
Proc Natl Acad Sci U S A. 2002;99(18):11616-21 - PMID: 12185247 - PMCID: PMC129318 - DOI: 10.1073/pnas.182095699

The C. elegans POU-domain transcription factor UNC-86 regulates the tph-1 tryptophan hydroxylase gene and neurite outgrowth in specific serotonergic neurons.

Sze JY, Zhang S, Li J, Ruvkun G
Development. 2002;129(16):3901-11 - PMID: 12135927

The Enterococcus faecalis fsrB gene, a key component of the fsr quorum-sensing system, is associated with virulence in the rabbit endophthalmitis model.

Mylonakis E, Engelbert M, Qin X, Sifri CD, Murray BE, Ausubel FM, Gilmore MS, Calderwood SB
Infect Immun. 2002;70(8):4678-81 - PMID: 12117982 - PMCID: PMC128160 - DOI: 10.1128/iai.70.8.4678-4681.2002

Longevity: don't hold your breath.

Lee SS, Ruvkun G
Nature. 2002;418(6895):287-8 - PMID: 12124610 - DOI: 10.1038/418287a

A conserved p38 MAP kinase pathway in Caenorhabditis elegans innate immunity.

Kim DH, Feinbaum R, Alloing G, Emerson FE, Garsin DA, Inoue H, Tanaka-Hino M, Hisamoto N, Matsumoto K, Tan MW, Ausubel FM
Science. 2002;297(5581):623-6 - PMID: 12142542 - DOI: 10.1126/science.1073759

Naturally occurring mutations in the largest extracellular loops of ABCA1 can disrupt its direct interaction with apolipoprotein A-I.

Fitzgerald ML, Morris AL, Rhee JS, Andersson LP, Mendez AJ, Freeman MW
J Biol Chem. 2002;277(36):33178-87 - PMID: 12084722 - DOI: 10.1074/jbc.M204996200

Decreased bone density in splenectomized Gaucher patients receiving enzyme replacement therapy.

Schiffmann R, Mankin H, Dambrosia JM, Xavier RJ, Kreps C, Hill SC, Barton NW, Rosenthal DI
Blood Cells Mol Dis. 2002;28(2):288-96 - PMID: 12064924

Sugar sensing and signaling in plants.

Rolland F, Moore B, Sheen J
Plant Cell. 2002;14 Suppl:S185-205 - PMID: 12045277 - PMCID: PMC151255 - DOI: 10.1105/tpc.010455

Signals involved in Arabidopsis resistance to Trichoplusia ni caterpillars induced by virulent and avirulent strains of the phytopathogen Pseudomonas syringae.

Cui J, Jander G, Racki LR, Kim PD, Pierce NE, Ausubel FM
Plant Physiol. 2002;129(2):551-64 - PMID: 12068100 - PMCID: PMC161673 - DOI: 10.1104/pp.010815

Two-component signal transduction pathways in Arabidopsis.

Hwang I, Chen HC, Sheen J
Plant Physiol. 2002;129(2):500-15 - PMID: 12068096 - PMCID: PMC161668 - DOI: 10.1104/pp.005504

Calcium signaling through protein kinases. The Arabidopsis calcium-dependent protein kinase gene family.

Cheng SH, Willmann MR, Chen HC, Sheen J
Plant Physiol. 2002;129(2):469-85 - PMID: 12068094 - PMCID: PMC1540234 - DOI: 10.1104/pp.005645

Phosphorelay and transcription control in cytokinin signal transduction.

Sheen J
Science. 2002;296(5573):1650-2 - PMID: 12040183 - DOI: 10.1126/science.1071883

Control of developmental timing by micrornas and their targets.

Pasquinelli AE, Ruvkun G
Annu Rev Cell Dev Biol. 2002;18:495-513 - PMID: 12142272 - DOI: 10.1146/annurev.cellbio.18.012502.105832

Regional measurement of canine skeletal muscle blood flow by positron emission tomography with H2(15)O.

Fischman AJ, Hsu H, Carter EA, Yu YM, Tompkins RG, Guerrero JL, Young VR, Alpert NM
J Appl Physiol. 2002;92(4):1709-16 - PMID: 11896041 - DOI: 10.1152/japplphysiol.00445.2001

Mapping of local renal blood flow with PET and H(2)(15)O.

Alpert NM, Rabito CA, Correia DJ, Babich JW, Littman BH, Tompkins RG, Rubin NT, Rubin RH, Fischman AJ
J Nucl Med. 2002;43(4):470-5 - PMID: 11937589

Polymorphic amplified typing sequences provide a novel approach to Escherichia coli O157:H7 strain typing.

Kudva IT, Evans PS, Perna NT, Barrett TJ, DeCastro GJ, Ausubel FM, Blattner FR, Calderwood SB
J Clin Microbiol. 2002;40(4):1152-9 - PMID: 11923324 - PMCID: PMC140341 - DOI: 10.1128/jcm.40.4.1152-1159.2002

The genome of M. acetivorans reveals extensive metabolic and physiological diversity.

Galagan JE, Nusbaum C, Roy A, Endrizzi MG, Macdonald P, FitzHugh W, Calvo S, Engels R, Smirnov S, Atnoor D, Brown A, Allen N, Naylor J, Stange-Thomann N, DeArellano K, Johnson R, Linton L, McEwan P, McKernan K, Talamas J, Tirrell A, Ye W, Zimmer A, Barber RD, Cann I, Graham DE, Grahame DA, Guss AM, Hedderich R, Ingram-Smith C, Kuettner HC, Krzycki JA, Leigh JA, Li W, Liu J, Mukhopadhyay B, Reeve JN, Smith K, Springer TA, Umayam LA, White O, White RH, Conway de Macario E, Ferry JG, Jarrell KF ...
Genome Res. 2002;12(4):532-42 - PMID: 11932238 - PMCID: PMC187521 - DOI: 10.1101/gr.223902

Strains of Escherichia coli O157:H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms.

Kudva IT, Evans PS, Perna NT, Barrett TJ, Ausubel FM, Blattner FR, Calderwood SB
J Bacteriol. 2002;184(7):1873-9 - PMID: 11889093 - PMCID: PMC134921 - DOI: 10.1128/jb.184.7.1873-1879.2002

Pseudomonas biofilm formation and antibiotic resistance are linked to phenotypic variation.

Drenkard E, Ausubel FM
Nature. 2002;416(6882):740-3 - PMID: 11961556 - DOI: 10.1038/416740a

Nuclear hormone receptors and cholesterol trafficking: the orphans find a new home.

Fitzgerald ML, Moore KJ, Freeman MW
J Mol Med (Berl). 2002;80(5):271-81 - PMID: 12021839 - DOI: 10.1007/s00109-001-0318-y

Identifying and modifying protein-DNA and protein-protein interactions using a bacterial two-hybrid selection system.

Joung JK
J Cell Biochem Suppl. 2002;Suppl 37:53-7 - PMID: 11842428

Inducible nitric oxide synthase plays a role in LPS-induced hyperglycemia and insulin resistance.

Sugita H, Kaneki M, Tokunaga E, Sugita M, Koike C, Yasuhara S, Tompkins RG, Martyn JA
Am J Physiol Endocrinol Metab. 2002;282(2):E386-94 - PMID: 11788371 - DOI: 10.1152/ajpendo.00087.2001

Inhibitory effects of apoptotic cell ingestion upon endotoxin-driven myeloid dendritic cell maturation.

Stuart LM, Lucas M, Simpson C, Lamb J, Savill J, Lacy-Hulbert A
J Immunol. 2002;168(4):1627-35 - PMID: 11823490 - DOI: 10.4049/jimmunol.168.4.1627

MAP kinase signalling cascade in Arabidopsis innate immunity.

Asai T, Tena G, Plotnikova J, Willmann MR, Chiu WL, Gomez-Gomez L, Boller T, Ausubel FM, Sheen J
Nature. 2002;415(6875):977-83 - PMID: 11875555 - DOI: 10.1038/415977a

Plasma L-5-oxoproline kinetics and whole blood glutathione synthesis rates in severely burned adult humans.

Yu YM, Ryan CM, Fei ZW, Lu XM, Castillo L, Schultz JT, Tompkins RG, Young VR
Am J Physiol Endocrinol Metab. 2002;282(2):E247-58 - PMID: 11788355 - DOI: 10.1152/ajpendo.00206.2001

Caenorhabditis elegans as a host for the study of host-pathogen interactions.

Aballay A, Ausubel FM
Curr Opin Microbiol. 2002;5(1):97-101 - PMID: 11834377

Identification of a novel Ras-regulated proapoptotic pathway.

Khokhlatchev A, Rabizadeh S, Xavier R, Nedwidek M, Chen T, Zhang XF, Seed B, Avruch J
Curr Biol. 2002;12(4):253-65 - PMID: 11864565 - DOI: 10.1016/s0960-9822(02)00683-8

Identification of virulence genes in a pathogenic strain of Pseudomonas aeruginosa by representational difference analysis.

Choi JY, Sifri CD, Goumnerov BC, Rahme LG, Ausubel FM, Calderwood SB
J Bacteriol. 2002;184(4):952-61 - PMID: 11807055 - PMCID: PMC134824 - DOI: 10.1128/jb.184.4.952-961.2002

Ductal lavage and the clinical management of women at high risk for breast carcinoma: a commentary.

O'Shaughnessy JA, Ljung BM, Dooley WC, Chang J, Kuerer HM, Hung DT, Grant MD, Khan SA, Phillips RF, Duvall K, Euhus DM, King BL, Anderson BO, Troyan SL, Kim J, Veronesi U, Cazzaniga M
Cancer. 2002;94(2):292-8 - PMID: 11900214 - DOI: 10.1002/cncr.10238

C/EBPalpha induces adipogenesis through PPARgamma: a unified pathway.

Rosen ED, Hsu CH, Wang X, Sakai S, Freeman MW, Gonzalez FJ, Spiegelman BM
Genes Dev. 2002;16(1):22-6 - PMID: 11782441 - PMCID: PMC155311 - DOI: 10.1101/gad.948702

Role of tumor necrosis factor receptor 2 (TNFR2) in colonic epithelial hyperplasia and chronic intestinal inflammation in mice.

Mizoguchi E, Mizoguchi A, Takedatsu H, Cario E, de Jong YP, Ooi CJ, Xavier RJ, Terhorst C, Podolsky DK, Bhan AK
Gastroenterology. 2002;122(1):134-44 - PMID: 11781288 - DOI: 10.1053/gast.2002.30347

Long-term consequences of toxic epidermal necrolysis in children.

Sheridan RL, Schulz JT, Ryan CM, Schnitzer JJ, Lawlor D, Driscoll DN, Donelan MB, Tompkins RG
Pediatrics. 2002;109(1):74-8 - PMID: 11773544 - DOI: 10.1542/peds.109.1.74

LBP, CD14, TLR4 and the murine innate immune response to a peritoneal Salmonella infection.

Bernheiden M, Heinrich JM, Minigo G, Schütt C, Stelter F, Freeman M, Golenbock D, Jack RS
J Endotoxin Res. 2001;7(6):447-50 - PMID: 11753215

Regulation of C. elegans DAF-16 and its human ortholog FKHRL1 by the daf-2 insulin-like signaling pathway.

Lee RY, Hench J, Ruvkun G
Curr Biol. 2001;11(24):1950-7 - PMID: 11747821 - DOI: 10.1016/s0960-9822(01)00595-4

Targeted disruption of the murine Fanconi anemia gene, Fancg/Xrcc9.

Yang Y, Kuang Y, Montes De Oca R, Hays T, Moreau L, Lu N, Seed B, D'Andrea AD
Blood. 2001;98(12):3435-40 - PMID: 11719385 - DOI: 10.1182/blood.v98.12.3435

Signal transduction in maize and Arabidopsis mesophyll protoplasts.

Sheen J
Plant Physiol. 2001;127(4):1466-75 - PMID: 11743090 - PMCID: PMC1540179

Differential roles of the Pseudomonas aeruginosa PA14 rpoN gene in pathogenicity in plants, nematodes, insects, and mice.

Hendrickson EL, Plotnikova J, Mahajan-Miklos S, Rahme LG, Ausubel FM
J Bacteriol. 2001;183(24):7126-34 - PMID: 11717271 - PMCID: PMC95561 - DOI: 10.1128/JB.183.24.7126-7134.2001

Long-term maintenance of cytochrome P450 activities by rat hepatocyte/3T3 cell co-cultures in heparinized human plasma.

Washizu J, Berthiaume F, Mokuno Y, Tompkins RG, Toner M, Yarmush ML
Tissue Eng. 2001;7(6):691-703 - PMID: 11749727 - DOI: 10.1089/107632701753337654

One-step purification of recombinant proteins using a nanomolar-affinity streptavidin-binding peptide, the SBP-Tag.

Keefe AD, Wilson DS, Seelig B, Szostak JW
Protein Expr Purif. 2001;23(3):440-6 - PMID: 11722181 - DOI: 10.1006/prep.2001.1515

The American Burn Association in the New Millennium.

Tompkins RG
J Burn Care Rehabil. 2001;22(6):369-374 - PMID: 11773770

The genetics of aging.

Finch CE, Ruvkun G
Annu Rev Genomics Hum Genet. 2001;2:435-62 - PMID: 11701657 - DOI: 10.1146/annurev.genom.2.1.435

Ductal lavage for detection of cellular atypia in women at high risk for breast cancer.

Dooley WC, Ljung BM, Veronesi U, Cazzaniga M, Elledge RM, O'Shaughnessy JA, Kuerer HM, Hung DT, Khan SA, Phillips RF, Ganz PA, Euhus DM, Esserman LJ, Haffty BG, King BL, Kelley MC, Anderson MM, Schmit PJ, Clark RR, Kass FC, Anderson BO, Troyan SL, Arias RD, Quiring JN, Love SM, Page DL, King EB
J Natl Cancer Inst. 2001;93(21):1624-32 - PMID: 11698566 - DOI: 10.1093/jnci/93.21.1624

In vitro evolution suggests multiple origins for the hammerhead ribozyme.

Salehi-Ashtiani K, Szostak JW
Nature. 2001;414(6859):82-4 - PMID: 11689947 - DOI: 10.1038/35102081

Isochorismate synthase is required to synthesize salicylic acid for plant defence.

Wildermuth MC, Dewdney J, Wu G, Ausubel FM
Nature. 2001;414(6863):562-5 - PMID: 11734859 - DOI: 10.1038/35107108

Endoplasmic reticulum chaperone gp96 is required for innate immunity but not cell viability.

Randow F, Seed B
Nat Cell Biol. 2001;3(10):891-6 - PMID: 11584270 - DOI: 10.1038/ncb1001-891

Molecular biology. Glimpses of a tiny RNA world.

Ruvkun G
Science. 2001;294(5543):797-9 - PMID: 11679654 - DOI: 10.1126/science.1066315

L-histidine decarboxylase decreases its own transcription through downregulation of ERK activity.

Colucci R, Fleming JV, Xavier R, Wang TC
Am J Physiol Gastrointest Liver Physiol. 2001;281(4):G1081-91 - PMID: 11557529 - DOI: 10.1152/ajpgi.2001.281.4.G1081

Plant mitogen-activated protein kinase signaling cascades.

Tena G, Asai T, Chiu WL, Sheen J
Curr Opin Plant Biol. 2001;4(5):392-400 - PMID: 11597496

Dissection of abscisic acid signal transduction pathways in barley aleurone layers.

Shen Q, Gomez-Cadenas A, Zhang P, Walker-Simmons MK, Sheen J, Ho TH
Plant Mol Biol. 2001;47(3):437-48 - PMID: 11587514

Peroxisome proliferator-activated receptors in macrophage biology: friend or foe?

Moore KJ, Fitzgerald ML, Freeman MW
Curr Opin Lipidol. 2001;12(5):519-27 - PMID: 11561171

A simple model host for identifying Gram-positive virulence factors.

Garsin DA, Sifri CD, Mylonakis E, Qin X, Singh KV, Murray BE, Calderwood SB, Ausubel FM
Proc Natl Acad Sci U S A. 2001;98(19):10892-7 - PMID: 11535834 - PMCID: PMC58570 - DOI: 10.1073/pnas.191378698

Two-component circuitry in Arabidopsis cytokinin signal transduction.

Hwang I, Sheen J
Nature. 2001;413(6854):383-9 - PMID: 11574878 - DOI: 10.1038/35096500

The roles of mucD and alginate in the virulence of Pseudomonas aeruginosa in plants, nematodes and mice.

Yorgey P, Rahme LG, Tan MW, Ausubel FM
Mol Microbiol. 2001;41(5):1063-76 - PMID: 11555287 - DOI: 10.1046/j.1365-2958.2001.02580.x

Hepatitis C virus replication is directly inhibited by IFN-alpha in a full-length binary expression system.

Chung RT, He W, Saquib A, Contreras AM, Xavier RJ, Chawla A, Wang TC, Schmidt EV
Proc Natl Acad Sci U S A. 2001;98(17):9847-52 - PMID: 11493707 - PMCID: PMC55541 - DOI: 10.1073/pnas.171319698

Hypoxia and acidosis independently up-regulate vascular endothelial growth factor transcription in brain tumors in vivo.

Fukumura D, Xu L, Chen Y, Gohongi T, Seed B, Jain RK
Cancer Res. 2001;61(16):6020-4 - PMID: 11507045

Intrahepatic amino acid and glucose metabolism in a D-galactosamine-induced rat liver failure model.

Arai K, Lee K, Berthiaume F, Tompkins RG, Yarmush ML
Hepatology. 2001;34(2):360-71 - PMID: 11481621 - DOI: 10.1053/jhep.2001.26515

Lipid rafts and pseudotyping.

Pickl WF, Pimentel-Muiños FX, Seed B
J Virol. 2001;75(15):7175-83 - PMID: 11435598 - PMCID: PMC114446 - DOI: 10.1128/JVI.75.15.7175-7183.2001

Molecular identification of phenylalanine ammonia-lyase as a substrate of a specific constitutively active Arabidopsis CDPK expressed in maize protoplasts.

Cheng SH, Sheen J, Gerrish C, Bolwell GP
FEBS Lett. 2001;503(2-3):185-8 - PMID: 11513879 - DOI: 10.1016/s0014-5793(01)02732-6

A fulminant hepatic failure model in the rat: involvement of interleukin-1beta and tumor necrosis factor-alpha.

Shito M, Balis UJ, Tompkins RG, Yarmush ML, Toner M
Dig Dis Sci. 2001;46(8):1700-8 - PMID: 11508670 - DOI: 10.1023/a:1010653504568

Initial experience with a composite autologous skin substitute.

Sheridan RL, Morgan JR, Cusick JL, Petras LM, Lydon MM, Tompkins RG
Burns. 2001;27(5):421-4 - PMID: 11451592

Antibiotic prophylaxis for group A streptococcal burn wound infection is not necessary.

Sheridan RL, Weber JM, Pasternack MS, Tompkins RG
J Trauma. 2001;51(2):352-5 - PMID: 11493799 - DOI: 10.1097/00005373-200108000-00022

Young age is not a predictor of mortality in burns.

Sheridan RL, Weber JM, Schnitzer JJ, Schulz JT, Ryan CM, Tompkins RG
Pediatr Crit Care Med. 2001;2(3):223-224 - PMID: 12793945

Genes and mechanisms related to RNA interference regulate expression of the small temporal RNAs that control C. elegans developmental timing.

Grishok A, Pasquinelli AE, Conte D, Li N, Parrish S, Ha I, Baillie DL, Fire A, Ruvkun G, Mello CC
Cell. 2001;106(1):23-34 - PMID: 11461699 - DOI: 10.1016/s0092-8674(01)00431-7

In vitro and in vivo evaluation of albumin synthesis rate of porcine hepatocytes in a flat-plate bioreactor.

Shito M, Kim NH, Baskaran H, Tilles AW, Tompkins RG, Yarmush ML, Toner M
Artif Organs. 2001;25(7):571-8 - PMID: 11493279

Evidence that dendritic cells infiltrate atherosclerotic lesions in apolipoprotein E-deficient mice.

Bobryshev YV, Taksir T, Lord RS, Freeman MW
Histol Histopathol. 2001;16(3):801-8 - PMID: 11510970 - DOI: 10.14670/HH-16.801

Identification of two sequences in the cytoplasmic tail of the human immunodeficiency virus type 1 envelope glycoprotein that inhibit cell surface expression.

Bültmann A, Muranyi W, Seed B, Haas J
J Virol. 2001;75(11):5263-76 - PMID: 11333908 - PMCID: PMC114932 - DOI: 10.1128/JVI.75.11.5263-5276.2001

The TASTY locus on chromosome 1 of Arabidopsis affects feeding of the insect herbivore Trichoplusia ni.

Jander G, Cui J, Nhan B, Pierce NE, Ausubel FM
Plant Physiol. 2001;126(2):890-8 - PMID: 11402216 - PMCID: PMC111178 - DOI: 10.1104/pp.126.2.890

Silanizing glassware.

Seed B
Curr Protoc Immunol. 2001;Appendix 3:Appendix 3K - PMID: 18432662 - DOI: 10.1002/0471142735.ima03ks21

Silanizing glassware.

Seed B
Curr Protoc Protein Sci. 2001;Appendix 3:Appendix 3E - PMID: 18429072 - DOI: 10.1002/0471140864.psa03es13

Silanizing glassware.

Seed B
Curr Protoc Mol Biol. 2001;Appendix 3:Appendix 3B - PMID: 18265032 - DOI: 10.1002/0471142727.mba03bs28

Silanizing glassware.

Seed B
Curr Protoc Cell Biol. 2001;Appendix 3:Appendix 3E - PMID: 18228287 - DOI: 10.1002/0471143030.cba03es08

Isotopic assays for reporter gene activity.

Kingston RE, Sheen J, Moore D
Curr Protoc Mol Biol. 2001;Chapter 9:Unit9.7A - PMID: 18265285 - DOI: 10.1002/0471142727.mb0907as29

Introduction of plasmid DNA into cells.

Seidman CE, Struhl K, Sheen J, Jessen T
Curr Protoc Mol Biol. 2001;Chapter 1:Unit1.8 - PMID: 18265047 - DOI: 10.1002/0471142727.mb0108s37

Gaucher disease. New approaches to an ancient disease.

Mankin HJ, Rosenthal DI, Xavier R
J Bone Joint Surg Am. 2001;83(5):748-62 - PMID: 11379747

Isotopic assays for reporter gene activity.

Kingston RE, Sheen J, Moore D
Curr Protoc Pharmacol. 2001;Chapter 6:Unit 6.4 - PMID: 21965075 - DOI: 10.1002/0471141755.ph0604s05

ATP-binding cassette transporter A1 contains an NH2-terminal signal anchor sequence that translocates the protein's first hydrophilic domain to the exoplasmic space.

Fitzgerald ML, Mendez AJ, Moore KJ, Andersson LP, Panjeton HA, Freeman MW
J Biol Chem. 2001;276(18):15137-45 - PMID: 11328826 - DOI: 10.1074/jbc.m100474200

Detection of breast cancer cells in ductal lavage fluid by methylation-specific PCR.

Evron E, Dooley WC, Umbricht CB, Rosenthal D, Sacchi N, Gabrielson E, Soito AB, Hung DT, Ljung B, Davidson NE, Sukumar S
Lancet. 2001;357(9265):1335-6 - PMID: 11343741 - DOI: 10.1016/s0140-6736(00)04501-3

Functional proteins from a random-sequence library.

Keefe AD, Szostak JW
Nature. 2001;410(6829):715-8 - PMID: 11287961 - PMCID: PMC4476321 - DOI: 10.1038/35070613

The use of mRNA display to select high-affinity protein-binding peptides.

Wilson DS, Keefe AD, Szostak JW
Proc Natl Acad Sci U S A. 2001;98(7):3750-5 - PMID: 11274392 - PMCID: PMC31124 - DOI: 10.1073/pnas.061028198

Regulation of DAF-2 receptor signaling by human insulin and ins-1, a member of the unusually large and diverse C. elegans insulin gene family.

Pierce SB, Costa M, Wisotzkey R, Devadhar S, Homburger SA, Buchman AR, Ferguson KC, Heller J, Platt DM, Pasquinelli AA, Liu LX, Doberstein SK, Ruvkun G
Genes Dev. 2001;15(6):672-86 - PMID: 11274053 - PMCID: PMC312654 - DOI: 10.1101/gad.867301

Regulation of ectodermal and excretory function by the C. elegans POU homeobox gene ceh-6.

Bürglin TR, Ruvkun G
Development. 2001;128(5):779-90 - PMID: 11171402

Arginine and ornithine kinetics in severely burned patients: increased rate of arginine disposal.

Yu YM, Ryan CM, Castillo L, Lu XM, Beaumier L, Tompkins RG, Young VR
Am J Physiol Endocrinol Metab. 2001;280(3):E509-17 - PMID: 11171607 - DOI: 10.1152/ajpendo.2001.280.3.E509

Manipulating intestinal cholesterol absorption and hepatic cholesterol and bile acid metabolism by activation of deorphanized nuclear receptors.

Rigotti A, Freeman MW
Gastroenterology. 2001;120(4):1054-5 - PMID: 11231965 - DOI: 10.1016/s0016-5085(01)83919-6

Programmed cell death mediated by ced-3 and ced-4 protects Caenorhabditis elegans from Salmonella typhimurium-mediated killing.

Aballay A, Ausubel FM
Proc Natl Acad Sci U S A. 2001;98(5):2735-9 - PMID: 11226309 - PMCID: PMC30208 - DOI: 10.1073/pnas.041613098

TBX1 is responsible for cardiovascular defects in velo-cardio-facial/DiGeorge syndrome.

Merscher S, Funke B, Epstein JA, Heyer J, Puech A, Lu MM, Xavier RJ, Demay MB, Russell RG, Factor S, Tokooya K, Jore BS, Lopez M, Pandita RK, Lia M, Carrion D, Xu H, Schorle H, Kobler JB, Scambler P, Wynshaw-Boris A, Skoultchi AI, Morrow BE, Kucherlapati R
Cell. 2001;104(4):619-29 - PMID: 11239417 - DOI: 10.1016/s0092-8674(01)00247-1

A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms.

Sachidanandam R, Weissman D, Schmidt SC, Kakol JM, Stein LD, Marth G, Sherry S, Mullikin JC, Mortimore BJ, Willey DL, Hunt SE, Cole CG, Coggill PC, Rice CM, Ning Z, Rogers J, Bentley DR, Kwok PY, Mardis ER, Yeh RT, Schultz B, Cook L, Davenport R, Dante M, Fulton L, Hillier L, Waterston RH, McPherson JD, Gilman B, Schaffner S, Van Etten WJ, Reich D, Higgins J, Daly MJ, Blumenstiel B, Baldwin J, Stange-Thomann N, Zody MC, Linton L, Lander ES, Altshuler D,
Nature. 2001;409(6822):928-33 - PMID: 11237013 - DOI: 10.1038/35057149

Initial sequencing and analysis of the human genome.

Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, Stange-Thomann N, Stojanovic N, Subramanian A, Wyman D, Rogers J, Sulston J, Ainscough R, Beck S, Bentley D, Burton J, Clee C, Carter N, Coulson A, Deadman R, Deloukas P, Dunham A, Dun ...
Nature. 2001;409(6822):860-921 - PMID: 11237011 - DOI: 10.1038/35057062

Isoform-specific mutations in the Caenorhabditis elegans heterochronic gene lin-14 affect stage-specific patterning.

Reinhart BJ, Ruvkun G
Genetics. 2001;157(1):199-209 - PMID: 11139502 - PMCID: PMC1461488

Mesophyll-specific, light and metabolic regulation of the C4 PPCZm1 promoter in transgenic maize.

Kausch AP, Owen TP, Zachwieja SJ, Flynn AR, Sheen J
Plant Mol Biol. 2001;45(1):1-15 - PMID: 11247600

The role of PPAR-gamma in macrophage differentiation and cholesterol uptake.

Moore KJ, Rosen ED, Fitzgerald ML, Randow F, Andersson LP, Altshuler D, Milstone DS, Mortensen RM, Spiegelman BM, Freeman MW
Nat Med. 2001;7(1):41-7 - PMID: 11135614 - DOI: 10.1038/83328

Synthesizing life.

Szostak JW, Bartel DP, Luisi PL
Nature. 2001;409(6818):387-90 - PMID: 11201752 - DOI: 10.1038/35053176

Phosphatidylinositol 3-kinase signaling inhibits DAF-16 DNA binding and function via 14-3-3-dependent and 14-3-3-independent pathways.

Cahill CM, Tzivion G, Nasrin N, Ogg S, Dore J, Ruvkun G, Alexander-Bridges M
J Biol Chem. 2000;276(16):13402-10 - PMID: 11124266 - DOI: 10.1074/jbc.M010042200

Arabidopsis genome. A milestone in plant biology.

Ausubel FM
Plant Physiol. 2000;124(4):1451-4 - PMID: 11115856 - PMCID: PMC1539293 - DOI: 10.1104/pp.124.4.1451

Pathogenesis of the human opportunistic pathogen Pseudomonas aeruginosa PA14 in Arabidopsis.

Plotnikova JM, Rahme LG, Ausubel FM
Plant Physiol. 2000;124(4):1766-74 - PMID: 11115892 - PMCID: PMC59873 - DOI: 10.1104/pp.124.4.1766

A simple procedure for the analysis of single nucleotide polymorphisms facilitates map-based cloning in Arabidopsis.

Drenkard E, Richter BG, Rozen S, Stutius LM, Angell NA, Mindrinos M, Cho RJ, Oefner PJ, Davis RW, Ausubel FM
Plant Physiol. 2000;124(4):1483-92 - PMID: 11115864 - PMCID: PMC1539302 - DOI: 10.1104/pp.124.4.1483

Mutational analysis of the Arabidopsis nucleotide binding site-leucine-rich repeat resistance gene RPS2.

Tao Y, Yuan F, Leister RT, Ausubel FM, Katagiri F
Plant Cell. 2000;12(12):2541-2554 - PMID: 11148296 - PMCID: PMC102236 - DOI: 10.1105/tpc.12.12.2541

Effects of overexpression of the amino-terminal fragment of apolipoprotein B on apolipoprotein B and lipoprotein production.

Li Z, Kako Y, Pang L, Freeman MW, Glick JM, Wang X, Goldberg IJ
J Lipid Res. 2000;41(12):1912-20 - PMID: 11108724

Episomal segregation of the adenovirus enhancer sequence by conditional genome rearrangement abrogates late viral gene expression.

Wang X, Zeng W, Murakawa M, Freeman MW, Seed B
J Virol. 2000;74(23):11296-303 - PMID: 11070029 - PMCID: PMC113234 - DOI: 10.1128/jvi.74.23.11296-11303.2000

Fas triggers an alternative, caspase-8-independent cell death pathway using the kinase RIP as effector molecule.

Holler N, Zaru R, Micheau O, Thome M, Attinger A, Valitutti S, Bodmer JL, Schneider P, Seed B, Tschopp J
Nat Immunol. 2000;1(6):489-95 - PMID: 11101870 - DOI: 10.1038/82732

Episomal segregation of the adenovirus enhancer sequence by conditional genome rearrangement abrogates late viral gene expression.

Wang X, Zeng W, Murakawa M, Freeman MW, Seed B
J Virol. 2000;74(23):11296-303 - PMID: 11070029 - PMCID: PMC113234 - DOI: 10.1128/jvi.74.23.11296-11303.2000

Graded expression of ceh-14 reporters in the hypodermis is induced by a gonadal signal.

Kagoshima H, Sommer R, Reinhart BJ, Cassata G, Ruvkun G, Bürglin TR
Dev Genes Evol. 2000;210(11):564-9 - PMID: 11180807 - DOI: 10.1007/s004270050347

Conservation of the sequence and temporal expression of let-7 heterochronic regulatory RNA.

Pasquinelli AE, Reinhart BJ, Slack F, Martindale MQ, Kuroda MI, Maller B, Hayward DC, Ball EE, Degnan B, Müller P, Spring J, Srinivasan A, Fishman M, Finnerty J, Corbo J, Levine M, Leahy P, Davidson E, Ruvkun G
Nature. 2000;408(6808):86-9 - PMID: 11081512 - DOI: 10.1038/35040556

Salmonella typhimurium proliferates and establishes a persistent infection in the intestine of Caenorhabditis elegans.

Aballay A, Yorgey P, Ausubel FM
Curr Biol. 2000;10(23):1539-42 - PMID: 11114525 - DOI: 10.1016/s0960-9822(00)00830-7

Cutaneous herpetic infections complicating burns.

Sheridan RL, Schulz JT, Weber JM, Ryan CM, Pasternack MS, Tompkins RG
Burns. 2000;26(7):621-4 - PMID: 10925184

The role of hexokinase in plant sugar signal transduction and growth and development.

Xiao W, Sheen J, Jang JC
Plant Mol Biol. 2000;44(4):451-61 - PMID: 11197321

Roles of salicylic acid, jasmonic acid, and ethylene in cpr-induced resistance in arabidopsis.

Clarke JD, Volko SM, Ledford H, Ausubel FM, Dong X
Plant Cell. 2000;12(11):2175-90 - PMID: 11090217 - PMCID: PMC150166 - DOI: 10.1105/tpc.12.11.2175

Pattern recognition receptors TLR4 and CD14 mediate response to respiratory syncytial virus.

Kurt-Jones EA, Popova L, Kwinn L, Haynes LM, Jones LP, Tripp RA, Walsh EE, Freeman MW, Golenbock DT, Anderson LJ, Finberg RW
Nat Immunol. 2000;1(5):398-401 - PMID: 11062499 - DOI: 10.1038/80833

A 10-year experience with toxic epidermal necrolysis.

Schulz JT, Sheridan RL, Ryan CM, MacKool B, Tompkins RG
J Burn Care Rehabil. 2000;21(3):199-204 - PMID: 10850900

Optimized synthesis of RNA-protein fusions for in vitro protein selection.

Liu R, Barrick JE, Szostak JW, Roberts RW
Methods Enzymol. 2000;318:268-93 - PMID: 10889994 - DOI: 10.1016/s0076-6879(00)18058-9

Optimization of rat hepatocyte culture in citrated human plasma.

Washizu J, Berthiaume F, Chan C, Tompkins RG, Toner M, Yarmush ML
J Surg Res. 2000;93(2):237-46 - PMID: 11027466 - DOI: 10.1006/jsre.2000.5986

Amino acid supplementation improves cell-specific functions of the rat hepatocytes exposed to human plasma.

Washizu J, Chan C, Berthiaume F, Tompkins RG, Toner M, Yarmush ML
Tissue Eng. 2000;6(5):497-504 - PMID: 11074936 - DOI: 10.1089/107632700750022143

Regulation of C. elegans life-span by insulinlike signaling in the nervous system.

Wolkow CA, Kimura KD, Lee MS, Ruvkun G
Science. 2000;290(5489):147-50 - PMID: 11021802 - DOI: 10.1126/science.290.5489.147

Ancient adaptation of the active site of tryptophanyl-tRNA synthetase for tryptophan binding.

Praetorius-Ibba M, Stange-Thomann N, Kitabatake M, Ali K, Söll I, Carter CW, Ibba M, Söll D
Biochemistry. 2000;39(43):13136-43 - PMID: 11052665 - DOI: 10.1021/bi001512t

Simulation of fungal-mediated cell death by fumonisin B1 and selection of fumonisin B1-resistant (fbr) Arabidopsis mutants.

Stone JM, Heard JE, Asai T, Ausubel FM
Plant Cell. 2000;12(10):1811-22 - PMID: 11041878 - PMCID: PMC149121 - DOI: 10.1105/tpc.12.10.1811

Fumonisin B1-induced cell death in arabidopsis protoplasts requires jasmonate-, ethylene-, and salicylate-dependent signaling pathways.

Asai T, Stone JM, Heard JE, Kovtun Y, Yorgey P, Sheen J, Ausubel FM
Plant Cell. 2000;12(10):1823-36 - PMID: 11041879 - PMCID: PMC149122 - DOI: 10.1105/tpc.12.10.1823

Three unique mutants of Arabidopsis identify eds loci required for limiting growth of a biotrophic fungal pathogen.

Dewdney J, Reuber TL, Wildermuth MC, Devoto A, Cui J, Stutius LM, Drummond EP, Ausubel FM
Plant J. 2000;24(2):205-18 - PMID: 11069695

Divergent response to LPS and bacteria in CD14-deficient murine macrophages.

Moore KJ, Andersson LP, Ingalls RR, Monks BG, Li R, Arnaout MA, Golenbock DT, Freeman MW
J Immunol. 2000;165(8):4272-80 - PMID: 11035061 - DOI: 10.4049/jimmunol.165.8.4272

In vitro selection and directed evolution.

Szostak JW
Harvey Lect. 2000;93:95-118 - PMID: 10941421

DAF-16 recruits the CREB-binding protein coactivator complex to the insulin-like growth factor binding protein 1 promoter in HepG2 cells.

Nasrin N, Ogg S, Cahill CM, Biggs W, Nui S, Dore J, Calvo D, Shi Y, Ruvkun G, Alexander-Bridges MC
Proc Natl Acad Sci U S A. 2000;97(19):10412-7 - PMID: 10973497 - PMCID: PMC27038 - DOI: 10.1073/pnas.190326997

Microbiology. How to get along--friendly microbes in a hostile world.

Xavier RJ, Podolsky DK
Science. 2000;289(5484):1483-4 - PMID: 10991734 - DOI: 10.1126/science.289.5484.1483

Isolation and characterization of disease resistance gene homologues from rice cultivar IR64.

Ilag LL, Yadav RC, Huang N, Ronald PC, Ausubel FM
Gene. 2000;255(2):245-55 - PMID: 11024284 - DOI: 10.1016/s0378-1119(00)00333-4

Expanding the structural and functional diversity of RNA: analog uridine triphosphates as candidates for in vitro selection of nucleic acids.

Vaish NK, Fraley AW, Szostak JW, McLaughlin LW
Nucleic Acids Res. 2000;28(17):3316-22 - PMID: 10954600 - PMCID: PMC110695 - DOI: 10.1093/nar/28.17.3316

Elucidating the molecular mechanisms of bacterial virulence using non-mammalian hosts.

Mahajan-Miklos S, Rahme LG, Ausubel FM
Mol Microbiol. 2000;37(5):981-8 - PMID: 10972817 - DOI: 10.1046/j.1365-2958.2000.02056.x

Mechanisms of NSAID-induced gastrointestinal injury defined using mutant mice.

Beck PL, Xavier R, Lu N, Nanda NN, Dinauer M, Podolsky DK, Seed B
Gastroenterology. 2000;119(3):699-705 - PMID: 10982764 - DOI: 10.1053/gast.2000.16497

What to do about high cholesterol

M Freeman, Consultant editor 2nd edition. PJ Skerret and SD Emond
President and Fellows of Harvard College. Harvard Health Publications. 2000;:ePub

Plants and animals share functionally common bacterial virulence factors.

Rahme LG, Ausubel FM, Cao H, Drenkard E, Goumnerov BC, Lau GW, Mahajan-Miklos S, Plotnikova J, Tan MW, Tsongalis J, Walendziewicz CL, Tompkins RG
Proc Natl Acad Sci U S A. 2000;97(16):8815-21 - PMID: 10922040 - PMCID: PMC34017 - DOI: 10.1073/pnas.97.16.8815

Analysis of Arabidopsis glucose insensitive mutants, gin5 and gin6, reveals a central role of the plant hormone ABA in the regulation of plant vegetative development by sugar.

Arenas-Huertero F, Arroyo A, Zhou L, Sheen J, León P
Genes Dev. 2000;14(16):2085-96 - PMID: 10950871 - PMCID: PMC316855

In vitro selection of functional nucleic acids.

Wilson DS, Szostak JW
Annu Rev Biochem. 2000;68:611-47 - PMID: 10872462 - DOI: 10.1146/annurev.biochem.68.1.611

Cellular cholesterol efflux in heterozygotes for tangier disease is markedly reduced and correlates with high density lipoprotein cholesterol concentration and particle size.

Brousseau ME, Eberhart GP, Dupuis J, Asztalos BF, Goldkamp AL, Schaefer EJ, Freeman MW
J Lipid Res. 2000;41(7):1125-35 - PMID: 10884295

Positive correlation between virulence of Pseudomonas aeruginosa mutants in mice and insects.

Jander G, Rahme LG, Ausubel FM
J Bacteriol. 2000;182(13):3843-5 - PMID: 10851003 - PMCID: PMC94559 - DOI: 10.1128/jb.182.13.3843-3845.2000

A bacterial two-hybrid selection system for studying protein-DNA and protein-protein interactions.

Joung JK, Ramm EI, Pabo CO
Proc Natl Acad Sci U S A. 2000;97(13):7382-7 - PMID: 10852947 - PMCID: PMC16554 - DOI: 10.1073/pnas.110149297

Virulence of the phytopathogen Pseudomonas syringae pv. maculicola is rpoN dependent.

Hendrickson EL, Guevera P, Peñaloza-Vàzquez A, Shao J, Bender C, Ausubel FM
J Bacteriol. 2000;182(12):3498-507 - PMID: 10852883 - PMCID: PMC101941 - DOI: 10.1128/jb.182.12.3498-3507.2000

The alternative sigma factor RpoN is required for hrp activity in Pseudomonas syringae pv. maculicola and acts at the level of hrpL transcription.

Hendrickson EL, Guevera P, Ausubel FM
J Bacteriol. 2000;182(12):3508-16 - PMID: 10852884 - PMCID: PMC101944 - DOI: 10.1128/jb.182.12.3508-3516.2000

Artificial skin.

Schulz JT, Tompkins RG, Burke JF
Annu Rev Med. 2000;51:231-44 - PMID: 10774462 - DOI: 10.1146/annurev.med.51.1.231

Blood glutathione synthesis rates in healthy adults receiving a sulfur amino acid-free diet.

Lyons J, Rauh-Pfeiffer A, Yu YM, Lu XM, Zurakowski D, Tompkins RG, Ajami AM, Young VR, Castillo L
Proc Natl Acad Sci U S A. 2000;97(10):5071-6 - PMID: 10792033 - PMCID: PMC25783 - DOI: 10.1073/pnas.090083297

The lin-41 RBCC gene acts in the C. elegans heterochronic pathway between the let-7 regulatory RNA and the LIN-29 transcription factor.

Slack FJ, Basson M, Liu Z, Ambros V, Horvitz HR, Ruvkun G
Mol Cell. 2000;5(4):659-69 - PMID: 10882102

Current expectations for survival in pediatric burns.

Sheridan RL, Remensnyder JP, Schnitzer JJ, Schulz JT, Ryan CM, Tompkins RG
Arch Pediatr Adolesc Med. 2000;154(3):245-9 - PMID: 10710021

Fractalkine is an epithelial and endothelial cell-derived chemoattractant for intraepithelial lymphocytes in the small intestinal mucosa.

Muehlhoefer A, Saubermann LJ, Gu X, Luedtke-Heckenkamp K, Xavier R, Blumberg RS, Podolsky DK, MacDermott RP, Reinecker HC
J Immunol. 2000;164(6):3368-76 - PMID: 10706732 - DOI: 10.4049/jimmunol.164.6.3368

Constructing high complexity synthetic libraries of long ORFs using in vitro selection.

Cho G, Keefe AD, Liu R, Wilson DS, Szostak JW
J Mol Biol. 2000;297(2):309-19 - PMID: 10715203 - DOI: 10.1006/jmbi.2000.3571

Novel mutations in the gene encoding ATP-binding cassette 1 in four tangier disease kindreds.

Brousseau ME, Schaefer EJ, Dupuis J, Eustace B, Van Eerdewegh P, Goldkamp AL, Thurston LM, FitzGerald MG, Yasek-McKenna D, O'Neill G, Eberhart GP, Weiffenbach B, Ordovas JM, Freeman MW, Brown RH, Gu JZ
J Lipid Res. 2000;41(3):433-41 - PMID: 10706591

Lipopolysaccharide induces scavenger receptor A expression in mouse macrophages: a divergent response relative to human THP-1 monocyte/macrophages.

Fitzgerald ML, Moore KJ, Freeman MW, Reed GL
J Immunol. 2000;164(5):2692-700 - PMID: 10679110 - DOI: 10.4049/jimmunol.164.5.2692

The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans.

Reinhart BJ, Slack FJ, Basson M, Pasquinelli AE, Bettinger JC, Rougvie AE, Horvitz HR, Ruvkun G
Nature. 2000;403(6772):901-6 - PMID: 10706289 - DOI: 10.1038/35002607

Food and metabolic signalling defects in a Caenorhabditis elegans serotonin-synthesis mutant.

Sze JY, Victor M, Loer C, Shi Y, Ruvkun G
Nature. 2000;403(6769):560-4 - PMID: 10676966 - DOI: 10.1038/35000609

Caenorhabditis elegans: a model genetic host to study Pseudomonas aeruginosa pathogenesis.

Tan MW, Ausubel FM
Curr Opin Microbiol. 2000;3(1):29-34 - PMID: 10679415

Stromelysin-1 (MMP-3) expression driven by a macrophage-specific promoter results in reduced viability in transgenic mice.

Fabunmi RP, Moore KJ, Libby P, Freeman MW
Atherosclerosis. 2000;148(2):375-86 - PMID: 10657574 - DOI: 10.1016/s0021-9150(99)00405-0

Management of severe toxic epidermal necrolysis in children.

Sheridan RL, Weber JM, Schulz JT, Ryan CM, Low HM, Tompkins RG
J Burn Care Rehabil. 2000;20(6):497-500 - PMID: 10613688

Ribozyme-catalyzed tRNA aminoacylation.

Lee N, Bessho Y, Wei K, Szostak JW, Suga H
Nat Struct Biol. 2000;7(1):28-33 - PMID: 10625423 - DOI: 10.1038/71225

A common muscarinic pathway for diapause recovery in the distantly related nematode species Caenorhabditis elegans and Ancylostoma caninum.

Tissenbaum HA, Hawdon J, Perregaux M, Hotez P, Guarente L, Ruvkun G
Proc Natl Acad Sci U S A. 2000;97(1):460-5 - PMID: 10618440 - PMCID: PMC26685 - DOI: 10.1073/pnas.97.1.460

Long-term outcome of children surviving massive burns.

Sheridan RL, Hinson MI, Liang MH, Nackel AF, Schoenfeld DA, Ryan CM, Mulligan JL, Tompkins RG
JAMA. 2000;283(1):69-73 - PMID: 10632282 - DOI: 10.1001/jama.283.1.69

A paradoxical reduction in susceptibility to colonic injury upon targeted transgenic ablation of goblet cells.

Itoh H, Beck PL, Inoue N, Xavier R, Podolsky DK
J Clin Invest. 1999;104(11):1539-47 - PMID: 10587517 - PMCID: PMC409855 - DOI: 10.1172/JCI6211

Regulated commitment of TNF receptor signaling: a molecular switch for death or activation.

Pimentel-Muiños FX, Seed B
Immunity. 1999;11(6):783-93 - PMID: 10626900

Low-dose inhaled nitric oxide in acutely burned children with profound respiratory failure.

Sheridan RL, Zapol WM, Ritz RH, Tompkins RG
Surgery. 1999;126(5):856-62 - PMID: 10568185

Arabidopsis thaliana PAD4 encodes a lipase-like gene that is important for salicylic acid signaling.

Jirage D, Tootle TL, Reuber TL, Frost LN, Feys BJ, Parker JE, Ausubel FM, Glazebrook J
Proc Natl Acad Sci U S A. 1999;96(23):13583-8 - PMID: 10557364 - PMCID: PMC23991 - DOI: 10.1073/pnas.96.23.13583

Genome-wide mapping with biallelic markers in Arabidopsis thaliana.

Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspiel N, Theologis A, Yang WH, Hubbell E, Au M, Chung EY, Lashkari D, Lemieux B, Dean C, Lipshutz RJ, Ausubel FM, Davis RW, Oefner PJ
Nat Genet. 1999;23(2):203-7 - PMID: 10508518 - DOI: 10.1038/13833

Cutaneous burn injury alters relative tricarboxylic acid cycle fluxes in rat liver.

Yarmush DM, MacDonald AD, Foy BD, Berthiaume F, Tompkins RG, Yarmush ML
J Burn Care Rehabil. 1999;20(4):292-302 - PMID: 10425591

Effluxed lipids: Tangier Island's latest export.

Freeman MW
Proc Natl Acad Sci U S A. 1999;96(20):10950-2 - PMID: 10500104 - PMCID: PMC34222 - DOI: 10.1073/pnas.96.20.10950

Themes from a NASA workshop on gene regulatory processes in development and evolution.

Davidson EH, Ruvkun G
J Exp Zool. 1999;285(2):104-15 - PMID: 10440721

Measurement of muscle protein synthesis by positron emission tomography with L-[methyl-11C]methionine: effects of transamination and transmethylation.

Carter EA, Yu YM, Alpert NM, Bonab AA, Tompkins RG, Fischman AJ
J Trauma. 1999;47(2):341-5 - PMID: 10452471 - DOI: 10.1097/00005373-199908000-00021

A unique mechanism of desensitization to lipolysis mediated by beta(3)-adrenoceptor in rats with thermal injury.

Ikezu T, Yasuhara S, Granneman JG, Kraemer FB, Okamoto T, Tompkins RG, Martyn JA
Am J Physiol. 1999;277(2):E316-24 - PMID: 10444428 - DOI: 10.1152/ajpendo.1999.277.2.E316

Leukotriene B4 receptor transgenic mice reveal novel protective roles for lipoxins and aspirin-triggered lipoxins in reperfusion.

Chiang N, Gronert K, Clish CB, O'Brien JA, Freeman MW, Serhan CN
J Clin Invest. 1999;104(3):309-16 - PMID: 10430612 - PMCID: PMC408424 - DOI: 10.1172/JCI7016

The Epstein-Barr virus oncoprotein latent membrane protein 1 engages the tumor necrosis factor receptor-associated proteins TRADD and receptor-interacting protein (RIP) but does not induce apoptosis or require RIP for NF-kappaB activation.

Izumi KM, Cahir McFarland ED, Ting AT, Riley EA, Seed B, Kieff ED
Mol Cell Biol. 1999;19(8):5759-67 - PMID: 10409763 - PMCID: PMC84426 - DOI: 10.1128/mcb.19.8.5759

Alternative olfactory neuron fates are specified by the LIM homeobox gene lim-4.

Sagasti A, Hobert O, Troemel ER, Ruvkun G, Bargmann CI
Genes Dev. 1999;13(14):1794-806 - PMID: 10421632 - PMCID: PMC316880 - DOI: 10.1101/gad.13.14.1794

The metabolic basis of the increase of the increase in energy expenditure in severely burned patients.

Yu YM, Tompkins RG, Ryan CM, Young VR
JPEN J Parenter Enteral Nutr. 1999;23(3):160-8 - PMID: 10338224 - DOI: 10.1177/0148607199023003160

A PDK1 homolog is necessary and sufficient to transduce AGE-1 PI3 kinase signals that regulate diapause in Caenorhabditis elegans.

Paradis S, Ailion M, Toker A, Thomas JH, Ruvkun G
Genes Dev. 1999;13(11):1438-52 - PMID: 10364160 - PMCID: PMC316759 - DOI: 10.1101/gad.13.11.1438

Pax genes in Caenorhabditis elegans: a new twist.

Hobert O, Ruvkun G
Trends Genet. 1999;15(6):214-6 - PMID: 10354580

A 15-year experience with varicella infections in a pediatric burn unit.

Sheridan RL, Weber JM, Pasternak MM, Mulligan JM, Tompkins RG
Burns. 1999;25(4):353-6 - PMID: 10431985

C4 GENE EXPRESSION.

Sheen J
Annu Rev Plant Physiol Plant Mol Biol. 1999;50:187-217 - PMID: 15012208 - DOI: 10.1146/annurev.arplant.50.1.187

Membrane compartmentation and the response to antigen.

Xavier R, Seed B
Curr Opin Immunol. 1999;11(3):265-9 - PMID: 10375560

Isolation and characterization of fluorophore-binding RNA aptamers.

Holeman LA, Robinson SL, Szostak JW, Wilson C
Fold Des. 1999;3(6):423-31 - PMID: 9889155 - DOI: 10.1016/S1359-0278(98)00059-5

The Caenorhabditis elegans lim-6 LIM homeobox gene regulates neurite outgrowth and function of particular GABAergic neurons.

Hobert O, Tessmar K, Ruvkun G
Development. 1999;126(7):1547-62 - PMID: 10068647

Acute hand burns in children: management and long-term outcome based on a 10-year experience with 698 injured hands.

Sheridan RL, Baryza MJ, Pessina MA, O'Neill KM, Cipullo HM, Donelan MB, Ryan CM, Schulz JT, Schnitzer JJ, Tompkins RG
Ann Surg. 1999;229(4):558-64 - PMID: 10203090 - PMCID: PMC1191743 - DOI: 10.1097/00000658-199904000-00016

Skin substitutes in burns.

Sheridan RL, Tompkins RG
Burns. 1999;25(2):97-103 - PMID: 10208382

Pseudomonas aeruginosa killing of Caenorhabditis elegans used to identify P. aeruginosa virulence factors.

Tan MW, Rahme LG, Sternberg JA, Tompkins RG, Ausubel FM
Proc Natl Acad Sci U S A. 1999;96(5):2408-13 - PMID: 10051655 - PMCID: PMC26797 - DOI: 10.1073/pnas.96.5.2408

A conserved LIM protein that affects muscular adherens junction integrity and mechanosensory function in Caenorhabditis elegans.

Hobert O, Moerman DG, Clark KA, Beckerle MC, Ruvkun G
J Cell Biol. 1999;144(1):45-57 - PMID: 9885243 - PMCID: PMC2148118 - DOI: 10.1083/jcb.144.1.45

Laser ablation of burns: initial clinical trial.

Sheridan RL, Lydon MM, Petras LM, Schomacker KT, Tompkins RG, Glatter RD, Parrish JA
Surgery. 1999;125(1):92-5 - PMID: 9889803

Killing of Caenorhabditis elegans by Pseudomonas aeruginosa used to model mammalian bacterial pathogenesis.

Tan MW, Mahajan-Miklos S, Ausubel FM
Proc Natl Acad Sci U S A. 1999;96(2):715-20 - PMID: 9892699 - PMCID: PMC15202 - DOI: 10.1073/pnas.96.2.715

Molecular mechanisms of bacterial virulence elucidated using a Pseudomonas aeruginosa-Caenorhabditis elegans pathogenesis model.

Mahajan-Miklos S, Tan MW, Rahme LG, Ausubel FM
Cell. 1999;96(1):47-56 - PMID: 9989496 - DOI: 10.1016/s0092-8674(00)80958-7

A common theme for LIM homeobox gene function across phylogeny?

Hobert O, Ruvkun G
Biol Bull. 1998;195(3):377-80 - PMID: 9924780 - DOI: 10.2307/1543153

Heterochronic genes in development and evolution.

Slack F, Ruvkun G
Biol Bull. 1998;195(3):375-6 - PMID: 9924779 - DOI: 10.2307/1543152

The C. elegans PTEN homolog, DAF-18, acts in the insulin receptor-like metabolic signaling pathway.

Ogg S, Ruvkun G
Mol Cell. 1998;2(6):887-93 - PMID: 9885576

A novel repeat domain that is often associated with RING finger and B-box motifs.

Slack FJ, Ruvkun G
Trends Biochem Sci. 1998;23(12):474-5 - PMID: 9868369

The taxonomy of developmental control in Caenorhabditis elegans.

Ruvkun G, Hobert O
Science. 1998;282(5396):2033-41 - PMID: 9851920 - DOI: 10.1126/science.282.5396.2033

Modulation of expression of the ToxR regulon in Vibrio cholerae by a member of the two-component family of response regulators.

Wong SM, Carroll PA, Rahme LG, Ausubel FM, Calderwood SB
Infect Immun. 1998;66(12):5854-61 - PMID: 9826365 - PMCID: PMC108741

Isolation of a fluorophore-specific DNA aptamer with weak redox activity.

Wilson C, Szostak JW
Chem Biol. 1998;5(11):609-17 - PMID: 9831529

Correlation of defense gene induction defects with powdery mildew susceptibility in Arabidopsis enhanced disease susceptibility mutants.

Reuber TL, Plotnikova JM, Dewdney J, Rogers EE, Wood W, Ausubel FM
Plant J. 1998;16(4):473-85 - PMID: 9881167

Characterization of a composite tissue model that supports clonal growth of human melanocytes in vitro and in vivo.

Medalie DA, Tompkins RG, Morgan JR
J Invest Dermatol. 1998;111(5):810-6 - PMID: 9804343 - DOI: 10.1046/j.1523-1747.1998.00368.x

Use of cleaved amplified polymorphic sequences (CAPS) as genetic markers in Arabidopsis thaliana.

Glazebrook J, Drenkard E, Preuss D, Ausubel FM
Methods Mol Biol. 1998;82:173-82 - PMID: 9664424

Muscle protein synthesis by positron-emission tomography with L-[methyl-11C]methionine in adult humans.

Fischman AJ, Yu YM, Livni E, Babich JW, Young VR, Alpert NM, Tompkins RG
Proc Natl Acad Sci U S A. 1998;95(22):12793-8 - PMID: 9788993 - PMCID: PMC23595 - DOI: 10.1073/pnas.95.22.12793

Health information in the developing world.

Lown B, Bukachi F, Xavier R
Lancet. 1998;352 Suppl 2:SII34-8 - PMID: 9798645 - DOI: 10.1016/s0140-6736(98)90300-2

In vitro-differentiated embryonic stem cell macrophages: a model system for studying atherosclerosis-associated macrophage functions.

Moore KJ, Fabunmi RP, Andersson LP, Freeman MW
Arterioscler Thromb Vasc Biol. 1998;18(10):1647-54 - PMID: 9763539

Maximal parenteral glucose oxidation in hypermetabolic young children: a stable isotope study.

Sheridan RL, Yu YM, Prelack K, Young VR, Burke JF, Tompkins RG
JPEN J Parenter Enteral Nutr. 1998;22(4):212-6 - PMID: 9661121 - DOI: 10.1177/0148607198022004212

Aging, life span, and senescence.

Guarente L, Ruvkun G, Amasino R
Proc Natl Acad Sci U S A. 1998;95(19):11034-6 - PMID: 9736682 - PMCID: PMC33892 - DOI: 10.1073/pnas.95.19.11034

Tumor induction of VEGF promoter activity in stromal cells.

Fukumura D, Xavier R, Sugiura T, Chen Y, Park EC, Lu N, Selig M, Nielsen G, Taksir T, Jain RK, Seed B
Cell. 1998;94(6):715-25 - PMID: 9753319 - DOI: 10.1016/s0092-8674(00)81731-6

PPARgamma and colorectal carcinoma: conflicts in a nuclear family.

Seed B
Nat Med. 1998;4(9):1004-5 - PMID: 9734386 - DOI: 10.1038/1990

Muskelin, a novel intracellular mediator of cell adhesive and cytoskeletal responses to thrombospondin-1.

Adams JC, Seed B, Lawler J
EMBO J. 1998;17(17):4964-74 - PMID: 9724633 - PMCID: PMC1170825 - DOI: 10.1093/emboj/17.17.4964

Caenorhabditis elegans Akt/PKB transduces insulin receptor-like signals from AGE-1 PI3 kinase to the DAF-16 transcription factor.

Paradis S, Ruvkun G
Genes Dev. 1998;12(16):2488-98 - PMID: 9716402 - PMCID: PMC317081 - DOI: 10.1101/gad.12.16.2488

Functional changes in scavenger receptor binding conformation are induced by charge mutants spanning the entire collagen domain.

Andersson L, Freeman MW
J Biol Chem. 1998;273(31):19592-601 - PMID: 9677385 - DOI: 10.1074/jbc.273.31.19592

Unusual metal ion catalysis in an acyl-transferase ribozyme.

Suga H, Cowan JA, Szostak JW
Biochemistry. 1998;37(28):10118-25 - PMID: 9665717 - DOI: 10.1021/bi980432a

Both C3a and C3a(desArg) regulate interleukin-6 synthesis in human peripheral blood mononuclear cells.

Takabayashi T, Vannier E, Burke JF, Tompkins RG, Gelfand JA, Clark BD
J Infect Dis. 1998;177(6):1622-8 - PMID: 9607842 - DOI: 10.1086/515316

Death in the burn unit: sterile multiple organ failure.

Sheridan RL, Ryan CM, Yin LM, Hurley J, Tompkins RG
Burns. 1998;24(4):307-11 - PMID: 9688194

Isolation of new Arabidopsis mutants with enhanced disease susceptibility to Pseudomonas syringae by direct screening.

Volko SM, Boller T, Ausubel FM
Genetics. 1998;149(2):537-48 - PMID: 9611172 - PMCID: PMC1460196

Membrane compartmentation is required for efficient T cell activation.

Xavier R, Brennan T, Li Q, McCormack C, Seed B
Immunity. 1998;8(6):723-32 - PMID: 9655486

SEK1/MKK4 is required for maintenance of a normal peripheral lymphoid compartment but not for lymphocyte development.

Swat W, Fujikawa K, Ganiatsas S, Yang D, Xavier RJ, Harris NL, Davidson L, Ferrini R, Davis RJ, Labow MA, Flavell RA, Zon LI, Alt FW
Immunity. 1998;8(5):625-34 - PMID: 9620683

A light-independent developmental mechanism potentiates flavonoid gene expression in Arabidopsis seedlings.

Kubasek WL, Ausubel FM, Shirley BW
Plant Mol Biol. 1998;37(2):217-23 - PMID: 9617795

Control of neural development and function in a thermoregulatory network by the LIM homeobox gene lin-11.

Hobert O, D'Alberti T, Liu Y, Ruvkun G
J Neurosci. 1998;18(6):2084-96 - PMID: 9482795

A rabbit model for metabolic studies after burn injury.

Hu RH, Yu YM, Costa D, Young VR, Ryan CM, Burke JF, Tompkins RG
J Surg Res. 1998;75(2):153-60 - PMID: 9655088 - DOI: 10.1006/jsre.1998.5274

Genetically modified human keratinocytes overexpressing PDGF-A enhance the performance of a composite skin graft.

Eming SA, Medalie DA, Tompkins RG, Yarmush ML, Morgan JR
Hum Gene Ther. 1998;9(4):529-39 - PMID: 9525314 - DOI: 10.1089/hum.1998.9.4-529

Decreased cholesterol efflux from fibroblasts of a patient without Tangier disease, but with markedly reduced high density lipoprotein cholesterol levels.

Eberhart GP, Mendez AJ, Freeman MW
J Clin Endocrinol Metab. 1998;83(3):836-46 - PMID: 9506737 - DOI: 10.1210/jcem.83.3.4642

Temporal pattern formation by heterochronic genes.

Slack F, Ruvkun G
Annu Rev Genet. 1998;31:611-34 - PMID: 9442909 - DOI: 10.1146/annurev.genet.31.1.611

Use of Arabidopsis for genetic dissection of plant defense responses.

Glazebrook J, Rogers EE, Ausubel FM
Annu Rev Genet. 1998;31:547-69 - PMID: 9442907 - DOI: 10.1146/annurev.genet.31.1.547

An insulin-like signaling pathway affects both longevity and reproduction in Caenorhabditis elegans.

Tissenbaum HA, Ruvkun G
Genetics. 1998;148(2):703-17 - PMID: 9504918 - PMCID: PMC1459840

Objective estimates of the probability of death from burn injuries.

Ryan CM, Schoenfeld DA, Thorpe WP, Sheridan RL, Cassem EH, Tompkins RG
N Engl J Med. 1998;338(6):362-6 - PMID: 9449729 - DOI: 10.1056/NEJM199802053380604

Increased immune response elicited by DNA vaccination with a synthetic gp120 sequence with optimized codon usage.

André S, Seed B, Eberle J, Schraut W, Bültmann A, Haas J
J Virol. 1998;72(2):1497-503 - PMID: 9445053 - PMCID: PMC124631

Structural and kinetic characterization of an acyl transferase ribozyme.

Suga H, Lohse PA, Szostak JW
J Am Chem Soc. 1998;120(6):1151-6 - PMID: 11541113 - DOI: 10.1021/ja972472s

The epidemiology of resistance to ofloxacin and oxacillin among clinical coagulase-negative staphylococcal isolates: analysis of risk factors and strain types.

Pegues DA, Colby C, Hibberd PL, Cohen LG, Ausubel FM, Calderwood SB, Hooper DC
Clin Infect Dis. 1998;26(1):72-9 - PMID: 9455512 - DOI: 10.1086/516270

PPAR-gamma agonists inhibit production of monocyte inflammatory cytokines.

Jiang C, Ting AT, Seed B
Nature. 1998;391(6662):82-6 - PMID: 9422509 - DOI: 10.1038/34184

Ice formation in isolated human hepatocytes and human liver tissue.

Bischof JC, Ryan CM, Tompkins RG, Yarmush ML, Toner M
ASAIO J. 1997;43(4):271-8 - PMID: 9242939

RNA-peptide fusions for the in vitro selection of peptides and proteins.

Roberts RW, Szostak JW
Proc Natl Acad Sci U S A. 1997;94(23):12297-302 - PMID: 9356443 - PMCID: PMC24913 - DOI: 10.1073/pnas.94.23.12297

Inactivation of the alpha C protein antigen gene, bca, by a novel shuttle/suicide vector results in attenuation of virulence and immunity in group B Streptococcus.

Li J, Kasper DL, Ausubel FM, Rosner B, Michel JL
Proc Natl Acad Sci U S A. 1997;94(24):13251-6 - PMID: 9371832 - PMCID: PMC24295 - DOI: 10.1073/pnas.94.24.13251

Use of model plant hosts to identify Pseudomonas aeruginosa virulence factors.

Rahme LG, Tan MW, Le L, Wong SM, Tompkins RG, Calderwood SB, Ausubel FM
Proc Natl Acad Sci U S A. 1997;94(24):13245-50 - PMID: 9371831 - PMCID: PMC24294 - DOI: 10.1073/pnas.94.24.13245

Mutant ATP-binding RNA aptamers reveal the structural basis for ligand binding.

Dieckmann T, Butcher SE, Sassanfar M, Szostak JW, Feigon J
J Mol Biol. 1997;273(2):467-78 - PMID: 9344753 - DOI: 10.1006/jmbi.1997.1329

The Fork head transcription factor DAF-16 transduces insulin-like metabolic and longevity signals in C. elegans.

Ogg S, Paradis S, Gottlieb S, Patterson GI, Lee L, Tissenbaum HA, Ruvkun G
Nature. 1997;389(6654):994-9 - PMID: 9353126 - DOI: 10.1038/40194

The DAF-3 Smad protein antagonizes TGF-beta-related receptor signaling in the Caenorhabditis elegans dauer pathway.

Patterson GI, Koweek A, Wong A, Liu Y, Ruvkun G
Genes Dev. 1997;11(20):2679-90 - PMID: 9334330 - PMCID: PMC316611 - DOI: 10.1101/gad.11.20.2679

Analysis of thermal injury-induced insulin resistance in rodents. Implication of postreceptor mechanisms.

Ikezu T, Okamoto T, Yonezawa K, Tompkins RG, Martyn JA
J Biol Chem. 1997;272(40):25289-95 - PMID: 9312146 - DOI: 10.1074/jbc.272.40.25289

Burns in children younger than two years of age: an experience with 200 consecutive admissions.

Sheridan RL, Ryan CM, Petras LM, Lydon MK, Weber JM, Tompkins RG
Pediatrics. 1997;100(4):721-3 - PMID: 9310533 - DOI: 10.1542/peds.100.4.721

Integrins and inside-out signal transduction: converging signals from PKC and PIP3.

Kolanus W, Seed B
Curr Opin Cell Biol. 1997;9(5):725-31 - PMID: 9330877

A nuclear genetic lesion affecting Saccharomyces cerevisiae mitochondrial translation is complemented by a homologous Bacillus gene.

Kim SI, Stange-Thomann N, Martins O, Hong KW, Söll D, Fox TD
J Bacteriol. 1997;179(17):5625-7 - PMID: 9287027 - PMCID: PMC179443 - DOI: 10.1128/jb.179.17.5625-5627.1997

In vitro selection of catalytic RNAs.

Chapman KB, Szostak JW
Curr Opin Struct Biol. 1997;4:618-22 - PMID: 11539575

Control of hypertrophic scar growth using selective photothermolysis.

Reiken SR, Wolfort SF, Berthiaume F, Compton C, Tompkins RG, Yarmush ML
Lasers Surg Med. 1997;21(1):7-12 - PMID: 9228634

Localization of radiolabeled chemotactic peptide at focal sites of Escherichia coli infection in rabbits: evidence for a receptor-specific mechanism.

Babich JW, Tompkins RG, Graham W, Barrow SA, Fischman AJ
J Nucl Med. 1997;38(8):1316-22 - PMID: 9255175

daf-2, an insulin receptor-like gene that regulates longevity and diapause in Caenorhabditis elegans.

Kimura KD, Tissenbaum HA, Liu Y, Ruvkun G
Science. 1997;277(5328):942-6 - PMID: 9252323 - DOI: 10.1126/science.277.5328.942

Regulation of interneuron function in the C. elegans thermoregulatory pathway by the ttx-3 LIM homeobox gene.

Hobert O, Mori I, Yamashita Y, Honda H, Ohshima Y, Liu Y, Ruvkun G
Neuron. 1997;19(2):345-57 - PMID: 9292724