Publications for All Faculty - 2014

High-density lipoprotein-mediated cholesterol efflux capacity is improved by treatment with antiretroviral therapy in acute human immunodeficiency virus infection.

Lo J, Rosenberg ES, Fitzgerald ML, Bazner SB, Ihenachor EJ, Hawxhurst V, Borkowska AH, Wei J, Zimmerman CO, Burdo TH, Williams KC, Freeman MW, Grinspoon SK
Open Forum Infect Dis. 2014;1(3):ofu108 - PMID: 25734176 - PMCID: PMC4324225 - DOI: 10.1093/ofid/ofu108

Complex host genetics influence the microbiome in inflammatory bowel disease.

Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ
Genome Med. 2014;6(12):107 - PMID: 25587358 - PMCID: PMC4292994 - DOI: 10.1186/s13073-014-0107-1

Morbidity and Survival Probability in Burn Patients in Modern Burn Care.

Jeschke MG, Pinto R, Kraft R, Nathens AB, Finnerty CC, Gamelli RL, Gibran NS, Klein MB, Arnoldo BD, Tompkins RG, Herndon DN,
Crit Care Med. 2014;43(4):808-15 - PMID: 25559438 - PMCID: PMC4359665 - DOI: 10.1097/CCM.0000000000000790

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

Pauli A, Norris ML, Valen E, Chew GL, Gagnon JA, Zimmerman S, Mitchell A, Ma J, Dubrulle J, Reyon D, Tsai SQ, Joung JK, Saghatelian A, Schier AF
Science. 2014;343(6172):1248636 - PMID: 24407481 - PMCID: PMC4107353 - DOI: 10.1126/science.1248636

Improving CRISPR-Cas nuclease specificity using truncated guide RNAs.

Fu Y, Sander JD, Reyon D, Cascio VM, Joung JK
Nat Biotechnol. 2014;32(3):279-84 - PMID: 24463574 - PMCID: PMC3988262 - DOI: 10.1038/nbt.2808

Effect of exercise on burn-induced changes in tissue-specific glucose metabolism.

Carter EA, Paul K, Bonab AA, Tompkins RG, Fischman AJ
J Burn Care Res. 2014;35(6):470-3 - PMID: 24476988 - PMCID: PMC4113562 - DOI: 10.1097/BCR.0000000000000036

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

Gupta A, Christensen RG, Bell HA, Goodwin M, Patel RY, Pandey M, Enuameh MS, Rayla AL, Zhu C, Thibodeau-Beganny S, Brodsky MH, Joung JK, Wolfe SA, Stormo GD
Nucleic Acids Res. 2014;42(8):4800-12 - PMID: 24523353 - PMCID: PMC4005693 - DOI: 10.1093/nar/gku132

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

Guilinger JP, Pattanayak V, Reyon D, Tsai SQ, Sander JD, Joung JK, Liu DR
Nat Methods. 2014;11(4):429-35 - PMID: 24531420 - PMCID: PMC4010127 - DOI: 10.1038/nmeth.2845

CRISPR-Cas systems for editing, regulating and targeting genomes.

Sander JD, Joung JK
Nat Biotechnol. 2014;32(4):347-55 - PMID: 24584096 - PMCID: PMC4022601 - DOI: 10.1038/nbt.2842

Pathways disrupted in human ALS motor neurons identified through genetic correction of mutant SOD1.

Kiskinis E, Sandoe J, Williams LA, Boulting GL, Moccia R, Wainger BJ, Han S, Peng T, Thams S, Mikkilineni S, Mellin C, Merkle FT, Davis-Dusenbery BN, Ziller M, Oakley D, Ichida J, Di Costanzo S, Atwater N, Maeder ML, Goodwin MJ, Nemesh J, Handsaker RE, Paull D, Noggle S, McCarroll SA, Joung JK, Woolf CJ, Brown RH, Eggan K
Cell Stem Cell. 2014;14(6):781-95 - PMID: 24704492 - PMCID: PMC4653065 - DOI: 10.1016/j.stem.2014.03.004

Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing.

Tsai SQ, Wyvekens N, Khayter C, Foden JA, Thapar V, Reyon D, Goodwin MJ, Aryee MJ, Joung JK
Nat Biotechnol. 2014;32(6):569-76 - PMID: 24770325 - PMCID: PMC4090141 - DOI: 10.1038/nbt.2908

Targeted mutagenesis of zebrafish antithrombin III triggers disseminated intravascular coagulation and thrombosis, revealing insight into function.

Liu Y, Kretz CA, Maeder ML, Richter CE, Tsao P, Vo AH, Huarng MC, Rode T, Hu Z, Mehra R, Olson ST, Joung JK, Shavit JA
Blood. 2014;124(1):142-50 - PMID: 24782510 - PMCID: PMC4125349 - DOI: 10.1182/blood-2014-03-561027

What's changed with genome editing?

Tsai SQ, Joung JK
Cell Stem Cell. 2014;15(1):3-4 - PMID: 24996161 - DOI: 10.1016/j.stem.2014.06.017

I?B kinase ? (IKBKB) mutations in lymphomas that constitutively activate canonical nuclear factor ?B (NF?B) signaling.

Kai X, Chellappa V, Donado C, Reyon D, Sekigami Y, Ataca D, Louissaint A, Mattoo H, Joung JK, Pillai S
J Biol Chem. 2014;289(39):26960-72 - PMID: 25107905 - PMCID: PMC4175336 - DOI: 10.1074/jbc.M114.598763

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

Hill SJ, Rolland T, Adelmant G, Xia X, Owen MS, Dricot A, Zack TI, Sahni N, Jacob Y, Hao T, McKinney KM, Clark AP, Reyon D, Tsai SQ, Joung JK, Beroukhim R, Marto JA, Vidal M, Gaudet S, Hill DE, Livingston DM
Genes Dev. 2014;28(17):1957-75 - PMID: 25184681 - PMCID: PMC4197947 - DOI: 10.1101/gad.241620.114

Genome editing: a tool for research and therapy: towards a functional understanding of variants for molecular diagnostics using genome editing.

Tsai SQ, Iafrate AJ, Joung JK
Nat Med. 2014;20(10):1103-4 - PMID: 25295940 - DOI: 10.1038/nm.3722

Cationic lipid-mediated delivery of proteins enables efficient protein-based genome editing in vitro and in vivo.

Zuris JA, Thompson DB, Shu Y, Guilinger JP, Bessen JL, Hu JH, Maeder ML, Joung JK, Chen ZY, Liu DR
Nat Biotechnol. 2014;33(1):73-80 - PMID: 25357182 - PMCID: PMC4289409 - DOI: 10.1038/nbt.3081

Targeted genome editing in human cells using CRISPR/Cas nucleases and truncated guide RNAs.

Fu Y, Reyon D, Joung JK
Methods Enzymol. 2014;546:21-45 - PMID: 25398334 - DOI: 10.1016/B978-0-12-801185-0.00002-7

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

Gjini E, Mansour MR, Sander JD, Moritz N, Nguyen AT, Kesarsing M, Gans E, He S, Chen S, Ko M, Kuang YY, Yang S, Zhou Y, Rodig S, Zon LI, Joung JK, Rao A, Look AT
Mol Cell Biol. 2014;35(5):789-804 - PMID: 25512612 - PMCID: PMC4323485 - DOI: 10.1128/MCB.00971-14

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases.

Tsai SQ, Zheng Z, Nguyen NT, Liebers M, Topkar VV, Thapar V, Wyvekens N, Khayter C, Iafrate AJ, Le LP, Aryee MJ, Joung JK
Nat Biotechnol. 2014;33(2):187-197 - PMID: 25513782 - PMCID: PMC4320685 - DOI: 10.1038/nbt.3117

Fanconi Anemia Gene Editing by the CRISPR/Cas9 System.

Osborn MJ, Gabriel R, Webber BR, DeFeo AP, McElroy AN, Jarjour J, Starker CG, Wagner JE, Joung JK, Voytas DF, von Kalle C, Schmidt M, Blazar BR, Tolar J
Hum Gene Ther. 2014;26(2):114-26 - PMID: 25545896 - PMCID: PMC4326027 - DOI: 10.1089/hum.2014.111

Mice are not men.

Warren HS, Tompkins RG, Moldawer LL, Seok J, Xu W, Mindrinos MN, Maier RV, Xiao W, Davis RW
Proc Natl Acad Sci U S A. 2014;112(4):E345 - PMID: 25540422 - PMCID: PMC4313842 - DOI: 10.1073/pnas.1414857111

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

O'Rourke EJ, Ruvkun G
Nat Cell Biol. 2014;17(1):104 - PMID: 25534088

Generation of functional RNAs from inactive oligonucleotide complexes by non-enzymatic primer extension.

Adamala K, Engelhart AE, Szostak JW
J Am Chem Soc. 2014;137(1):483-9 - PMID: 25521912 - PMCID: PMC4984999 - DOI: 10.1021/ja511564d

Recovery Trajectories After Burn Injury in Young Adults: Does Burn Size Matter?

Ryan CM, Lee A, Kazis LE, Schneider JC, Shapiro GD, Sheridan RL, Meyer WJ, Palmieri T, Pidcock FS, Reilly D, Tompkins RG,
J Burn Care Res. 2014;36(1):118-29 - PMID: 25501787 - DOI: 10.1097/BCR.0000000000000214

Early life environment and natural history of inflammatory bowel diseases.

Guo AY, Stevens BW, Wilson RG, Russell CN, Cohen MA, Sturgeon HC, Thornton A, Giallourakis C, Khalili H, Nguyen DD, Sauk J, Yajnik V, Xavier RJ, Ananthakrishnan AN
BMC Gastroenterol. 2014;14(1):216 - PMID: 25510175 - PMCID: PMC4300207 - DOI: 10.1186/s12876-014-0216-8

Pathogens.

Govindan JA, Ruvkun G
Virulence. 2014;5(7):695-696 - PMID: 25513769 - PMCID: PMC4189874 - DOI: 10.4161/viru.36667

Spontaneous Neutrophil Migration Patterns during Sepsis after Major Burns.

Jones CN, Moore M, Dimisko L, Alexander A, Ibrahim A, Hassell BA, Warren HS, Tompkins RG, Fagan SP, Irimia D
PLoS One. 2014;9(12):e114509 - PMID: 25489947 - PMCID: PMC4260850 - DOI: 10.1371/journal.pone.0114509

Gene Pathways That Delay Caenorhabditis elegans Reproductive Senescence.

Wang MC, Oakley HD, Carr CE, Sowa JN, Ruvkun G
PLoS Genet. 2014;10(12):e1004752 - PMID: 25474471 - PMCID: PMC4256158 - DOI: 10.1371/journal.pgen.1004752

BCG-induced trained immunity in NK cells: Role for non-specific protection to infection.

Kleinnijenhuis J, Quintin J, Preijers F, Joosten LA, Jacobs C, Xavier RJ, van der Meer JW, van Crevel R, Netea MG
Clin Immunol. 2014;155(2):213-219 - PMID: 25451159 - PMCID: PMC5084088 - DOI: 10.1016/j.clim.2014.10.005

Genetics of immune-mediated disorders: from genome-wide association to molecular mechanism.

Kumar V, Wijmenga C, Xavier RJ
Curr Opin Immunol. 2014;31C:51-57 - PMID: 25458995 - PMCID: PMC5080657 - DOI: 10.1016/j.coi.2014.09.007

Controlled growth of filamentous fatty acid vesicles under flow.

Hentrich C, Szostak JW
Langmuir. 2014;30(49):14916-25 - PMID: 25402759 - PMCID: PMC4985002 - DOI: 10.1021/la503933x

Cas9-Based Genome Editing in Arabidopsis and Tobacco.

Li JF, Zhang D, Sheen J
Methods Enzymol. 2014;546C:459-472 - PMID: 25398353 - DOI: 10.1016/B978-0-12-801185-0.00022-2

Autophagy and checkpoints for intracellular pathogen defense.

Paulus GL, Xavier RJ
Curr Opin Gastroenterol. 2014;31(1):14-23 - PMID: 25394238 - PMCID: PMC4330559 - DOI: 10.1097/MOG.0000000000000134

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

Buffen K, Oosting M, Quintin J, Ng A, Kleinnijenhuis J, Kumar V, van de Vosse E, Wijmenga C, van Crevel R, Oosterwijk E, Grotenhuis AJ, Vermeulen SH, Kiemeney LA, van de Veerdonk FL, Chamilos G, Xavier RJ, van der Meer JW, Netea MG, Joosten LA
PLoS Pathog. 2014;10(10):e1004485 - PMID: 25356988 - PMCID: PMC4214925 - DOI: 10.1371/journal.ppat.1004485

Inertial focusing cytometer with integrated optics for particle characterization.

Kotz KT, Petrofsky AC, Haghgooie R, Granier R, Toner M, Tompkins RG
Technology (Singap World Sci). 2014;1(1):27-36 - PMID: 25346940 - PMCID: PMC4206911 - DOI: 10.1142/S233954781350009X

Twists and turns: my career path and concerns about the future.

Ausubel FM
Genetics. 2014;198(2):431-4 - PMID: 25316778 - PMCID: PMC4196596 - DOI: 10.1534/genetics.114.169102

Chain-Length Heterogeneity Allows for the Assembly of Fatty Acid Vesicles in Dilute Solutions.

Budin I, Prwyes N, Zhang N, Szostak JW
Biophys J. 2014;107(7):1582-1590 - PMID: 25296310 - PMCID: PMC4190651 - DOI: 10.1016/j.bpj.2014.07.067

Pathogens.

Govindan JA, Ruvkun G
Virulence. 2014;5(7):ePub - PMID: 25290904 - PMCID: PMC4189874

Next-Gen Sequencing-Based Mapping and Identification of Ethyl Methanesulfonate-Induced Mutations in Arabidopsis thaliana.

Zhang XC, Millet Y, Ausubel FM, Borowsky M
Curr Protoc Mol Biol. 2014;108:7.18.1-7.18.16 - PMID: 25271717 - DOI: 10.1002/0471142727.mb0718s108

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

Liao J, Jijon HB, Kim IR, Goel G, Doan A, Sokol H, Bauer H, Herrmann BG, Lassen KG, Xavier RJ
PLoS One. 2014;9(9):e108777 - PMID: 25268627 - PMCID: PMC4182575 - DOI: 10.1371/journal.pone.0108777

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling.

Platt RJ, Chen S, Zhou Y, Yim MJ, Swiech L, Kempton HR, Dahlman JE, Parnas O, Eisenhaure TM, Jovanovic M, Graham DB, Jhunjhunwala S, Heidenreich M, Xavier RJ, Langer R, Anderson DG, Hacohen N, Regev A, Feng G, Sharp PA, Zhang F
Cell. 2014;159(2):440-55 - PMID: 25263330 - PMCID: PMC4265475 - DOI: 10.1016/j.cell.2014.09.014

mTOR- and HIF-1?-mediated aerobic glycolysis as metabolic basis for trained immunity.

Cheng SC, Quintin J, Cramer RA, Shepardson KM, Saeed S, Kumar V, Giamarellos-Bourboulis EJ, Martens JH, Rao NA, Aghajanirefah A, Manjeri GR, Li Y, Ifrim DC, Arts RJ, van der Meer BM, Deen PM, Logie C, O'Neill LA, Willems P, van de Veerdonk FL, van der Meer JW, Ng A, Joosten LA, Wijmenga C, Stunnenberg HG, Xavier RJ, Netea MG
Science. 2014;345(6204):1250684 - PMID: 25258083 - PMCID: PMC4226238 - DOI: 10.1126/science.1250684

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity.

Saeed S, Quintin J, Kerstens HH, Rao NA, Aghajanirefah A, Matarese F, Cheng SC, Ratter J, Berentsen K, van der Ent MA, Sharifi N, Janssen-Megens EM, Ter Huurne M, Mandoli A, van Schaik T, Ng A, Burden F, Downes K, Frontini M, Kumar V, Giamarellos-Bourboulis EJ, Ouwehand WH, van der Meer JW, Joosten LA, Wijmenga C, Martens JH, Xavier RJ, Logie C, Netea MG, Stunnenberg HG
Science. 2014;345(6204):1251086 - PMID: 25258085 - PMCID: PMC4242194 - DOI: 10.1126/science.1251086

Treatment of heterotopic ossification through remote ATP hydrolysis.

Peterson JR, De La Rosa S, Eboda O, Cilwa KE, Agarwal S, Buchman SR, Cederna PS, Xi C, Morris MD, Herndon DN, Xiao W, Tompkins RG, Krebsbach PH, Wang SC, Levi B
Sci Transl Med. 2014;6(255):255ra132 - PMID: 25253675 - PMCID: PMC4353731 - DOI: 10.1126/scitranslmed.3008810

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

Draberova L, Bugajev V, Potuckova L, Halova I, Bambouskova M, Polakovicova I, Xavier RJ, Seed B, Draber P
Mol Cell Biol. 2014;34(23):4285-300 - PMID: 25246632 - PMCID: PMC4248753 - DOI: 10.1128/MCB.00983-14

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

Sundberg TB, Xavier RJ, Schreiber SL, Shamji AF
Curr Opin Chem Biol. 2014;23C:23-30 - PMID: 25222143 - PMCID: PMC5087273 - DOI: 10.1016/j.cbpa.2014.08.013

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

Kumar V, Cheng SC, Johnson MD, Smeekens SP, Wojtowicz A, Giamarellos-Bourboulis E, Karjalainen J, Franke L, Withoff S, Plantinga TS, van de Veerdonk FL, van der Meer JW, Joosten LA, Sokol H, Bauer H, Herrmann BG, Bochud PY, Marchetti O, Perfect JR, Xavier RJ, Kullberg BJ, Wijmenga C, Netea MG
Nat Commun. 2014;5:4675 - PMID: 25197941 - PMCID: PMC5142444 - DOI: 10.1038/ncomms5675

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

Sheng J, Larsen A, Heuberger BD, Blain JC, Szostak JW
J Am Chem Soc. 2014;136(39):13916-24 - PMID: 25188906 - PMCID: PMC4183603 - DOI: 10.1021/ja508015a

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

Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE
Nat Biotechnol. 2014;32(12):1262-1267 - PMID: 25184501 - PMCID: PMC4262738 - DOI: 10.1038/nbt.3026

HIV-1 Protein Nef Inhibits Activity of ATP Binding Cassette Transporter A1 by Targeting Endoplasmic Reticulum Chaperone Calnexin.

Jennelle L, Hunegnaw R, Dubrovsky L, Pushkarsky T, Fitzgerald ML, Sviridov D, Popratiloff A, Brichacek B, Bukrinsky M
J Biol Chem. 2014;289(42):28870-84 - PMID: 25170080 - PMCID: PMC4200247 - DOI: 10.1074/jbc.M114.583591

Multivariate inference of pathway activity in host immunity and response to therapeutics.

Goel G, Conway KL, Jaeger M, Netea MG, Xavier RJ
Nucleic Acids Res. 2014;42(16):10288-306 - PMID: 25147207 - PMCID: PMC4176341 - DOI: 10.1093/nar/gku722

An alteration in ATG16L1 stability in Crohn disease.

Lassen KG, Xavier RJ
Autophagy. 2014;10(10):1858-1860 - PMID: 25136803 - PMCID: PMC4198368 - DOI: 10.4161/auto.29963

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

Sundberg TB, Choi HG, Song JH, Russell CN, Hussain MM, Graham DB, Khor B, Gagnon J, O'Connell DJ, Narayan K, Dan?ík V, Perez JR, Reinecker HC, Gray NS, Schreiber SL, Xavier RJ, Shamji AF
Proc Natl Acad Sci U S A. 2014;111(34):12468-12473 - PMID: 25114223 - PMCID: PMC4151730 - DOI: 10.1073/pnas.1412308111

Single Hind Limb Burn Injury to Mice Alters Nuclear Factor-?B Expression and [18F] 2-Fluoro-2-Deoxy-D-Glucose Uptake.

Carter EA, Hamrahi V, Paul K, Bonab AA, Jung W, Tompkins RG, Fischman AJ
J Burn Care Res. 2014;35(6):e373-e378 - PMID: 25100541 - PMCID: PMC4229441 - DOI: 10.1097/BCR.0000000000000035

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

Mammarella ND, Cheng Z, Fu ZQ, Daudi A, Bolwell GP, Dong X, Ausubel FM
Phytochemistry. 2014;112:110-121 - PMID: 25096754 - PMCID: PMC4314520 - DOI: 10.1016/j.phytochem.2014.07.010

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

Wolf SE, Tompkins RG, Herndon DN
Surg Clin North Am. 2014;94(4):917-930 - PMID: 25085097 - DOI: 10.1016/j.suc.2014.05.012

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

Wivagg CN, Bhattacharyya RP, Hung DT
J Antibiot (Tokyo). 2014;67(9):645-654 - PMID: 25052484 - DOI: 10.1038/ja.2014.94

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

Garcia SM, Tabach Y, Lourenço GF, Armakola M, Ruvkun G
Nat Struct Mol Biol. 2014;21(8):712-720 - PMID: 25038802 - PMCID: PMC4125460 - DOI: 10.1038/nsmb.2858

Application of Gaussia luciferase in bicistronic and non-conventional secretion reporter constructs.

Luft C, Freeman J, Elliott D, Al-Tamimi N, Kriston-Vizi J, Heintze J, Lindenschmidt I, Seed B, Ketteler R
BMC Biochem. 2014;15(1):14 - PMID: 25007711 - PMCID: PMC4099409 - DOI: 10.1186/1471-2091-15-14

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

Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LA
J Clin Invest. 2014;124(8):3617-33 - PMID: 25003194 - PMCID: PMC4109533 - DOI: 10.1172/JCI75436

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

Wu HY, Liu KH, Wang YC, Wu JF, Chiu WL, Chen CY, Wu SH, Sheen J, Lai EM
Plant Methods. 2014;10:19 - PMID: 24987449 - PMCID: PMC4076510 - DOI: 10.1186/1746-4811-10-19

Inflammatory Bowel Disease as a Model for Translating the Microbiome.

Huttenhower C, Kostic AD, Xavier RJ
Immunity. 2014;40(6):843-854 - PMID: 24950204 - PMCID: PMC4135443 - DOI: 10.1016/j.immuni.2014.05.013

Prediction of Multiple Infections After Severe Burn Trauma: A Prospective Cohort Study.

Yan S, Tsurumi A, Que YA, Ryan CM, Bandyopadhaya A, Morgan AA, Flaherty PJ, Tompkins RG, Rahme LG
Ann Surg. 2014;261(4):781-792 - PMID: 24950278 - PMCID: PMC4284150 - DOI: 10.1097/SLA.0000000000000759

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
Ann Surg. 2014;261(5):1006-12 - PMID: 24950285 - PMCID: PMC4272342 - DOI: 10.1097/SLA.0000000000000764

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

Wei SC, Tan YY, Weng MT, Lai LC, Hsiao JH, Chuang EY, Shun CT, Wu DC, Kao AW, Chuang CS, Ni YH, Shieh MJ, Tung CC, Chen Y, Wang CY, Xavier RJ, Podolsky DK, Wong JM
PLoS One. 2014;9(6):e100515 - PMID: 24945726 - PMCID: PMC4063938 - DOI: 10.1371/journal.pone.0100515

Detecting differential protein expression in large-scale population proteomics.

Ryu SY, Qian WJ, Camp DG, Smith RD, Tompkins RG, Davis RW, Xiao W
Bioinformatics. 2014;30(19):2741-6 - PMID: 24928210 - PMCID: PMC4173009 - DOI: 10.1093/bioinformatics/btu341

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

Pukkila-Worley R, Feinbaum RL, McEwan DL, Conery AL, Ausubel FM
PLoS Pathog. 2014;10(5):e1004143 - PMID: 24875643 - PMCID: PMC4038581 - DOI: 10.1371/journal.ppat.1004143

Deficits in receptor-mediated endocytosis and recycling in cells from mice bearing a disruption of the Gpr107 locus.

Zhou GL, Na SY, Niedra R, Seed B
J Cell Sci. 2014;127(Pt 18):3916-27 - PMID: 24849652 - DOI: 10.1242/jcs.135269

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

Tam JM, Mansour MK, Khan NS, Seward M, Puranam S, Tanne A, Sokolovska A, Becker CE, Acharya M, Baird MA, Choi AM, Davidson MW, Segal BH, Lacy-Hulbert A, Stuart LM, Xavier RJ, Vyas JM
J Infect Dis. 2014;210(11):1844-54 - PMID: 24842831 - PMCID: PMC4271056 - DOI: 10.1093/infdis/jiu290

Pseudomonas aeruginosa PA14 Pathogenesis in Caenorhabditis elegans.

Kirienko NV, Cezairliyan BO, Ausubel FM, Powell JR
Methods Mol Biol. 2014;1149:653-69 - PMID: 24818940 - DOI: 10.1007/978-1-4939-0473-0_50

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

Pan CY, Chen JC, Sheen JF, Lin TL, Chen JY
Antimicrob Agents Chemother. 2014;58(8):4264-4274 - PMID: 24820078 - PMCID: PMC4135991 - DOI: 10.1128/AAC.02958-14

Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense.

Lassen KG, Kuballa P, Conway KL, Patel KK, Becker CE, Peloquin JM, Villablanca EJ, Norman JM, Liu TC, Heath RJ, Becker ML, Fagbami L, Horn H, Mercer J, Yilmaz OH, Jaffe JD, Shamji AF, Bhan AK, Carr SA, Daly MJ, Virgin HW, Schreiber SL, Stappenbeck TS, Xavier RJ
Proc Natl Acad Sci U S A. 2014;111(21):7741-7746 - PMID: 24821797 - PMCID: PMC4040621 - DOI: 10.1073/pnas.1407001111

In vivo high-resolution magic angle spinning proton NMR spectroscopy of Drosophila melanogaster flies as a model system to investigate mitochondrial dysfunction in Drosophila GST2 mutants.

Righi V, Apidianakis Y, Psychogios N, Rahme LG, Tompkins RG, Tzika AA
Int J Mol Med. 2014;34(1):327-33 - PMID: 24789699 - DOI: 10.3892/ijmm.2014.1757

Benchmarking outcomes in the critically injured burn patient.

Klein MB, Goverman J, Hayden DL, Fagan SP, McDonald-Smith GP, Alexander AK, Gamelli RL, Gibran NS, Finnerty CC, Jeschke MG, Arnoldo B, Wispelwey B, Mindrinos MN, Xiao W, Honari SE, Mason PH, Schoenfeld DA, Herndon DN, Tompkins RG,
Ann Surg. 2014;259(5):833-41 - PMID: 24722222 - PMCID: PMC4283803 - DOI: 10.1097/SLA.0000000000000438

Caenorhabditis elegans pathways that surveil and defend mitochondria.

Liu Y, Samuel BS, Breen PC, Ruvkun G
Nature. 2014;508(7496):406-10 - PMID: 24695221 - PMCID: PMC4102179 - DOI: 10.1038/nature13204

MUT-14 and SMUT-1 DEAD Box RNA Helicases Have Overlapping Roles in Germline RNAi and Endogenous siRNA Formation.

Phillips CM, Montgomery BE, Breen PC, Roovers EF, Rim YS, Ohsumi TK, Newman MA, van Wolfswinkel JC, Ketting RF, Ruvkun G, Montgomery TA
Curr Biol. 2014;24(8):839-44 - PMID: 24684932 - PMCID: PMC4010136 - DOI: 10.1016/j.cub.2014.02.060

Survival From Burns in the New Millennium: 70 Years' Experience From a Single Institution.

Tompkins RG
Ann Surg. 2014;261(2):263-268 - PMID: 24670865 - PMCID: PMC4372065 - DOI: 10.1097/SLA.0000000000000623

Epitope-tagged protein-based artificial miRNA screens for optimized gene silencing in plants.

Li JF, Zhang D, Sheen J
Nat Protoc. 2014;9(4):939-49 - PMID: 24675734 - PMCID: PMC4208271 - DOI: 10.1038/nprot.2014.061

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

Ananthakrishnan AN, Nguyen DD, Sauk J, Yajnik V, Xavier RJ
Inflamm Bowel Dis. 2014;20(5):783-9 - PMID: 24651583 - PMCID: PMC4113010 - DOI: 10.1097/MIB.0000000000000014

High-Throughput Screening for Novel Anti-Infectives Using a C. elegans Pathogenesis Model.

Conery AL, Larkins-Ford J, Ausubel FM, Kirienko NV
Curr Protoc Chem Biol. 2014;6(1):25-37 - PMID: 24652621 - PMCID: PMC4021578 - DOI: 10.1002/9780470559277.ch130160

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

Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ
Cell Host Microbe. 2014;15(3):382-92 - PMID: 24629344 - PMCID: PMC4059512 - DOI: 10.1016/j.chom.2014.02.005

Progress Toward Synthetic Cells.

Blain JC, Szostak JW
Annu Rev Biochem. 2014;83:615-640 - PMID: 24606140 - DOI: 10.1146/annurev-biochem-080411-124036

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
J Surg Res. 2014;188(2):473-9 - PMID: 24582214 - PMCID: PMC3988254 - DOI: 10.1016/j.jss.2014.01.011

Enterococcus infection biology: Lessons from invertebrate host models.

Yuen GJ, Ausubel FM
J Microbiol. 2014;52(3):200-10 - PMID: 24585051 - PMCID: PMC4556283 - DOI: 10.1007/s12275-014-4011-6

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

Stanley SA, Barczak AK, Silvis MR, Luo SS, Sogi K, Vokes M, Bray MA, Carpenter AE, Moore CB, Siddiqi N, Rubin EJ, Hung DT
PLoS Pathog. 2014;10(2):e1003946 - PMID: 24586159 - PMCID: PMC3930586 - DOI: 10.1371/journal.ppat.1003946

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

Pulloor NK, Nair S, Kostic AD, Bist P, Weaver JD, Riley AM, Tyagi R, Uchil PD, York JD, Snyder SH, García-Sastre A, Potter BV, Lin R, Shears SB, Xavier RJ, Krishnan MN
PLoS Pathog. 2014;10(2):e1003981 - PMID: 24586175 - PMCID: PMC3937324 - DOI: 10.1371/journal.ppat.1003981

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

Rajamuthiah R, Fuchs BB, Jayamani E, Kim Y, Larkins-Ford J, Conery A, Ausubel FM, Mylonakis E
PLoS One. 2014;9(2):e89189 - PMID: 24586584 - PMCID: PMC3929655 - DOI: 10.1371/journal.pone.0089189

Rapid RNA Exchange in Aqueous Two-Phase System and Coacervate Droplets.

Jia TZ, Hentrich C, Szostak JW
Orig Life Evol Biosph. 2014;44(1):1-12 - PMID: 24577897 - PMCID: PMC4141154 - DOI: 10.1007/s11084-014-9355-8

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

Kostic AD, Xavier RJ, Gevers D
Gastroenterology. 2014;146(6):1489-99 - PMID: 24560869 - PMCID: PMC4034132 - DOI: 10.1053/j.gastro.2014.02.009

Long-term posttraumatic stress symptoms vary inversely with early opiate dosing in children recovering from serious burns: Effects durable at 4 years.

Sheridan RL, Stoddard FJ, Kazis LE, Lee A, Li NC, Kagan RJ, Palmieri TL, Meyer WJ, Nicolai M, Stubbs TK, Chan G, Hinson MI, Herndon DN, Tompkins RG,
J Trauma Acute Care Surg. 2014;76(3):828-832 - PMID: 24553556 - DOI: 10.1097/TA.0b013e3182ab111c

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

de Luca A, Smeekens SP, Casagrande A, Iannitti R, Conway KL, Gresnigt MS, Begun J, Plantinga TS, Joosten LA, van der Meer JW, Chamilos G, Netea MG, Xavier RJ, Dinarello CA, Romani L, van de Veerdonk FL
Proc Natl Acad Sci U S A. 2014;111(9):3526-31 - PMID: 24550444 - PMCID: PMC3948220 - DOI: 10.1073/pnas.1322831111

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

Zanni MV, Kelesidis T, Fitzgerald ML, Lo J, Abbara S, Wai B, Marmarelis E, Hernandez NJ, Yang OO, Currier JS, Grinspoon SK
Antivir Ther. 2014;19(8):805-11 - PMID: 24535655 - PMCID: PMC4423391 - DOI: 10.3851/IMP2756

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

Sheng J, Li L, Engelhart AE, Gan J, Wang J, Szostak JW
Proc Natl Acad Sci U S A. 2014;111(8):3050-5 - PMID: 24516151 - PMCID: PMC3939906 - DOI: 10.1073/pnas.1317799111

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

Li L, Szostak JW
J Am Chem Soc. 2014;136(7):2858-65 - PMID: 24499340 - PMCID: PMC3982932 - DOI: 10.1021/ja412079b

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

Fowler SA, Ananthakrishnan AN, Gardet A, Stevens CR, Korzenik JR, Sands BE, Daly MJ, Xavier RJ, Yajnik V
J Crohns Colitis. 2014;8(8):845-51 - PMID: 24461721 - PMCID: PMC4237062 - DOI: 10.1016/j.crohns.2014.01.003

Autophagy is essential for cardiac morphogenesis during vertebrate development.

Lee E, Koo Y, Ng A, Wei Y, Luby-Phelps K, Juraszek A, Xavier RJ, Cleaver O, Levine B, Amatruda JF
Autophagy. 2014;10(4):572-87 - PMID: 24441423 - PMCID: PMC4091146 - DOI: 10.4161/auto.27649

Synthesis and Non-Enzymatic Template-Directed Polymerization of 2'-Amino-2'-Deoxythreose Nucleotides.

Blain JC, Ricardo A, Szostak JW
J Am Chem Soc. 2014;136(5):2033-9 - PMID: 24409991 - PMCID: PMC4105081 - DOI: 10.1021/ja411950n

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
Am J Gastroenterol. 2014;109(3):395-400 - PMID: 24419484 - PMCID: PMC4225079 - DOI: 10.1038/ajg.2013.464

TOR Signaling Networks in Plant Growth and Metabolism.

Xiong Y, Sheen J
Plant Physiol. 2014;164(2):499-512 - PMID: 24385567 - PMCID: PMC3912084 - DOI: 10.1104/pp.113.229948

Master Regulators in Plant Glucose Signaling Networks.

Sheen J
2014;57(2):67-79 - PMID: 25530701 - PMCID: PMC4270195 - DOI: 10.1007/s12374-014-0902-7