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Betin V, Penaranda C, Bandyopadhyay N, Yang R, Abitua A, Bhattacharyya RP, Fan A, Avraham R, Livny J, Shoresh N, Hung DT

Hybridization-based capture of pathogen mRNA enables paired host-pathogen transcriptional analysis.
Sci Rep. 2019;9(1):19244 - PMID: 31848386 - PMCID: PMC6917760 - DOI: 10.1038/s41598-019-55633-6

Dreckmann SC, Amini-Nik S, Tompkins RG, Vojvodic M, Jeschke MG

Genome-wide comparisons of gene expression in adult versus elderly burn patients.
PLoS One. 2019;14(12):e0226425 - PMID: 31834907 - PMCID: PMC6910697 - DOI: 10.1371/journal.pone.0226425

Jiang X, Hall AB, Xavier RJ, Alm EJ

Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools.
PLoS One. 2019;14(12):e0223680 - PMID: 31830054 - PMCID: PMC6907783 - DOI: 10.1371/journal.pone.0223680

Vasquez-Rifo A, Veksler-Lublinsky I, Cheng Z, Ausubel FM, Ambros V

The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans.
Genome Biol. 2019;20(1):270 - PMID: 31823826 - PMCID: PMC6902481 - DOI: 10.1186/s13059-019-1890-1

Bhattacharyya RP, Bandyopadhyay N, Ma P, Son SS, Liu J, He LL, Wu L, Khafizov R, Boykin R, Cerqueira GC, Pironti A, Rudy RF, Patel MM, Yang R, Skerry J, Nazarian E, Musser KA, Taylor J, Pierce VM, Earl AM, Cosimi LA, Shoresh N, Beechem J, Livny J, Hung DT

Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination.
Nat Med. 2019;25(12):1858-1864 - PMID: 31768064 - PMCID: PMC6930013 - DOI: 10.1038/s41591-019-0650-9

Zhou L, Kim S, Ho KH, O'Flaherty DK, Giurgiu C, Wright TH, Szostak JW

Non-enzymatic primer extension with strand displacement.
Elife. 2019;8:ePub - PMID: 31702557 - PMCID: PMC6872209 - DOI: 10.7554/eLife.51888

Ogura A, Tsurumi A, Que YA, Almpani M, Zheng H, Tompkins RG, Ryan CM, Rahme LG

Associations between clinical characteristics and the development of multiple organ failure after severe burns in adult patients.
Burns. 2019;45(8):1775-1782 - PMID: 31690472 - DOI: 10.1016/j.burns.2019.02.014

Wang A, Szostak JW

Lipid constituents of model protocell membranes.
Emerg Top Life Sci. 2019;3(5):537-542 - PMID: 33523161 - DOI: 10.1042/ETLS20190021

Maheshwari P, Du H, Sheen J, Assmann SM, Albert R

Model-driven discovery of calcium-related protein-phosphatase inhibition in plant guard cell signaling.
PLoS Comput Biol. 2019;15(10):e1007429 - PMID: 31658257 - PMCID: PMC6837631 - DOI: 10.1371/journal.pcbi.1007429

Wright TH, Giurgiu C, Zhang W, Radakovic A, O'Flaherty DK, Zhou L, Szostak JW

Prebiotically Plausible 'Patching' of RNA Backbone Cleavage Through a 3'-5' Pyrophosphate Linkage.
J Am Chem Soc. 2019;141(45):18104-18112 - PMID: 31651170 - PMCID: PMC7577263 - DOI: 10.1021/jacs.9b08237

Johnson EO, Hung DT

A point of inflection and reflection on systems chemical biology.
ACS Chem Biol. 2019;14(12):2497-2511 - PMID: 31613592 - DOI: 10.1021/acschembio.9b00714

Govindan JA, Jayamani E, Ruvkun G

ROS-based lethality of Caenorhabditis elegans mitochondrial electron transport mutants grown on Escherichia coli siderophore iron release mutants.
Proc Natl Acad Sci U S A. 2019;116(43):21651-21658 - PMID: 31591219 - PMCID: PMC6815122 - DOI: 10.1073/pnas.1912628116

Xu H, Ding J, Porter CBM, Wallrapp A, Tabaka M, Ma S, Fu S, Guo X, Riesenfeld SJ, Su C, Dionne D, Nguyen LT, Lefkovith A, Ashenberg O, Burkett PR, Shi HN, Rozenblatt-Rosen O, Graham DB, Kuchroo VK, Regev A, Xavier RJ

Transcriptional Atlas of Intestinal Immune Cells Reveals that Neuropeptide α-CGRP Modulates Group 2 Innate Lymphoid Cell Responses.
Immunity. 2019;51(4):696-708.e9 - PMID: 31618654 - PMCID: PMC6991097 - DOI: 10.1016/j.immuni.2019.09.004

Grünewald J, Zhou R, Iyer S, Lareau CA, Garcia SP, Aryee MJ, Joung JK

CRISPR DNA base editors with reduced RNA off-target and self-editing activities.
Nat Biotechnol. 2019;37(9):1041-1048 - PMID: 31477922 - PMCID: PMC6730565 - DOI: 10.1038/s41587-019-0236-6

Elmaleh DR, Farlow MR, Conti PS, Tompkins RG, Kundakovic L, Tanzi RE

Developing Effective Alzheimer's Disease Therapies: Clinical Experience and Future Directions.
J Alzheimers Dis. 2019;71(3):715-732 - PMID: 31476157 - PMCID: PMC6839593 - DOI: 10.3233/JAD-190507

Khor B, Conway KL, Omar AS, Biton M, Haber AL, Rogel N, Baxt LA, Begun J, Kuballa P, Gagnon JD, Lassen KG, Regev A, Xavier RJ

Distinct Tissue-Specific Roles for the Disease-Associated Autophagy Genes ATG16L2 and ATG16L1.
J Immunol. 2019;203(7):1820-1829 - PMID: 31451676 - PMCID: PMC6761021 - DOI: 10.4049/jimmunol.1800419

Lelyveld VS, O'Flaherty DK, Zhou L, Izgu EC, Szostak JW

DNA polymerase activity on synthetic N3'→P5' phosphoramidate DNA templates.
Nucleic Acids Res. 2019;47(17):8941-8949 - PMID: 31428779 - PMCID: PMC6755091 - DOI: 10.1093/nar/gkz707

Goel G, Tye-Din JA, Qiao SW, Russell AK, Mayassi T, Ciszewski C, Sarna VK, Wang S, Goldstein KE, Dzuris JL, Williams LJ, Xavier RJ, Lundin KEA, Jabri B, Sollid LM, Anderson RP

Cytokine release and gastrointestinal symptoms after gluten challenge in celiac disease.
Sci Adv. 2019;5(8):eaaw7756 - PMID: 31457091 - PMCID: PMC6685723 - DOI: 10.1126/sciadv.aaw7756

Todd ZR, Szabla R, Szostak JW, Sasselov DD

UV photostability of three 2-aminoazoles with key roles in prebiotic chemistry on the early earth.
Chem Commun (Camb). 2019;55(70):10388-10391 - PMID: 31380533 - PMCID: PMC9631353 - DOI: 10.1039/c9cc05265h

Plichta DR, Graham DB, Subramanian S, Xavier RJ

Therapeutic Opportunities in Inflammatory Bowel Disease: Mechanistic Dissection of Host-Microbiome Relationships.
Cell. 2019;178(5):1041-1056 - PMID: 31442399 - PMCID: PMC6778965 - DOI: 10.1016/j.cell.2019.07.045

Kim W, Zou G, Hari TPA, Wilt IK, Zhu W, Galle N, Faizi HA, Hendricks GL, Tori K, Pan W, Huang X, Steele AD, Csatary EE, Dekarske MM, Rosen JL, Ribeiro NQ, Lee K, Port J, Fuchs BB, Vlahovska PM, Wuest WM, Gao H, Ausubel FM, Mylonakis E

A selective membrane-targeting repurposed antibiotic with activity against persistent methicillin-resistant Staphylococcus aureus.
Proc Natl Acad Sci U S A. 2019;116(33):16529-16534 - PMID: 31358625 - PMCID: PMC6697817 - DOI: 10.1073/pnas.1904700116

Mallick H, Franzosa EA, Mclver LJ, Banerjee S, Sirota-Madi A, Kostic AD, Clish CB, Vlamakis H, Xavier RJ, Huttenhower C

Predictive metabolomic profiling of microbial communities using amplicon or metagenomic sequences.
Nat Commun. 2019;10(1):3136 - PMID: 31316056 - PMCID: PMC6637180 - DOI: 10.1038/s41467-019-10927-1

Halvorsen YD, Walford GA, Massaro J, Aftring RP, Freeman MW

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.
Diabetes Obes Metab. 2019;21(11):2496-2504 - PMID: 31297965 - DOI: 10.1111/dom.13833

Zhang W, Pal A, Ricardo A, Szostak JW

Template-directed Nonenzymatic Primer Extension Using 2-methylimidazole-activated Morpholino Derivatives of Guanosine and Cytidine.
J Am Chem Soc. 2019;141(30):12159-12166 - PMID: 31298852 - PMCID: PMC7547883 - DOI: 10.1021/jacs.9b06453

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

Allele-specific gene editing prevents deafness in a model of dominant progressive hearing loss.
Nat Med. 2019;25(7):1123-1130 - PMID: 31270503 - PMCID: PMC6802276 - DOI: 10.1038/s41591-019-0500-9

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

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.
Cell. 2019;178(3):714-730.e22 - PMID: 31348891 - PMCID: PMC6662628 - DOI: 10.1016/j.cell.2019.06.029

Ramon M, Dang TVT, Broeckx T, Hulsmans S, Crepin N, Sheen J, Rolland F

Default Activation and Nuclear Translocation of the Plant Cellular Energy Sensor SnRK1 Regulate Metabolic Stress Responses and Development.
Plant Cell. 2019;31(7):1614-1632 - PMID: 33590001 - DOI: 10.1105/tpc.18.00500

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

Intra- and Inter-cellular Rewiring of the Human Colon during Ulcerative Colitis.
Cell. 2019;178(3):714-730.e22 - PMID: 31348891 - PMCID: PMC6662628 - DOI: 10.1016/j.cell.2019.06.029

Freeman MW, Singh AK, Guidon AC, Arvikar SL, Goldstein RH, Clement NF

Case 22-2019: A 65-Year-Old Woman with Weakness, Dark Urine, and Dysphagia.
N Engl J Med. 2019;381(3):275-283 - PMID: 31314973 - DOI: 10.1056/NEJMcpc1900589

Schirmer M, Garner A, Vlamakis H, Xavier RJ

Microbial genes and pathways in inflammatory bowel disease.
Nat Rev Microbiol. 2019;17(8):497-511 - PMID: 31249397 - PMCID: PMC6759048 - DOI: 10.1038/s41579-019-0213-6

Romano KP, Warrier T, Poulsen BE, Nguyen PH, Loftis AR, Saebi A, Pentelute BL, Hung DT

Mutations in pmrB confer cross-resistance between the LptD inhibitor POL7080 and colistin in Pseudomonas aeruginosa.
Antimicrob Agents Chemother. 2019;63(9):ePub - PMID: 31235628 - PMCID: PMC6709506 - DOI: 10.1128/AAC.00511-19

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, Schnappinger D, Hung DT

Large-scale chemical-genetics yields new M. tuberculosis inhibitor classes.
Nature. 2019;571(7763):72-78 - PMID: 31217586 - DOI: 10.1038/s41586-019-1315-z

Mojarro A, Hachey J, Bailey R, Brown M, Doebler R, Ruvkun G, Zuber MT, Carr CE

Nucleic Acid Extraction and Sequencing from Low-Biomass Synthetic Mars Analog Soils for In Situ Life Detection.
Astrobiology. 2019;19(9):1139-1152 - PMID: 31204862 - PMCID: PMC6708270 - DOI: 10.1089/ast.2018.1929

Henke MT, Kenny DJ, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J

Ruminococcus gnavus, a member of the human gut microbiome associated with Crohn's disease, produces an inflammatory polysaccharide.
Proc Natl Acad Sci U S A. 2019;116(26):12672-12677 - PMID: 31182571 - PMCID: PMC6601261 - DOI: 10.1073/pnas.1904099116

O'Flaherty DK, Zhou L, Szostak JW

Nonenzymatic template-directed synthesis of mixed-sequence 3'-NP-DNA up to 25 nucleotides long inside model protocells.
J Am Chem Soc. 2019;141(26):10481-10488 - PMID: 31180644 - PMCID: PMC7547854 - DOI: 10.1021/jacs.9b04858

Strecker J, Ladha A, Gardner Z, Schmid-Burgk JL, Makarova KS, Koonin EV, Zhang F

RNA-guided DNA insertion with CRISPR-associated transposases.
Science. 2019;365(6448):48-53 - PMID: 31171706 - PMCID: PMC6659118 - DOI: 10.1126/science.aax9181

Armakola M, Ruvkun G

Regulation of Caenorhabditis elegans neuronal polarity by heterochronic genes.
Proc Natl Acad Sci U S A. 2019;116(25):12327-12336 - PMID: 31164416 - PMCID: PMC6589651 - DOI: 10.1073/pnas.1820928116

Halvorsen YD, Lock JP, Zhou W, Zhu F, Freeman MW

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.
Diabetes Obes Metab. 2019;21(10):2248-2256 - PMID: 31161692 - DOI: 10.1111/dom.13801

Ansaldo E, Slayden LC, Ching KL, Koch MA, Wolf NK, Plichta DR, Brown EM, Graham DB, Xavier RJ, Moon JJ, Barton GM

Akkermansia muciniphila induces intestinal adaptive immune responses during homeostasis.
Science. 2019;364(6446):1179-1184 - PMID: 31221858 - PMCID: PMC6645389 - DOI: 10.1126/science.aaw7479

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, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ

Correction: Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population.
PLoS Genet. 2019;15(5):e1008190 - PMID: 31145742 - PMCID: PMC6542503 - DOI: 10.1371/journal.pgen.1008190

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

Conservation of the structure and function of bacterial tryptophan synthases.
IUCrJ. 2019;6(Pt 4):649-664 - PMID: 31316809 - PMCID: PMC6608616 - DOI: 10.1107/S2052252519005955

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

Multi-omics of the gut microbial ecosystem in inflammatory bowel diseases.
Nature. 2019;569(7758):655-662 - PMID: 31142855 - PMCID: PMC6650278 - DOI: 10.1038/s41586-019-1237-9

Melia JMP, Lin R, Xavier RJ, Thompson RB, Fu D, Wan F, Sears CL, Donowitz M

Induction of the metal transporter ZIP8 by interferon gamma in intestinal epithelial cells: Potential role of metal dyshomeostasis in Crohn's disease.
Biochem Biophys Res Commun. 2019;515(2):325-331 - PMID: 31151823 - DOI: 10.1016/j.bbrc.2019.05.137

Ramon M, Dang TVT, Broeckx T, Hulsmans S, Crepin N, Sheen J, Rolland FA

Default activation and nuclear translocation of the plant cellular energy sensor SnRK1 regulate metabolic stress responses and development.
Plant Cell. 2019;31(7):1614-1632 - PMID: 31123051 - PMCID: PMC6635846 - DOI: 10.1105/tpc.18.00500

Allegretti AS, Zhang W, Zhou W, Thurber TK, Rigby SP, Bowman-Stroud C, Trescoli C, Serusclat P, Freeman MW, Halvorsen YC

Safety and Effectiveness of Bexagliflozin in Patients With Type 2 Diabetes Mellitus and Stage 3a/3b CKD.
Am J Kidney Dis. 2019;74(3):328-337 - PMID: 31101403 - PMCID: PMC10077840 - DOI: 10.1053/j.ajkd.2019.03.417

Ferder IC, Fung L, Ohguchi Y, Zhang X, Lassen KG, Capen D, Brown D, Xavier RJ, Wang N

Meiotic gatekeeper STRA8 suppresses autophagy by repressing Nr1d1 expression during spermatogenesis in mice.
PLoS Genet. 2019;15(5):e1008084 - PMID: 31059511 - PMCID: PMC6502318 - DOI: 10.1371/journal.pgen.1008084

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

Bacteroides-Derived Sphingolipids Are Critical for Maintaining Intestinal Homeostasis and Symbiosis.
Cell Host Microbe. 2019;25(5):668-680.e7 - PMID: 31071294 - PMCID: PMC6544385 - DOI: 10.1016/j.chom.2019.04.002

Poulsen BE, Yang R, Clatworthy AE, White T, Osmulski SJ, Li L, Penaranda C, Lander ES, Shoresh N, Hung DT

Defining the core essential genome of Pseudomonas aeruginosa.
Proc Natl Acad Sci U S A. 2019;116(20):10072-10080 - PMID: 31036669 - PMCID: PMC6525520 - DOI: 10.1073/pnas.1900570116

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

Publisher Correction: Definitions and guidelines for research on antibiotic persistence.
Nat Rev Microbiol. 2019;17(7):460 - PMID: 31036919 - PMCID: PMC7609342 - DOI: 10.1038/s41579-019-0207-4

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

Hypoxia Rescues Frataxin Loss by Restoring Iron Sulfur Cluster Biogenesis.
Cell. 2019;177(6):1507-1521.e16 - PMID: 31031004 - PMCID: PMC6911770 - DOI: 10.1016/j.cell.2019.03.045

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

Tetraspanin CD82 Organizes Dectin-1 into Signaling Domains to Mediate Cellular Responses to Candida albicans.
J Immunol. 2019;202(11):3256-3266 - PMID: 31010852 - PMCID: PMC6529278 - DOI: 10.4049/jimmunol.1801384

Grünewald J, Zhou R, Garcia SP, Iyer S, Lareau CA, Aryee MJ, Joung JK

Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors.
Nature. 2019;569(7756):433-437 - PMID: 30995674 - PMCID: PMC6657343 - DOI: 10.1038/s41586-019-1161-z

Zhao S, Lieberman TD, Poyet M, Kauffman KM, Gibbons SM, Groussin M, Xavier RJ, Alm EJ

Adaptive Evolution within Gut Microbiomes of Healthy People.
Cell Host Microbe. 2019;25(5):656-667.e8 - PMID: 31028005 - PMCID: PMC6749991 - DOI: 10.1016/j.chom.2019.03.007

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

Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk: A Cross-Sectional Study.
Circ Res. 2019;124(12):1808-1820 - PMID: 30971183 - DOI: 10.1161/CIRCRESAHA.118.314642

Lehrbach NJ, Ruvkun G

Endoplasmic reticulum-associated SKN-1A/Nrf1 mediates a cytoplasmic unfolded protein response and promotes longevity.
Elife. 2019;8:ePub - PMID: 30973820 - PMCID: PMC6459674 - DOI: 10.7554/eLife.44425

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

Author Correction: Gut microbiome structure and metabolic activity in inflammatory bowel disease.
Nat Microbiol. 2019;4(5):898 - PMID: 30971771 - DOI: 10.1038/s41564-019-0442-5

Brown EM, Kenny DJ, Xavier RJ

Gut Microbiota Regulation of T Cells During Inflammation and Autoimmunity.
Annu Rev Immunol. 2019;37:599-624 - PMID: 31026411 - DOI: 10.1146/annurev-immunol-042718-041841

Lehrbach NJ, Breen PC, Ruvkun G

Protein Sequence Editing of SKN-1A/Nrf1 by Peptide:N-Glycanase Controls Proteasome Gene Expression.
Cell. 2019;177(3):737-750.e15 - PMID: 31002798 - PMCID: PMC6574124 - DOI: 10.1016/j.cell.2019.03.035

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, Gibson G, Xavier RJ, Kugathasan S, Walters T, Denson LA

Clinical and biological predictors of response to standardised paediatric colitis therapy (PROTECT): a multicentre inception cohort study.
Lancet. 2019;393(10182):1708-1720 - PMID: 30935734 - PMCID: PMC6501846 - DOI: 10.1016/S0140-6736(18)32592-3

Warnhoff K, Ruvkun G

Molybdenum cofactor transfer from bacteria to nematode mediates sulfite detoxification.
Nat Chem Biol. 2019;15(5):480-488 - PMID: 30911177 - PMCID: PMC6470025 - DOI: 10.1038/s41589-019-0249-y

Walton T, Zhang W, Li L, Tam CP, Szostak JW

The mechanism of nonenzymatic template copying with imidazole-activated nucleotides.
Angew Chem Int Ed Engl. 2019;58(32):10812-10819 - PMID: 30908802 - DOI: 10.1002/anie.201902050

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

Rapid identification and phylogenetic classification of diverse bacterial pathogens in a multiplexed hybridization assay targeting ribosomal RNA.
Sci Rep. 2019;9(1):4516 - PMID: 30872641 - PMCID: PMC6418090 - DOI: 10.1038/s41598-019-40792-3

Strom KR, Szostak JW, Prywes N

Transfer of Sequence Information and Replication of Diimine Duplexes.
J Org Chem. 2019;84(7):3754-3761 - PMID: 30855962 - PMCID: PMC7547894 - DOI: 10.1021/acs.joc.9b00095

Wein MN, Foretz M, Fisher DE, Xavier RJ, Kronenberg HM

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

Adopt a moratorium on heritable genome editing.
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Clement K, Rees H, Canver MC, Gehrke JM, Farouni R, Hsu JY, Cole MA, Liu DR, Joung JK, Bauer DE, Pinello L

CRISPResso2 provides accurate and rapid genome editing sequence analysis.
Nat Biotechnol. 2019;37(3):224-226 - PMID: 30809026 - PMCID: PMC6533916 - DOI: 10.1038/s41587-019-0032-3

Mao K, Ji F, Breen P, Sewell A, Han M, Sadreyev R, Ruvkun G

Mitochondrial Dysfunction in C. elegans Activates Mitochondrial Relocalization and Nuclear Hormone Receptor-Dependent Detoxification Genes.
Cell Metab. 2019;29(5):1182-1191.e4 - PMID: 30799287 - PMCID: PMC6506380 - DOI: 10.1016/j.cmet.2019.01.022

Kniazeva M, Ruvkun G

Rhizobium induces DNA damage in Caenorhabditis elegans intestinal cells.
Proc Natl Acad Sci U S A. 2019;116(9):3784-3792 - PMID: 30808764 - PMCID: PMC6397575 - DOI: 10.1073/pnas.1815656116

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

Spatial and Temporal Mapping of Human Innate Lymphoid Cells Reveals Elements of Tissue Specificity.
Immunity. 2019;50(2):505-519.e4 - PMID: 30770247 - PMCID: PMC6594374 - DOI: 10.1016/j.immuni.2019.01.012

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

Engineered CRISPR-Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing.
Nat Biotechnol. 2019;37(3):276-282 - PMID: 30742127 - PMCID: PMC6401248 - DOI: 10.1038/s41587-018-0011-0

Wu Y, Shi L, Li L, Fu L, Liu Y, Xiong Y, Sheen J

Integration of nutrient, energy, light and hormone signalling via TOR in plants.
J Exp Bot. 2019;70(8):2227-2238 - PMID: 30715492 - PMCID: PMC6463029 - DOI: 10.1093/jxb/erz028

Penaranda C, Hung DT

Single-Cell RNA Sequencing to Understand Host-Pathogen Interactions.
ACS Infect Dis. 2019;5(3):336-344 - PMID: 30702856 - DOI: 10.1021/acsinfecdis.8b00369

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

SLC39A8 missense variant is associated with Crohn's disease but does not have a major impact on gut microbiome composition in healthy subjects.
PLoS One. 2019;14(1):e0211328 - PMID: 30703110 - PMCID: PMC6354981 - DOI: 10.1371/journal.pone.0211328

Matsushita-Ishiodori Y, Hanczyc MM, Wang A, Szostak JW, Yomo T

Using Imaging Flow Cytometry to Quantify and Optimize Giant Vesicle Production by Water-in-oil Emulsion Transfer Methods.
Langmuir. 2019;35(6):2375-2382 - PMID: 30645943 - DOI: 10.1021/acs.langmuir.8b03635

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

A defined commensal consortium elicits CD8 T cells and anti-cancer immunity.
Nature. 2019;565(7741):600-605 - PMID: 30675064 - DOI: 10.1038/s41586-019-0878-z

Strecker J, Jones S, Koopal B, Schmid-Burgk J, Zetsche B, Gao L, Makarova KS, Koonin EV, Zhang F

Engineering of CRISPR-Cas12b for human genome editing.
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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

The Crohn's disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response.
Elife. 2019;8:ePub - PMID: 30666959 - PMCID: PMC6342529 - DOI: 10.7554/eLife.39982

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

Noncanonical ATG8-ABS3 interaction controls senescence in plants.
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Nakazawa H, Ikeda K, Shinozaki S, Yasuhara S, Yu YM, Martyn JAJ, Tompkins RG, Yorozu T, Inoue S, Kaneki M

Coenzyme Q10 protects against burn-induced mitochondrial dysfunction and impaired insulin signaling in mouse skeletal muscle.
FEBS Open Bio. 2019;9(2):348-363 - PMID: 30761259 - PMCID: PMC6356165 - DOI: 10.1002/2211-5463.12580

Xiaofang Jiang, A. Brantley Hall, Timothy D. Arthur, Damian R. Plichta, Christian T. Covington, Mathilde Poyet, Jessica Crothers, Peter L. Moses, Andrew C. Tolonen, Hera Vlamakis, Eric J. Alm, Ramnik J. Xavier

Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut
Science. 2019;363, Issue 6423:181-187 - PMID: 30630933 - PMCID: PMC6543533 - DOI: 10.1126/science.aau5238

Wang A, Chan Miller C, Szostak JW

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

Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.
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Walton T, Pazienza L, Szostak JW

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

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.
Nat Microbiol. 2019;4(3):470-479 - PMID: 30559407 - PMCID: PMC6384140 - DOI: 10.1038/s41564-018-0321-5

Lee H, Jun YS, Cha OK, Sheen J

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

Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis.
Mucosal Immunol. 2019;12(2):491-502 - PMID: 30542108 - PMCID: PMC6375755 - DOI: 10.1038/s41385-018-0114-4

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

Gut microbiome structure and metabolic activity in inflammatory bowel disease.
Nat Microbiol. 2019;4(2):293-305 - PMID: 30531976 - PMCID: PMC6342642 - DOI: 10.1038/s41564-018-0306-4

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

Single-cell RNA Sequencing of Blood and Ileal T cells From Patients With Crohn's Disease Reveals Tissue-specific Characteristics and Drug Targets.
Gastroenterology. 2019;156(3):812-815.e22 - PMID: 30391472 - PMCID: PMC6759855 - DOI: 10.1053/j.gastro.2018.10.046

Wang C, Bauckman KA, Ross ASB, Symington JW, Ligon MM, Scholtes G, Kumar A, Chang HW, Twentyman J, Fashemi BE, Xavier RJ, Mysorekar IU

A non-canonical autophagy-dependent role of the ATG16L1T300A variant in urothelial vesicular trafficking and uropathogenic Escherichia coli persistence.
Autophagy. 2019;15(3):527-542 - PMID: 30335568 - PMCID: PMC6351132 - DOI: 10.1080/15548627.2018.1535290

Kasotakis G, Starr N, Nelson E, Sarkar B, Burke PA, Remick DG, Tompkins RG, Inflammation and Host Response to Injury Investigators

Platelet transfusion increases risk for acute respiratory distress syndrome in non-massively transfused blunt trauma patients.
Eur J Trauma Emerg Surg. 2019;45(4):671-679 - PMID: 29627883 - DOI: 10.1007/s00068-018-0953-4
Total: 90