Publications for All Faculty - 2017

  • Gibbons SM, Kearney SM, Smillie CS, Alm EJ Two dynamic regimes in the human gut microbiome. PLoS Comput Biol. 2017;13(2):e1005364 - PMID: 28222117 - PMCID: PMC5340412 - DOI: 10.1371/journal.pcbi.1005364

  • Groussin M, Mazel F, Sanders JG, Smillie CS, Lavergne S, Thuiller W, Alm EJ Unraveling the processes shaping mammalian gut microbiomes over evolutionary time. Nat Commun. 2017;8:14319 - PMID: 28230052 - PMCID: PMC5331214 - DOI: 10.1038/ncomms14319

  • Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y, Tirosh I, Beyaz S, Dionne D, Zhang M, Raychowdhury R, Garrett WS, Rozenblatt-Rosen O, Shi HN, Yilmaz O, Xavier RJ, Regev A A single-cell survey of the small intestinal epithelium. Nature. 2017;551(7680):333-339 - PMID: 29144463 - PMCID: PMC6022292 - DOI: 10.1038/nature24489

  • Kim HJ, Wu CY, Yu HM, Sheen J, Lee H1. Dual CLAVATA3 Peptides in Arabidopsis Shoot Stem Cell Signaling. J Plant Biol. 2017;60(5):506-512 - PMID: 30310351 - PMCID: PMC6176727 - DOI: 10.1007/s12374-017-0083-2

  • Kim HJ, Wu CY, Yu HM, Sheen J, Lee H Dual CLAVATA3 Peptides in Arabidopsis Shoot Stem Cell Signaling. J Plant Biol. 2017;60(5):506-512 - PMID: 30310351 - PMCID: PMC6176727 - DOI: 10.1007/s12374-017-0083-2

  • Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y, Tirosh I, Beyaz S, Dionne D, Zhang M, Raychowdhury R, Garrett WS, Rozenblatt-Rosen O, Shi HN, Yilmaz O, Xavier RJ, Regev A A single-cell survey of the small intestinal epithelium. Nature. 2017;:ePub

  • Rogers KW, Lord ND, Gagnon JA, Pauli A, Zimmerman S, Aksel DC, Reyon D, Tsai SQ, Joung JK, Schier AF Nodal patterning without Lefty inhibitory feedback is functional but fragile. Elife. 2017;6:ePub - PMID: 29215332 - PMCID: PMC5720593 - DOI: 10.7554/eLife.28785

  • Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R, Bertha M, Cohen M, Garber J, Khalili H, Gevers D, Ananthakrishnan AN, Kugathasan S, Lander ES, Blainey P, Vlamakis H, Xavier RJ, Huttenhower C A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients. Genome Med. 2017;9(1):103 - PMID: 29183332 - PMCID: PMC5704459 - DOI: 10.1186/s13073-017-0490-5

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

  • Jia TZ, Fahrenbach AC, Kamat NP, Adamala KP, Szostak JW Retraction: Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication. Nat Chem. 2017;9(12):1286 - PMID: 29168488 - PMCID: PMC7412977 - DOI: 10.1038/nchem.2885

  • Li Z, Zhang D, Xiong X, Yan B, Xie W, Sheen J, Li JF A potent Cas9-derived gene activator for plant and mammalian cells. Nat Plants. 2017;3(12):930-936 - PMID: 29158545 - PMCID: PMC5894343 - DOI: 10.1038/s41477-017-0046-0

  • Ni J, Shen TD, Chen EZ, Bittinger K, Bailey A, Roggiani M, Sirota-Madi A, Friedman ES, Chau L, Lin A, Nissim I, Scott J, Lauder A, Hoffmann C, Rivas G, Albenberg L, Baldassano RN, Braun J, Xavier RJ, Clish CB, Yudkoff M, Li H, Goulian M, Bushman FD, Lewis JD, Wu GD A role for bacterial urease in gut dysbiosis and Crohn's disease. Sci Transl Med. 2017;9(416):ePub - PMID: 29141885 - PMCID: PMC5808452 - DOI: 10.1126/scitranslmed.aah6888

  • Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y, Tirosh I, Beyaz S, Dionne D, Zhang M, Raychowdhury R, Garrett WS, Rozenblatt-Rosen O, Shi HN, Yilmaz O, Xavier RJ, Regev A A single-cell survey of the small intestinal epithelium. Nature. 2017;551(7680):333-339 - PMID: 29144463 - PMCID: PMC6022292 - DOI: 10.1038/nature24489

  • Giurgiu C, Li L, O'Flaherty DK, Tam CP, Szostak JW A Mechanistic Explanation for the Regioselectivity of Nonenzymatic RNA Primer Extension. J Am Chem Soc. 2017;139(46):16741-16747 - PMID: 29112424 - PMCID: PMC6326530 - DOI: 10.1021/jacs.7b08784

  • Tak YE, Kleinstiver BP, Nuñez JK, Hsu JY, Horng JE, Gong J, Weissman JS, Joung JK Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors. Nat Methods. 2017;14(12):1163-1166 - PMID: 29083402 - PMCID: PMC5909187 - DOI: 10.1038/nmeth.4483

  • Murano T, Najibi M, Paulus GLC, Adiliaghdam F, Valencia-Guerrero A, Selig M, Wang X, Jeffrey K, Xavier RJ, Lassen KG, Irazoqui JE Transcription factor TFEB cell-autonomously modulates susceptibility to intestinal epithelial cell injury in vivo. Sci Rep. 2017;7(1):13938 - PMID: 29066772 - PMCID: PMC5655326 - DOI: 10.1038/s41598-017-14370-4

  • Leshchiner ES, Rush JS, Durney MA, Cao Z, Dančík V, Chittick B, Wu H, Petrone A, Bittker JA, Phillips A, Perez JR, Shamji AF, Kaushik VK, Daly MJ, Graham DB, Schreiber SL, Xavier RJ Small-molecule inhibitors directly target CARD9 and mimic its protective variant in inflammatory bowel disease. Proc Natl Acad Sci U S A. 2017;114(43):11392-11397 - PMID: 29073062 - PMCID: PMC5664502 - DOI: 10.1073/pnas.1705748114

  • Avital G, Avraham R, Fan A, Hashimshony T, Hung DT, Yanai I scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing. Genome Biol. 2017;18(1):200 - PMID: 29073931 - PMCID: PMC5658913 - DOI: 10.1186/s13059-017-1340-x

  • Li Y, Lv M, Su C, Long S, Zhang W, Conway KL, Li W, Xavier RJ, Shi HN p40 (phox) -Deficient Mice Exhibit Impaired Bacterial Clearance and Enhanced Pro-inflammatory Responses during Salmonella enterica serovar Typhimurium Infection. Front Immunol. 2017;8:1270 - PMID: 29062317 - PMCID: PMC5640886 - DOI: 10.3389/fimmu.2017.01270

  • 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 Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation. Science. 2017;358(6361):359-365 - PMID: 29051379 - PMCID: PMC5682622 - DOI: 10.1126/science.aan4526

  • Walton T, Szostak JW A kinetic model of nonenzymatic RNA polymerization by cytidine-5'-phosphoro-2-aminoimidazolide. Biochemistry. 2017;56(43):5739-5747 - PMID: 29022704 - PMCID: PMC6340129 - DOI: 10.1021/acs.biochem.7b00792

  • Pontefract A, Zhu TF, Walker VK, Hepburn H, Lui C, Zuber MT, Ruvkun G, Carr CE Microbial Diversity in a Hypersaline Sulfate Lake: A Terrestrial Analog of Ancient Mars. Front Microbiol. 2017;8:1819 - PMID: 29018418 - PMCID: PMC5623196 - DOI: 10.3389/fmicb.2017.01819

  • Ransey E, Björkbom A, Lelyveld VS, Biecek P, Pantano L, Szostak JW, Sliz P Comparative analysis of LIN28-RNA binding sites identified at single nucleotide resolution. RNA Biol. 2017;14(12):0 - PMID: 28945502 - PMCID: PMC5731800 - DOI: 10.1080/15476286.2017.1356566

  • Chen JS, Dagdas YS, Kleinstiver BP, Welch MM, Sousa AA, Harrington LB, Sternberg SH, Joung JK, Yildiz A, Doudna JA Enhanced proofreading governs CRISPR-Cas9 targeting accuracy. Nature. 2017;550(7676):407-410 - PMID: 28931002 - PMCID: PMC5918688 - DOI: 10.1038/nature24268

  • Koeva M, Gutu AD, Hebert W, Wager JD, Yonker LM, O'Toole GA, Ausubel FM, Moskowitz SM, Joseph-McCarthy D An Anti-Persister Strategy for the Treatment of Chronic Pseudomonas aeruginosa Infections. Antimicrob Agents Chemother. 2017;61(12):ePub - PMID: 28923873 - PMCID: PMC5700368 - DOI: 10.1128/AAC.00987-17

  • 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 SHANK3 Regulates Intestinal Barrier Function Through Modulating ZO-1 Expression Through the PKCε-dependent Pathway. Inflamm Bowel Dis. 2017;:ePub - PMID: 28922251

  • 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 SHANK3 Regulates Intestinal Barrier Function Through Modulating ZO-1 Expression Through the PKCε-dependent Pathway. Inflamm Bowel Dis. 2017;23(10):1730-1740 - PMID: 28906292 - DOI: 10.1097/MIB.0000000000001250

  • Franco LH, Nair VR, Scharn CR, Xavier RJ, Torrealba JR, Shiloh MU, Levine B The Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis and Anti-tuberculous Host Defense. Cell Host Microbe. 2017;22(3):421-423 - PMID: 28910640 - PMCID: PMC5818210 - DOI: 10.1016/j.chom.2017.08.005

  • Goodwin JM, Dowdle WE, DeJesus R, Wang Z, Bergman P, Kobylarz M, Lindeman A, Xavier RJ, McAllister G, Nyfeler B, Hoffman G, Murphy LO Autophagy-Independent Lysosomal Targeting Regulated by ULK1/2-FIP200 and ATG9. Cell Rep. 2017;20(10):2341-2356 - PMID: 28877469 - PMCID: PMC5699710 - DOI: 10.1016/j.celrep.2017.08.034

  • Cezairliyan B, Ausubel FM Investment in secreted enzymes during nutrient-limited growth is utility dependent. Proc Natl Acad Sci U S A. 2017;114(37):E7796-E7802 - PMID: 28847943 - PMCID: PMC5604031 - DOI: 10.1073/pnas.1708580114

  • Hall AB, Tolonen AC, Xavier RJ Human genetic variation and the gut microbiome in disease. Nat Rev Genet. 2017;18(11):690-699 - PMID: 28824167 - DOI: 10.1038/nrg.2017.63

  • 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 Erratum: E3 Ubiquitin ligase ZNRF4 negatively regulates NOD2 signalling and induces tolerance to MDP. Nat Commun. 2017;8:16141 - PMID: 28820178 - PMCID: PMC5562926 - DOI: 10.1038/ncomms16141

  • 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 Small-molecule studies identify CDK8 as a regulator of IL-10 in myeloid cells. Nat Chem Biol. 2017;13(10):1102-1108 - PMID: 28805801 - PMCID: PMC5693369 - DOI: 10.1038/nchembio.2458

  • 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 Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140. Sci Immunol. 2017;2(9):ePub - PMID: 28783698 - PMCID: PMC5549562 - DOI: 10.1126/sciimmunol.aag3160

  • 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 NIH Centers for Accelerated Innovations Program: principles, practices, successes and challenges. Nat Rev Drug Discov. 2017;16(10):663-664 - PMID: 28775338 - PMCID: PMC5963257 - DOI: 10.1038/nrd.2017.131

  • Bel S, Pendse M, Wang Y, Li Y, Ruhn KA, Hassell B, Leal T, Winter SE, Xavier RJ, Hooper LV Paneth cells secrete lysozyme via secretory autophagy during bacterial infection of the intestine. Science. 2017;357(6355):1047-1052 - PMID: 28751470 - PMCID: PMC5702267 - DOI: 10.1126/science.aal4677

  • 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 Burn-induced muscle metabolic derangements and mitochondrial dysfunction are associated with activation of HIF-1α and mTORC1: Role of protein farnesylation. Sci Rep. 2017;7(1):6618 - PMID: 28747716 - PMCID: PMC5529411 - DOI: 10.1038/s41598-017-07011-3

  • Mojarro A, Ruvkun G, Zuber MT, Carr CE Nucleic Acid Extraction from Synthetic Mars Analog Soils for in situ Life Detection. Astrobiology. 2017;17(8):747-760 - PMID: 28704064 - PMCID: PMC5567878 - DOI: 10.1089/ast.2016.1535

  • 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 Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation. Cell Host Microbe. 2017;22(1):25-37.e6 - PMID: 28704649 - PMCID: PMC5672633 - DOI: 10.1016/j.chom.2017.06.007

  • 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 Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children. Proc Natl Acad Sci U S A. 2017;114(30):E6166-E6175 - PMID: 28696303 - PMCID: PMC5544325 - DOI: 10.1073/pnas.1706359114

  • Zhang W, Tam CP, Walton T, Fahrenbach AC, Birrane G, Szostak JW Insight into the mechanism of nonenzymatic RNA primer extension from the structure of an RNA-GpppG complex. Proc Natl Acad Sci U S A. 2017;114(29):7659-7664 - PMID: 28673998 - PMCID: PMC5530681 - DOI: 10.1073/pnas.1704006114

  • 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 A small-molecule allosteric inhibitor of Mycobacterium tuberculosis tryptophan synthase. Nat Chem Biol. 2017;13(9):943-950 - PMID: 28671682 - PMCID: PMC6886523 - DOI: 10.1038/nchembio.2420

  • 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 E3 Ubiquitin ligase ZNRF4 negatively regulates NOD2 signalling and induces tolerance to MDP. Nat Commun. 2017;8:15865 - PMID: 28656966 - PMCID: PMC5493756 - DOI: 10.1038/ncomms15865

  • 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, Duerr RH, Mathew CG, Rioux JD, McGovern DPB, Cho JH, Georges M, Daly MJ, Barrett JC Fine-mapping inflammatory bowel disease loci to single-variant resolution. Nature. 2017;547(7662):173-178 - PMID: 28658209 - PMCID: PMC5511510 - DOI: 10.1038/nature22969

  • Jayamani E, Tharmalingam N, Rajamuthiah R, Coleman JJ, Kim W, Okoli I, Hernandez AM, Lee K, Nau GJ, Ausubel FM, Mylonakis E Characterization of a Francisella tularensis-Caenorhabditis elegans pathosystem for the evaluation of therapeutic compounds. Antimicrob Agents Chemother. 2017;61(9):ePub - PMID: 28652232 - PMCID: PMC5571314 - DOI: 10.1128/AAC.00310-17

  • Fahrenbach AC, Giurgiu C, Tam CP, Li L, Hongo Y, Aono M, Szostak JW Common and Potentially Prebiotic Origin for Precursors of Nucleotide Synthesis and Activation. J Am Chem Soc. 2017;139(26):8780-8783 - PMID: 28640999 - PMCID: PMC6326526 - DOI: 10.1021/jacs.7b01562

  • Tolonen AC, Xavier RJ Dissecting the human microbiome with single-cell genomics. Genome Med. 2017;9(1):56 - PMID: 28615076 - PMCID: PMC5471897 - DOI: 10.1186/s13073-017-0448-7

  • 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 Discovery of nitrate-CPK-NLP signalling in central nutrient-growth networks. Nature. 2017;545(7654):311-316 - PMID: 28489820 - PMCID: PMC5823009 - DOI: 10.1038/nature22077

  • 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 Genome editing of factor X in zebrafish reveals unexpected tolerance of severe defects in the common pathway. Blood. 2017;130(5):666-676 - PMID: 28576875 - PMCID: PMC5542852 - DOI: 10.1182/blood-2017-02-765206

  • Zhao Q, Harbour SN, Kolde R, Latorre IJ, Tun HM, Schoeb TR, Turner H, Moon JJ, Khafipour E, Xavier RJ, Weaver CT, Elson CO Selective Induction of Homeostatic Th17 Cells in the Murine Intestine by Cholera Toxin Interacting with the Microbiota. J Immunol. 2017;199(1):312-322 - PMID: 28539431 - PMCID: PMC5539960 - DOI: 10.4049/jimmunol.1700171

  • Stairs S, Nikmal A, Bucar DK, Zheng SL, Szostak JW, Powner MW Divergent prebiotic synthesis of pyrimidine and 8-oxo-purine ribonucleotides. Nat Commun. 2017;8:15270 - PMID: 28524845 - PMCID: PMC5454461 - DOI: 10.1038/ncomms15270

  • Frydman GH, Metcalf Pate KA, Marini RP, de Laforcade AM, Bosch I, Bakthavatchalu V, Muthupalani S, Swennes AG, Lyons CE, Tompkins RG, Fox JG Adult-onset, chronic, cyclic thrombocytopenia in a Rhesus macaque (Macaca mulatta) after dengue virus vaccination and viral challenge. Vet Clin Pathol. 2017;46(2):238-247 - PMID: 28518476 - PMCID: PMC5977396 - DOI: 10.1111/vcp.12497

  • Szostak JW The Narrow Road to the Deep Past. Angew Chem Int Ed Engl. 2017;56(37):11037-11043 - PMID: 28514493 - DOI: 10.1002/anie.201704048

  • 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 Epitope-specific immunotherapy targeting CD4-positive T cells in coeliac disease: two randomised, double-blind, placebo-controlled phase 1 studies. Lancet Gastroenterol Hepatol. 2017;2(7):479-493 - PMID: 28506538 - PMCID: PMC5676538 - DOI: 10.1016/S2468-1253(17)30110-3

  • 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 Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence. PLoS Pathog. 2017;13(5):e1006363 - PMID: 28505176 - PMCID: PMC5444860 - DOI: 10.1371/journal.ppat.1006363

  • Ananthakrishnan AN, Luo C, Yajnik V, Khalili H, Garber JJ, Stevens BW, Cleland T, Xavier RJ Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases. Cell Host Microbe. 2017;21(5):603-610.e3 - PMID: 28494241 - PMCID: PMC5705050 - DOI: 10.1016/j.chom.2017.04.010

  • Tsai SQ, Nguyen NT, Malagon-Lopez J, Topkar VV, Aryee MJ, Joung JK CIRCLE-seq: a highly sensitive in vitro screen for genome-wide CRISPR-Cas9 nuclease off-targets. Nat Methods. 2017;14(6):607-614 - PMID: 28459458 - PMCID: PMC5924695 - DOI: 10.1038/nmeth.4278

  • 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 Camptothecin resistance is determined by the regulation of topoisomerase I degradation mediated by ubiquitin proteasome pathway. Oncotarget. 2017;8(27):43733-43751 - PMID: 28415827 - PMCID: PMC5546437 - DOI: 10.18632/oncotarget.16376

  • 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 Nucleic acid detection with CRISPR-Cas13a/C2c2. Science. 2017;356(6336):438-442 - PMID: 28408723 - PMCID: PMC5526198 - DOI: 10.1126/science.aam9321

  • 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 Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease. Science. 2017;356(6333):44-50 - PMID: 28386004 - PMCID: PMC5506690 - DOI: 10.1126/science.aah5298

  • Frydman GH, Marini RP, Bakthavatchalu V, Biddle KE, Muthupalani S, Vanderburg CR, Lai B, Bendapudi PK, Tompkins RG, Fox JG Local and Systemic Changes Associated with Long-term, Percutaneous, Static Implantation of Titanium Alloys in Rhesus Macaques (Macaca mulatta). Comp Med. 2017;67(2):165-175 - PMID: 28381317 - PMCID: PMC5402736

  • Gevers D, Kugathasan S, Knights D, Kostic AD, Knight R, Xavier RJ A Microbiome Foundation for the Study of Crohn's Disease. Cell Host Microbe. 2017;21(3):301-304 - PMID: 28279336 - PMCID: PMC5684696 - DOI: 10.1016/j.chom.2017.02.012

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

  • 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, Forrester R, Francois C, Franklin H, Freeman MW, Furst H, Gage LP, Galakatos N, Gallagher BM, Geraghty JA, Gill S, Goeddel DV, Goldsmith MA, Gowen M, Goyal V, Graney T, Grayzel D, Greene B, Grint P, Gutierrez-Ramos JC, Haney B, Ha-Ngoc T, Harris T, Hasnain F, Hata YS, Hecht P, Henshaw L, Heyman R, Hoppenot H, Horvitz HR, Hughes TE, Hutton WS, Isaacs ST, Jenkins A, Jonker J, Kaplan J, Karsen P, Keiper J, Kim J, Kindler J, King R, King V, Kjellson N, Koenig S, Koenig G, Kolchinsky P, Laikind P, Langer RB, Lee JJ, Leff JS, Leicher BA, Leschly N, Levin A, Levin M, Levine AJ, Levy A, Liu DR, Lodish HF, Lopatin U, Love TW, Macdonald G, Maderis GJ, Mahadevia A, Mahanthappa NK, Martin JF, Martin A, Martucci WE, McArthur JG, McCann CM, McCarthy SA, McDonough CG, Mendlein J, Miller L, Miralles D, Moch KI, More B, Myers AG, Narachi MA, Nashat A, Nelson W, Newell WJ, Olle B, Osborn JE, Owens JC, Pande A, Papadopoulos S, Parker HS, Parmar KM, Patterson MR, Paul SM, Perez R, Perry M, Pfeffer CG, Powell M, Pruzanski M, Purcell DJ, Rakhit A, Ramamoorthi K, Rastetter W, Rawcliffe AA, Reid LE, Renaud RC, Rhodes JP, Rieflin WJ, Robins C, Rocklage SM, Rosenblatt M, Rosin JG, Rutter WJ, Saha S, Samuels C, Sato VL, Scangos G, Scarlett JA, Schenkein D, Schreiber SL, Schwab A, Sekhri P, Shah R, Shenk T, Siegall CB, Simon NJ, Simonian N, Stein J, Su M, Szela MT, Taglietti M, Tandon N, Termeer H, Thornberry NA, Tolar M, Ulevitch R, Vaishnaw AK, VanLent A, Varsavsky M, Vlasuk GP, Vounatsos M, Waksal SG, Warma N, Watts RJ, Werber Y, Westphal C, Wierenga W, Williams DE, Williams LR, Xanthopoulos KG, Zohar D, Zweifach SS US immigration order strikes against biotech. Nat Biotechnol. 2017;35(3):204-206 - PMID: 28267733 - DOI: 10.1038/nbt.3824

  • 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 Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study. Lancet. 2017;389(10080):1710-1718 - PMID: 28259484 - PMCID: PMC5719489 - DOI: 10.1016/S0140-6736(17)30317-3

  • 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 Corrigendum: SIKs control osteocyte responses to parathyroid hormone. Nat Commun. 2017;8:14745 - PMID: 28224982 - PMCID: PMC5322529 - DOI: 10.1038/ncomms14745

  • Chung HS, Sheen J MAPK Assays in Arabidopsis MAMP-PRR Signal Transduction. Methods Mol Biol. 2017;1578:155-166 - PMID: 28220422 - DOI: 10.1007/978-1-4939-6859-6_12

  • 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 Ribosomal mutations promote the evolution of antibiotic resistance in a multidrug environment. Elife. 2017;6:ePub - PMID: 28220755 - PMCID: PMC5319836 - DOI: 10.7554/eLife.20420

  • Li L, Prywes N, Tam CP, O'Flaherty DK, Lelyveld VS, Izgu EC, Pal A, Szostak JW Enhanced Nonenzymatic RNA Copying with 2-Aminoimidazole Activated Nucleotides. J Am Chem Soc. 2017;139(5):1810-1813 - PMID: 28117989 - PMCID: PMC6326525 - DOI: 10.1021/jacs.6b13148

  • Urbach JM, Ausubel FM The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events. Proc Natl Acad Sci U S A. 2017;114(5):1063-1068 - PMID: 28096345 - PMCID: PMC5293065 - DOI: 10.1073/pnas.1619730114

  • 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 Multi-institute analysis of carbapenem resistance reveals remarkable diversity, unexplained mechanisms, and limited clonal outbreaks. Proc Natl Acad Sci U S A. 2017;114(5):1135-1140 - PMID: 28096418 - PMCID: PMC5293017 - DOI: 10.1073/pnas.1616248114

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

  • Tam CP, Fahrenbach AC, Björkbom A, Prywes N, Izgu EC, Szostak JW Downstream Oligonucleotides Strongly Enhance the Affinity of GMP to RNA Primer-Template Complexes. J Am Chem Soc. 2017;139(2):571-574 - PMID: 28055190 - PMCID: PMC7547879 - DOI: 10.1021/jacs.6b09760

  • Nowyhed HN, Chandra S, Kiosses W, Marcovecchio P, Andary F, Zhao M, Fitzgerald ML, Kronenberg M, Hedrick CC ATP Binding Cassette Transporter ABCA7 Regulates NKT Cell Development and Function by Controlling CD1d Expression and Lipid Raft Content. Sci Rep. 2017;7:40273 - PMID: 28091533 - PMCID: PMC5238393 - DOI: 10.1038/srep40273

  • Franco LH, Nair VR, Scharn CR, Xavier RJ, Torrealba JR, Shiloh MU, Levine B The Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis and Anti-tuberculous Host Defense. Cell Host Microbe. 2017;21(1):59-72 - PMID: 28017659 - PMCID: PMC5699477 - DOI: 10.1016/j.chom.2016.11.002

  • 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 Visceral Adiposity, Genetic Susceptibility, and Risk of Complications Among Individuals with Crohn's Disease. Inflamm Bowel Dis. 2017;23(1):82-88 - PMID: 27893544 - PMCID: PMC5177457 - DOI: 10.1097/MIB.0000000000000978

  • 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 The Role of the Histone Methyltransferase Enhancer of Zeste Homolog 2 (EZH2) in the Pathobiological Mechanisms Underlying Inflammatory Bowel Disease (IBD). J Biol Chem. 2017;292(2):706-722 - PMID: 27909059 - PMCID: PMC5241744 - DOI: 10.1074/jbc.M116.749663

  • Stevens BW, Borren NZ, Velonias G, Conway G, Cleland T, Andrews E, Khalili H, Garber JJ, Xavier RJ, Yajnik V, Ananthakrishnan AN Erratum to: Vedolizumab Therapy Is Associated with an Improvement in Sleep Quality and Mood in Inflammatory Bowel Diseases. Dig Dis Sci. 2017;62(2):552 - PMID: 27864657 - DOI: 10.1007/s10620-016-4380-2

  • Li P, Tompkins RG, Xiao W, KERIS: kaleidoscope of gene responses to inflammation between species. Nucleic Acids Res. 2017;45(D1):D908-D914 - PMID: 27789704 - PMCID: PMC5210651 - DOI: 10.1093/nar/gkw974

  • Stevens BW, Borren NZ, Velonias G, Conway G, Cleland T, Andrews E, Khalili H, Garber JG, Xavier RJ, Yajnik V, Ananthakrishnan AN Vedolizumab Therapy Is Associated with an Improvement in Sleep Quality and Mood in Inflammatory Bowel Diseases. Dig Dis Sci. 2017;62(1):197-206 - PMID: 27796768 - PMCID: PMC5218976 - DOI: 10.1007/s10620-016-4356-2

  • Frydman GH, Le A, Ellett F, Jorgensen J, Fox JG, Tompkins RG, Irimia D Changes in neutrophil migration patterns upon contact with platelets in a microfluidic assay. J Leukoc Biol. 2017;101(3):797-806 - PMID: 27630219 - PMCID: PMC5295852 - DOI: 10.1189/jlb.1TA1115-517RR

  • Kashiwagi S, Khan MA, Yasuhara S, Goto T, Tompkins RG, Kaneki M, Martyn JA Prevention of Burn-Induced Inflammatory Responses and Muscle Wasting By GTS-21, A Specific Agonist for ?7 Nicotinic Acetylcholine Receptors. Shock. 2017;47(1):61-69 - PMID: 27529131 - PMCID: PMC5167674 - DOI: 10.1097/SHK.0000000000000729

  • 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 Impaired antibacterial autophagy links granulomatous intestinal inflammation in Niemann-Pick disease type C1 and XIAP deficiency with NOD2 variants in Crohn's disease. Gut. 2017;66(6):1060-1073 - PMID: 26953272 - PMCID: PMC5532464 - DOI: 10.1136/gutjnl-2015-310382