Publications

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;:ePub - PMID: 28931002

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;:ePub - PMID: 28923873

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

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

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

Obesity, but not physical activity, is associated with higher prevalence of asymptomatic diverticulosis.

Mashayekhi R, Bellavance DR, Chin SM, Maxner B, Staller K, Xavier RJ, Chung DC, Khalili H
Clin Gastroenterol Hepatol. 2017;:ePub - PMID: 28899671

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
Cell Rep. 2017;20(10):2341-2356 - PMID: 28877469

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

Cezairliyan B, Ausubel FM
Proc Natl Acad Sci U S A. 2017;:ePub - PMID: 28847943

Human genetic variation and the gut microbiome in disease.

Hall AB, Tolonen AC, Xavier RJ
Nat Rev Genet. 2017;:ePub - PMID: 28824167

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

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;:ePub - PMID: 28805801

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

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;:ePub - PMID: 28775338

Metagenomic Sequencing of an Echovirus 30 Genome From Cerebrospinal Fluid of a Patient With Aseptic Meningitis and Orchitis.

Piantadosi A, Mukerji SS, Chitneni P, Cho TA, Cosimi LA, Hung DT, Goldberg MB, Sabeti PC, Kuritzkes DR, Grad YH
Open Forum Infect Dis. 2017;4(3):ofx138 - PMID: 28761901 - PMCID: PMC5534216

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
Science. 2017;:ePub - PMID: 28751470

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

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

Mojarro A, Ruvkun G, Zuber MT, Carr CE
Astrobiology. 2017;:ePub - PMID: 28704064

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

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;:ePub - PMID: 28696303

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;:ePub - PMID: 28673998

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;:ePub - PMID: 28671682

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

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;:ePub - PMID: 28658209

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;:ePub - PMID: 28652232

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;:ePub - PMID: 28640999

Dissecting the human microbiome with single-cell genomics.

Tolonen AC, Xavier RJ
Genome Med. 2017;9(1):56 - PMID: 28615076

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

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;:ePub - PMID: 28576875

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;:ePub - PMID: 28539431

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

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;:ePub - PMID: 28518476

The Narrow Road to the Deep Past.

Szostak JW
Angew Chem Int Ed Engl. 2017;:ePub - PMID: 28514493

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;:ePub - PMID: 28506538

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

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

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

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;:ePub - PMID: 28415827

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

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

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

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

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;:ePub - PMID: 28282360

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

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

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

MAPK Assays in Arabidopsis MAMP-PRR Signal Transduction.

Chung HS, Sheen J
Methods Mol Biol. 2017;1578:155-166 - PMID: 28220422

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

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

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

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

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

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

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