Publications for All Faculty

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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

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

Strecker J, Stinus S, Caballero MP, Szilard RK, Chang M, Durocher D

A sharp Pif1-dependent threshold separates DNA double-strand breaks from critically short telomeres.
Elife. 2017;6:ePub - PMID: 28826474 - PMCID: PMC5595431 - DOI: 10.7554/eLife.23783

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

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

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

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

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

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

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

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

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

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

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

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

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

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
Total: 2501