Publications for All Faculty

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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
Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Savova G, Shaw SY, Churchill S, Burke KE, Karlson EW, Murphy SN, Kohane I, Liao KP, Xavier RJ

Use of narrative concepts in the EHR to validate genetic determinants of treatment response in a virtual inflammatory bowel disease cohort.

Clin Gastroenterol Hepatol. 2020;18(8):1890-1892 - PMID: 31404664 - DOI: 10.1016/j.cgh.2019.08.005
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
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
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
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
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
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
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
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
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
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
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
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
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
Total: 2477