Publications for All Faculty - 2020

  • Carr CE, Bryan NC, Saboda KN, Bhattaru SA, Ruvkun G, Zuber MT Nanopore sequencing at Mars, Europa, and microgravity conditions. NPJ Microgravity. 2020;6(1):24 - PMID: 34489469 - DOI: 10.1038/s41526-020-00113-9

  • Carey KL, Paulus GLC, Wang L, Balce DR, Luo JW, Bergman P, Ferder IC, Kong L, Renaud N, Singh S, Kost-Alimova M, Nyfeler B, Lassen KG, Virgin HW, Xavier RJ TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41. Cell Rep. 2020;33(6):108371 - PMID: 33176151 - PMCID: PMC7686957 - DOI: 10.1016/j.celrep.2020.108371

  • Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors. Nat Med. 2020;26(5):792-802 - PMID: 32405060 - PMCID: PMC7220853 - DOI: 10.1038/s41591-020-0844-1

  • Gomes ALC, Johns NI, Yang A, Velez-Cortes F, Smillie CS, Smith MB, Alm EJ, Wang HH Genome and sequence determinants governing the expression of horizontally acquired DNA in bacteria. ISME J. 2020;14(9):2347-2357 - PMID: 32514119 - PMCID: PMC7608860 - DOI: 10.1038/s41396-020-0696-1

  • Filbin MR, Mehta A, Schneider AM, Kays KR, Guess JR, Gentili M, Fenyves BG, Charland NC, Gonye ALK, Gushterova I, Khanna HK, LaSalle TJ, Lavin-Parsons KM, Lilly BM, Lodenstein CL, Manakongtreecheep K, Margolin JD, McKaig BN, Rojas-Lopez M, Russo BC, Sharma N, Tantivit J, Thomas MF, Gerszten RE, Heimberg GS, Hoover PJ, Lieb DJ, Lin B, Ngo D, Pelka K, Reyes M, Smillie CS, Waghray A, Wood TE, Zajac AS, Jennings LL, Grundberg I, Bhattacharyya RP, Parry BA, Villani AC, Sade-Feldman M, Hacohen N, Goldberg MB Plasma proteomics reveals tissue-specific cell death and mediators of cell-cell interactions in severe COVID-19 patients. bioRxiv. 2020;:ePub - PMID: 33173871 - PMCID: PMC7654866 - DOI: 10.1101/2020.11.02.365536

  • O'Flaherty DK, Zhou L, Szostak JW Nonenzymatic RNA-templated Synthesis of N3'→P5' Phosphoramidate DNA. Bio Protoc. 2020;10(17):e3734 - PMID: 33659395 - PMCID: PMC7842504 - DOI: 10.21769/BioProtoc.3734

  • Mao K, Breen P, Ruvkun G Mitochondrial dysfunction induces RNA interference in C. elegans through a pathway homologous to the mammalian RIG-I antiviral response. PLoS Biol. 2020;18(12):e3000996 - PMID: 33264285 - PMCID: PMC7735679 - DOI: 10.1371/journal.pbio.3000996

  • Lee K, Escobar I, Jang Y, Kim W, Ausubel FM, Mylonakis E In the Model Host Caenorhabditis elegans, Sphingosine-1-Phosphate-Mediated Signaling Increases Immunity toward Human Opportunistic Bacteria. Int J Mol Sci. 2020;21(21):ePub - PMID: 33105563 - PMCID: PMC7672543 - DOI: 10.3390/ijms21217813

  • Nakata T, Creasey EA, Kadoki M, Lin H, Selig MK, Yao J, Lefkovith A, Daly MJ, Graham DB, Xavier RJ A missense variant in SLC39A8 confers risk for Crohn's disease by disrupting manganese homeostasis and intestinal barrier integrity. Proc Natl Acad Sci U S A. 2020;117(46):28930-28938 - PMID: 33139556 - PMCID: PMC7682327 - DOI: 10.1073/pnas.2014742117

  • Carey KL, Paulus GLC, Wang L, Balce DR, Luo JW, Bergman P, Ferder IC, Kong L, Renaud N, Singh S, Kost-Alimova M, Nyfeler B, Lassen KG, Virgin HW, Xavier RJ TFEB Transcriptional Responses Reveal Negative Feedback by BHLHE40 and BHLHE41. Cell Rep. 2020;33(6):108371 - PMID: 33176151 - PMCID: PMC7686957 - DOI: 10.1016/j.celrep.2020.108371

  • Xie F, Dai S, Zhao Y, Huang P, Yu S, Ren B, Wang Q, Ji Z, Alterovitz G, Zhang Q, Zhang J, Chen X, Jiang L, Song F, Liu H, Ausubel FM, Liu X, Dai H, Zhang L Generation of Fluorinated Amychelin Siderophores against Pseudomonas aeruginosa Infections by a Combination of Genome Mining and Mutasynthesis. Cell Chem Biol. 2020;27(12):1532-1543.e6 - PMID: 33186541 - DOI: 10.1016/j.chembiol.2020.10.009

  • Strom KR, Szostak JW Solid-Phase Synthesis of Sequence-Defined Informational Oligomers. J Org Chem. 2020;85(21):13929-13938 - PMID: 33064001 - DOI: 10.1021/acs.joc.0c01977

  • Xu W, Rush JS, Graham DB, Cao Z, Xavier RJ USP15 Deubiquitinates CARD9 to Downregulate C-Type Lectin Receptor-Mediated Signaling. Immunohorizons. 2020;4(10):670-678 - PMID: 33093067 - PMCID: PMC7758836 - DOI: 10.4049/immunohorizons.2000036

  • Tsurumi A, Flaherty PJ, Que YA, Ryan CM, Mendoza AE, Almpani M, Bandyopadhaya A, Ogura A, Dhole YV, Goodfield LF, Tompkins RG, Rahme LG Multi-biomarker Prediction Models for Multiple Infection Episodes Following Blunt Trauma. iScience. 2020;23(11):101659 - PMID: 33047099 - PMCID: PMC7539926 - DOI: 10.1016/j.isci.2020.101659

  • Drokhlyansky E, Smillie CS, Van Wittenberghe N, Ericsson M, Griffin GK, Eraslan G, Dionne D, Cuoco MS, Goder-Reiser MN, Sharova T, Kuksenko O, Aguirre AJ, Boland GM, Graham D, Rozenblatt-Rosen O, Xavier RJ, Regev A The Human and Mouse Enteric Nervous System at Single-Cell Resolution. Cell. 2020;182(6):1606-1622.e23 - PMID: 32888429 - PMCID: PMC8358727 - DOI: 10.1016/j.cell.2020.08.003

  • Kong L, Lloyd-Price J, Vatanen T, Seksik P, Beaugerie L, Simon T, Vlamakis H, Sokol H, Xavier RJ Linking strain engraftment in fecal microbiota transplantation with maintenance of remission in Crohn's disease. Gastroenterology. 2020;159(6):2193-2202.e5 - PMID: 32860788 - PMCID: PMC7725862 - DOI: 10.1053/j.gastro.2020.08.045

  • Zhou L, O'Flaherty DK, Szostak JW Assembly of a ribozyme ligase from short oligomers by nonenzymatic ligation. J Am Chem Soc. 2020;142(37):15961-15965 - PMID: 32820909 - DOI: 10.1021/jacs.0c06722

  • Zhang SJ, Duzdevich D, Szostak JW Potentially Prebiotic Activation Chemistry Compatible with Nonenzymatic RNA Copying. J Am Chem Soc. 2020;142(35):14810-14813 - PMID: 32794700 - DOI: 10.1021/jacs.0c05300

  • Borren NZ, Plichta D, Joshi AD, Bonilla G, Sadreyev R, Vlamakis H, Xavier RJ, Ananthakrishnan AN Multi-"-Omics" Profiling in Patients With Quiescent Inflammatory Bowel Disease Identifies Biomarkers Predicting Relapse. Inflamm Bowel Dis. 2020;26(10):1524-1532 - PMID: 32766830 - PMCID: PMC7500522 - DOI: 10.1093/ibd/izaa183

  • Khader R, Tharmalingam N, Mishra B, Felix L, Ausubel FM, Kelso MJ, Mylonakis E Characterization of Five Novel Anti-MRSA Compounds Identified Using a Whole-Animal Caenorhabditis elegans/Galleria mellonella Sequential-Screening Approach. Antibiotics (Basel). 2020;9(8):ePub - PMID: 32726955 - PMCID: PMC7459823 - DOI: 10.3390/antibiotics9080449

  • Wei W, Ruvkun G Lysosomal activity regulates Caenorhabditis elegans mitochondrial dynamics through vitamin B12 metabolism. Proc Natl Acad Sci U S A. 2020;117(33):19970-19981 - PMID: 32737159 - PMCID: PMC7443905 - DOI: 10.1073/pnas.2008021117

  • Virgin HW, Cuervo AM, Xavier RJ Beth Cindy Levine (1960-2020). Science. 2020;369(6502):378 - PMID: 32703867 - DOI: 10.1126/science.abd6216

  • Xavier RJ Growth and the Microbiome - Integrating Global Health with Basic Science. N Engl J Med. 2020;383(4):391-393 - PMID: 32706538 - DOI: 10.1056/NEJMe2017496

  • Kindt JT, Szostak JW, Wang A Bulk Self-Assembly of Giant, Unilamellar Vesicles. ACS Nano. 2020;14(11):14627-14634 - PMID: 32602696 - PMCID: PMC8172239 - DOI: 10.1021/acsnano.0c03125

  • Kim W, Zou G, Pan W, Fricke N, Faizi HA, Kim SM, Khader R, Li S, Lee K, Escorba I, Vlahovska PM, Gao H, Ausubel FM, Mylonakis E The Neutrally Charged Diarylurea Compound PQ401 Kills Antibiotic-Resistant and Antibiotic-Tolerant Staphylococcus aureus. MBio. 2020;11(3):ePub - PMID: 32605985 - PMCID: PMC7327171 - DOI: 10.1128/mBio.01140-20

  • Clement K, Hsu JY, Canver MC, Joung JK, Pinello L Technologies and Computational Analysis Strategies for CRISPR Applications. Mol Cell. 2020;79(1):11-29 - PMID: 32619467 - PMCID: PMC7497852 - DOI: 10.1016/j.molcel.2020.06.012

  • Varma M, Kadoki M, Lefkovith A, Conway KL, Gao K, Mohanan V, Tusi BK, Graham DB, Latorre IJ, Tolonen AC, Khor B, Ng A, Xavier RJ Cell Type- and Stimulation-Dependent Transcriptional Programs Regulated by Atg16L1 and Its Crohn's Disease Risk Variant T300A. J Immunol. 2020;205(2):414-424 - PMID: 32522834 - PMCID: PMC7364322 - DOI: 10.4049/jimmunol.1900750

  • Kenny DJ, Plichta DR, Shungin D, Koppel N, Hall AB, Fu B, Vasan RS, Shaw SY, Vlamakis H, Balskus EP, Xavier RJ Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level. Cell Host Microbe. 2020;28(2):245-257.e6 - PMID: 32544460 - PMCID: PMC7435688 - DOI: 10.1016/j.chom.2020.05.013

  • Zhou L, O'Flaherty DK, Szostak JW Template-directed copying of RNA by non-enzymatic ligation. Angew Chem Int Ed Engl. 2020;59(36):15682-15687 - PMID: 32558121 - PMCID: PMC7496532 - DOI: 10.1002/anie.202004934

  • Grünewald J, Zhou R, Lareau CA, Garcia SP, Iyer S, Miller BR, Langner LM, Hsu JY, Aryee MJ, Joung JK A dual-deaminase CRISPR base editor enables concurrent adenine and cytosine editing. Nat Biotechnol. 2020;38(7):861-864 - PMID: 32483364 - PMCID: PMC7723518 - DOI: 10.1038/s41587-020-0535-y

  • Ackerman CM, Myhrvold C, Thakku SG, Freije CA, Metsky HC, Yang DK, Ye SH, Boehm CK, Kosoko-Thoroddsen TF, Kehe J, Nguyen TG, Carter A, Kulesa A, Barnes JR, Dugan VG, Hung DT, Blainey PC, Sabeti PC Massively multiplexed nucleic acid detection with Cas13. Nature. 2020;582(7811):277-282 - PMID: 32349121 - PMCID: PMC7332423 - DOI: 10.1038/s41586-020-2279-8

  • Duzdevich D, Carr CE, Szostak JW Deep sequencing of non-enzymatic RNA primer extension. Nucleic Acids Res. 2020;48(12):e70 - PMID: 32427335 - PMCID: PMC7337528 - DOI: 10.1093/nar/gkaa400

  • Ernst CM, Braxton JR, Rodriguez-Osorio CA, Zagieboylo AP, Li L, Pironti A, Manson AL, Nair AV, Benson M, Cummins K, Clatworthy AE, Earl AM, Cosimi LA, Hung DT Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae. Nat Med. 2020;26(5):705-711 - PMID: 32284589 - DOI: 10.1038/s41591-020-0825-4

  • Todd ZR, Fahrenbach AC, Ranjan S, Magnani CJ, Szostak JW, Sasselov DD Ultraviolet-Driven Deamination of Cytidine Ribonucleotides Under Planetary Conditions. Astrobiology. 2020;20(7):878-888 - PMID: 32267736 - DOI: 10.1089/ast.2019.2182

  • Lelyveld VS, Zhang W, Szostak JW Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase. Proc Natl Acad Sci U S A. 2020;117(13):7276-7283 - PMID: 32188786 - PMCID: PMC7132125 - DOI: 10.1073/pnas.1922400117

  • Frydman GH, Tessier SN, Wong KHK, Vanderburg CR, Fox JG, Toner M, Tompkins RG, Irimia D Megakaryocytes contain extranuclear histones and may be a source of platelet-associated histones during sepsis. Sci Rep. 2020;10(1):4621 - PMID: 32165642 - PMCID: PMC7067782 - DOI: 10.1038/s41598-020-61309-3

  • Netea MG, Domínguez-Andrés J, Barreiro LB, Chavakis T, Divangahi M, Fuchs E, Joosten LAB, van der Meer JWM, Mhlanga MM, Mulder WJM, Riksen NP, Schlitzer A, Schultze JL, Stabell Benn C, Sun JC, Xavier RJ, Latz E Defining trained immunity and its role in health and disease. Nat Rev Immunol. 2020;20(6):375-388 - PMID: 32132681 - PMCID: PMC7186935 - DOI: 10.1038/s41577-020-0285-6

  • Walton T, DasGupta S, Duzdevich D, Oh SS, Szostak JW In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole-activated substrates. Proc Natl Acad Sci U S A. 2020;117(11):5741-5748 - PMID: 32123094 - PMCID: PMC7084097 - DOI: 10.1073/pnas.1914367117

  • Fischer SEJ, Ruvkun G Caenorhabditis elegans ADAR editing and the ERI-6/7/MOV10 RNAi pathway silence endogenous viral elements and LTR retrotransposons. Proc Natl Acad Sci U S A. 2020;117(11):5987-5996 - PMID: 32123111 - PMCID: PMC7084138 - DOI: 10.1073/pnas.1919028117

  • Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC Global chemical effects of the microbiome include new bile-acid conjugations. Nature. 2020;579(7797):123-129 - PMID: 32103176 - PMCID: PMC7252668 - DOI: 10.1038/s41586-020-2047-9

  • Graham DB, Xavier RJ Pathway paradigms revealed from the genetics of inflammatory bowel disease. Nature. 2020;578(7796):527-539 - PMID: 32103191 - PMCID: PMC7871366 - DOI: 10.1038/s41586-020-2025-2

  • Reyes M, Filbin MR, Bhattacharyya RP, Billman K, Eisenhaure T, Hung DT, Levy BD, Baron RM, Blainey PC, Goldberg MB, Hacohen N An immune-cell signature of bacterial sepsis. Nat Med. 2020;26(3):333-340 - PMID: 32066974 - PMCID: PMC7235950 - DOI: 10.1038/s41591-020-0752-4

  • Fornelos N, Franzosa EA, Bishai J, Annand JW, Oka A, Lloyd-Price J, Arthur TD, Garner A, Avila-Pacheco J, Haiser HJ, Tolonen AC, Porter JA, Clish CB, Sartor RB, Huttenhower C, Vlamakis H, Xavier RJ Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease. Nat Microbiol. 2020;5(3):486-497 - PMID: 31959971 - PMCID: PMC7047597 - DOI: 10.1038/s41564-019-0655-7

  • Ennamorati M, Vasudevan C, Clerkin K, Halvorsen S, Verma S, Ibrahim S, Prosper S, Porter C, Yeliseyev V, Kim M, Gardecki J, Sassi S, Tearney G, Cherayil BJ, Bry L, Seed B, Jain N Intestinal microbes influence development of thymic lymphocytes in early life. Proc Natl Acad Sci U S A. 2020;117(5):2570-2578 - PMID: 31964813 - PMCID: PMC7007548 - DOI: 10.1073/pnas.1915047117

  • Liu KH, Diener A, Lin Z, Liu C, Sheen J Primary nitrate responses via calcium signalling and diverse protein phosphorylation. J Exp Bot. 2020;71(15):4428-4441 - PMID: 31985788 - PMCID: PMC7382375 - DOI: 10.1093/jxb/eraa047

  • Brady KJS, Ni P, Grant GG, Thorpe CR, Nadler D, Lee A, Shapiro G, Kogosov A, Palmieri TL, Tompkins RG, Schneider JC, Kazis LE, Ryan CM Translation and Cross-Cultural Validation of the English Young Adult Burn Outcome Questionnaire (YABOQ) in Spanish. J Burn Care Res. 2020;41(3):640-646 - PMID: 31930334 - DOI: 10.1093/jbcr/iraa011

  • Kim SC, Zhou L, Zhang W, O'Flaherty DK, Rondo-Brovetto V, Szostak JW A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2'-deoxynucleotides. J Am Chem Soc. 2020;142(5):2317-2326 - PMID: 31913615 - PMCID: PMC7577264 - DOI: 10.1021/jacs.9b11239

  • Chizzolini F, Passalacqua LFM, Oumais M, Dingilian AI, Szostak JW, Lupták A Large phenotypic enhancement of structured random RNA pools. J Am Chem Soc. 2020;142(4):1941-1951 - PMID: 31887027 - DOI: 10.1021/jacs.9b11396

  • Halvorsen YD, Walford G, Thurber T, Russell H, Massaro M, Freeman MW A Twelve-Week, Randomized, Double-Blind, Placebo-Controlled, Four-Arm Dose-Finding Phase 2 Study Evaluating Bexagliflozin as a Monotherapy for Adults with Type 2 Diabetes. Diabetes Obes Metab. 2020;22(4):566-573 - PMID: 31749238 - DOI: 10.1111/dom.13928

  • Johnson EO, Office E, Kawate T, Orzechowski M, Hung DT A large-scale chemical-genetic strategy enables design of antimicrobial combination chemotherapy in Mycobacteria. ACS Infect Dis. 2020;6(1):56-63 - PMID: 31721551 - PMCID: PMC6958538 - DOI: 10.1021/acsinfecdis.9b00373

  • 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

  • Raymond SL, Hawkins RB, Wang Z, Mira JC, Stortz JA, Han F, Lanz JD, Hennessy LV, Brumback BA, Baker HV, Efron PA, Brakenridge SC, Xiao W, Tompkins RG, Cuschieri J, Moore FA, Maier RV, Moldawer LL Prospective Validation of a Transcriptomic Metric in Severe Trauma. Ann Surg. 2020;271(5):802-810 - PMID: 30688688 - PMCID: PMC6656642 - DOI: 10.1097/SLA.0000000000003204