Publications for All Faculty - 2018

  • Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, Zhang M, Tirosh I, Dionne D, Nguyen LT, Xifaras ME, Shalek AK, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz OH, Regev A, Xavier RJ T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. Cell. 2018;175(5):1307-1320.e22 - PMID: 30392957 - PMCID: PMC6239889 - DOI: 10.1016/j.cell.2018.10.008

  • Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, Sadowsky MJ, Allegretti JR, Smith MB, Xavier RJ, Alm EJ Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation. Cell Host Microbe. 2018;23(2):229-240.e5 - PMID: 29447696 - PMCID: PMC8318347 - DOI: 10.1016/j.chom.2018.01.003

  • Johns NI, Gomes ALC, Yim SS, Yang A, Blazejewski T, Smillie CS, Smith MB, Alm EJ, Kosuri S, Wang HH Metagenomic mining of regulatory elements enables programmable species-selective gene expression. Nat Methods. 2018;15(5):323-329 - PMID: 30052624 - PMCID: PMC6065261 - DOI: 10.1038/nmeth.4633

  • Canver MC, Joung JK, Pinello L Impact of Genetic Variation on CRISPR-Cas Targeting. CRISPR J. 2018;1:159-170 - PMID: 31021199 - PMCID: PMC6319324 - DOI: 10.1089/crispr.2017.0016

  • Shi L, Wu Y, Sheen J TOR signaling in plants: conservation and innovation. Development. 2018;145(13):ePub - PMID: 29986898 - PMCID: PMC6053665 - DOI: 10.1242/dev.160887

  • Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome. Sci Transl Med. 2018;10(472):ePub - PMID: 30567928 - DOI: 10.1126/scitranslmed.aap8914

  • Chen GH, Liu MJ, Xiong Y, Sheen J, Wu SH TOR and RPS6 transmit light signals to enhance protein translation in deetiolating Arabidopsis seedlings. Proc Natl Acad Sci U S A. 2018;115(50):12823-12828 - PMID: 30482859 - PMCID: PMC6294885 - DOI: 10.1073/pnas.1809526115

  • Kim SC, O'Flaherty DK, Zhou L, Lelyveld VS, Szostak JW Inosine, but none of the 8-oxo-purines, is a plausible component of a primordial version of RNA. Proc Natl Acad Sci U S A. 2018;115(52):13318-13323 - PMID: 30509978 - PMCID: PMC6310819 - DOI: 10.1073/pnas.1814367115

  • Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data. Nat Methods. 2018;15(12):992-993 - PMID: 30504875 - PMCID: PMC6620603 - DOI: 10.1038/s41592-018-0225-6

  • Tan JMJ, Mellouk N, Osborne SE, Ammendolia DA, Dyer DN, Li R, Brunen D, van Rijn JM, Huang J, Czuczman MA, Cemma MA, Won AM, Yip CM, Xavier RJ, MacDuff DA, Reggiori F, Debnath J, Yoshimori T, Kim PK, Fairn GD, Coyaud E, Raught B, Muise AM, Higgins DE, Brumell JH An ATG16L1-dependent pathway promotes plasma membrane repair and limits Listeria monocytogenes cell-to-cell spread. Nat Microbiol. 2018;3(12):1472-1485 - PMID: 30478389 - DOI: 10.1038/s41564-018-0293-5

  • Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, Zhang M, Tirosh I, Dionne D, Nguyen LT, Xifaras ME, Shalek AK, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz OH, Regev A, Xavier RJ T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation. Cell. 2018;175(5):1307-1320.e22 - PMID: 30392957 - PMCID: PMC6239889 - DOI: 10.1016/j.cell.2018.10.008

  • Lin XX, Sen I, Janssens GE, Zhou X, Fonslow BR, Edgar D, Stroustrup N, Swoboda P, Yates JR, Ruvkun G, Riedel CG DAF-16/FOXO and HLH-30/TFEB function as combinatorial transcription factors to promote stress resistance and longevity. Nat Commun. 2018;9(1):4400 - PMID: 30353013 - PMCID: PMC6199276 - DOI: 10.1038/s41467-018-06624-0

  • Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ The human gut microbiome in early-onset type 1 diabetes from the TEDDY study. Nature. 2018;562(7728):589-594 - PMID: 30356183 - PMCID: PMC6296767 - DOI: 10.1038/s41586-018-0620-2

  • Stewart CJ, Ajami NJ, O'Brien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni H, Metcalf GA, Muzny D, Gibbs RA, Vatanen T, Huttenhower C, Xavier RJ, Rewers M, Hagopian W, Toppari J, Ziegler AG, She JX, Akolkar B, Lernmark A, Hyoty H, Vehik K, Krischer JP, Petrosino JF Temporal development of the gut microbiome in early childhood from the TEDDY study. Nature. 2018;562(7728):583-588 - PMID: 30356187 - PMCID: PMC6415775 - DOI: 10.1038/s41586-018-0617-x

  • Graham DB, Luo C, O'Connell DJ, Lefkovith A, Brown EM, Yassour M, Varma M, Abelin JG, Conway KL, Jasso GJ, Matar CG, Carr SA, Xavier RJ Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes. Nat Med. 2018;24(11):1762-1772 - PMID: 30349087 - PMCID: PMC6312190 - DOI: 10.1038/s41591-018-0203-7

  • Jin L, Engelhart AE, Zhang W, Adamala KP, Szostak JW Catalysis of Template-directed Nonenzymatic RNA Copying by Iron (II). J Am Chem Soc. 2018;140(44):15016-15021 - PMID: 30335371 - PMCID: PMC7547886 - DOI: 10.1021/jacs.8b09617

  • Dong D, Zhou H, Na SY, Niedra R, Peng Y, Wang H, Seed B, Zhou GL GPR108, an NF-κB activator suppressed by TIRAP, negatively regulates TLR-triggered immune responses. PLoS One. 2018;13(10):e0205303 - PMID: 30332431 - PMCID: PMC6192633 - DOI: 10.1371/journal.pone.0205303

  • Fang C, Lee KK, Nietupski R, Bates RH, Fernandez-Menendez R, Lopez-Roman EM, Guijarro-Lopez L, Yin Y, Peng Z, Gomez JE, Fisher S, Barros-Aguirre D, Hubbard BK, Serrano-Wu MH, Hung DT Discovery of heterocyclic replacements for the coumarin core of anti-tubercular FadD32 inhibitors. Bioorg Med Chem Lett. 2018;28(22):3529-3533 - PMID: 30316633 - PMCID: PMC6233306 - DOI: 10.1016/j.bmcl.2018.09.037

  • Schirmer M, Denson L, Vlamakis H, Franzosa EA, Thomas S, Gotman NM, Rufo P, Baker SS, Sauer C, Markowitz J, Pfefferkorn M, Oliva-Hemker M, Rosh J, Otley A, Boyle B, Mack D, Baldassano R, Keljo D, LeLeiko N, Heyman M, Griffiths A, Patel AS, Noe J, Kugathasan S, Walters T, Huttenhower C, Hyams J, Xavier RJ Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course. Cell Host Microbe. 2018;24(4):600-610.e4 - PMID: 30308161 - PMCID: PMC6277984 - DOI: 10.1016/j.chom.2018.09.009

  • Tillman EJ, Richardson CE, Cattie DJ, Reddy KC, Lehrbach NJ, Droste R, Ruvkun G, Kim DH Endoplasmic Reticulum Homeostasis Is Modulated by the Forkhead Transcription Factor FKH-9 During Infection of Caenorhabditis elegans. Genetics. 2018;210(4):1329-1337 - PMID: 30287474 - PMCID: PMC6283152 - DOI: 10.1534/genetics.118.301450

  • Akcakaya P, Bobbin ML, Guo JA, Malagon-Lopez J, Clement K, Garcia SP, Fellows MD, Porritt MJ, Firth MA, Carreras A, Baccega T, Seeliger F, Bjursell M, Tsai SQ, Nguyen NT, Nitsch R, Mayr LM, Pinello L, Bohlooly-Y M, Aryee MJ, Maresca M, Joung JK In vivo CRISPR editing with no detectable genome-wide off-target mutations. Nature. 2018;561(7723):416-419 - PMID: 30209390 - PMCID: PMC6194229 - DOI: 10.1038/s41586-018-0500-9

  • Ausubel FM Tracing My Roots: How I Became a Plant Biologist. Annu Rev Genet. 2018;52:1-20 - PMID: 30192637 - DOI: 10.1146/annurev-genet-120417-031722

  • Joyce GF, Szostak JW Protocells and RNA Self-Replication. Cold Spring Harb Perspect Biol. 2018;10(9):ePub - PMID: 30181195 - PMCID: PMC6120706 - DOI: 10.1101/cshperspect.a034801

  • Wein MN, Foretz M, Fisher DE, Xavier RJ, Kronenberg HM Salt-Inducible Kinases: Physiology, Regulation by cAMP, and Therapeutic Potential. Trends Endocrinol Metab. 2018;29(10):723-735 - PMID: 30150136 - PMCID: PMC6151151 - DOI: 10.1016/j.tem.2018.08.004

  • Kim W, Steele AD, Zhu W, Csatary EE, Fricke N, Dekarske MM, Jayamani E, Pan W, Kwon B, Sinitsa IF, Rosen JL, Conery AL, Fuchs BB, Vlahovska PM, Ausubel FM, Gao H, Wuest WM, Mylonakis E Discovery and Optimization of nTZDpa as an Antibiotic Effective Against Bacterial Persisters. ACS Infect Dis. 2018;4(11):1540-1545 - PMID: 30132650 - PMCID: PMC6468991 - DOI: 10.1021/acsinfecdis.8b00161

  • Moretti F, Bergman P, Dodgson S, Marcellin D, Claerr I, Goodwin JM, DeJesus R, Kang Z, Antczak C, Begue D, Bonenfant D, Graff A, Genoud C, Reece-Hoyes JS, Russ C, Yang Z, Hoffman GR, Mueller M, Murphy LO, Xavier RJ, Nyfeler B TMEM41B is a novel regulator of autophagy and lipid mobilization. EMBO Rep. 2018;19(9):ePub - PMID: 30126924 - PMCID: PMC6123663 - DOI: 10.15252/embr.201845889

  • Ma P, Laibinis HH, Ernst CM, Hung DT Carbapenem resistance caused by high-level expression of OXA-663 β-lactamase in an OmpK36-deficient Klebsiella pneumoniae clinical isolate. Antimicrob Agents Chemother. 2018;62(11):ePub - PMID: 30126962 - PMCID: PMC6201135 - DOI: 10.1128/AAC.01281-18

  • Bhattacharyya RP, Thakku SG, Hung DT Harnessing CRISPR Effectors for Infectious Disease Diagnostics. ACS Infect Dis. 2018;4(9):1278-1282 - PMID: 30113801 - DOI: 10.1021/acsinfecdis.8b00170

  • Carr CE, Bryan NC, Saboda KN, Bhattaru SA, Ruvkun G, Zuber MT Acceleration profiles and processing methods for parabolic flight. NPJ Microgravity. 2018;4:14 - PMID: 30109261 - PMCID: PMC6081456 - DOI: 10.1038/s41526-018-0050-3

  • Pontefract A, Hachey J, Zuber MT, Ruvkun G, Carr CE Sequencing nothing: Exploring failure modes of nanopore sensing and implications for life detection. Life Sci Space Res (Amst). 2018;18:80-86 - PMID: 30100151 - DOI: 10.1016/j.lssr.2018.05.004

  • Natividad JM, Agus A, Planchais J, Lamas B, Jarry AC, Martin R, Michel ML, Chong-Nguyen C, Roussel R, Straube M, Jegou S, McQuitty C, Le Gall M, da Costa G, Lecornet E, Michaudel C, Modoux M, Glodt J, Bridonneau C, Sovran B, Dupraz L, Bado A, Richard ML, Langella P, Hansel B, Launay JM, Xavier RJ, Duboc H, Sokol H Impaired Aryl Hydrocarbon Receptor Ligand Production by the Gut Microbiota Is a Key Factor in Metabolic Syndrome. Cell Metab. 2018;28(5):737-749.e4 - PMID: 30057068 - DOI: 10.1016/j.cmet.2018.07.001

  • Gehrke JM, Cervantes O, Clement MK, Wu Y, Zeng J, Bauer DE, Pinello L, Joung JK An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities. Nat Biotechnol. 2018;36(10):977-982 - PMID: 30059493 - PMCID: PMC6181770 - DOI: 10.1038/nbt.4199

  • Graham DB, Jasso GJ, Mok A, Goel G, Ng ACY, Kolde R, Varma M, Doench JG, Root DE, Clish CB, Carr SA, Xavier RJ Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes. Cell Rep. 2018;24(4):838-850 - PMID: 30044981 - PMCID: PMC6156773 - DOI: 10.1016/j.celrep.2018.06.081

  • Yassour M, Jason E, Hogstrom LJ, Arthur TD, Tripathi S, Siljander H, Selvenius J, Oikarinen S, Hyöty H, Virtanen SM, Ilonen J, Ferretti P, Pasolli E, Tett A, Asnicar F, Segata N, Vlamakis H, Lander ES, Huttenhower C, Knip M, Xavier RJ Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life. Cell Host Microbe. 2018;24(1):146-154.e4 - PMID: 30001517 - PMCID: PMC6091882 - DOI: 10.1016/j.chom.2018.06.007

  • Ambros V, Ruvkun G Recent Molecular Genetic Explorations of Caenorhabditis elegans MicroRNAs. Genetics. 2018;209(3):651-673 - PMID: 29967059 - PMCID: PMC6028246 - DOI: 10.1534/genetics.118.300291

  • Schirmer M, Kumar V, Netea MG, Xavier RJ The causes and consequences of variation in human cytokine production in health. Curr Opin Immunol. 2018;54:50-58 - PMID: 29913309 - DOI: 10.1016/j.coi.2018.05.012

  • Zhang W, Walton T, Li L, Szostak JW Crystallographic observation of nonenzymatic RNA primer extension. Elife. 2018;7:ePub - PMID: 29851379 - PMCID: PMC5980232 - DOI: 10.7554/eLife.36422

  • Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, International IBD Genetics Consortium, NIDDK IBD Genetics Consortium, T2D-GENES Consortium, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkkila M, Kontula K, Palotie A, Brant SR, Duerr RH, Silverberg MS, Rioux JD, Weersma RK, Franke A, Jostins L, Anderson CA, Barrett JC, MacArthur DG, Jalas C, Sokol H, Xavier RJ, Pulver A, Cho JH, McGovern DPB, Daly MJ Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population. PLoS Genet. 2018;14(5):e1007329 - PMID: 29795570 - PMCID: PMC5967709 - DOI: 10.1371/journal.pgen.1007329

  • Bakker OB, Aguirre-Gamboa R, Sanna S, Oosting M, Smeekens SP, Jaeger M, Zorro M, Võsa U, Withoff S, Netea-Maier RT, Koenen HJPM, Joosten I, Xavier RJ, Franke L, Joosten LAB, Kumar V, Wijmenga C, Netea MG, Li Y Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses. Nat Immunol. 2018;19(7):776-786 - PMID: 29784908 - PMCID: PMC6022810 - DOI: 10.1038/s41590-018-0121-3

  • Pitt B, Bakris GL, Weir MR, Freeman MW, Lainscak M, Mayo MR, Garza D, Zawadzki R, Berman L, Bushinsky DA Long-term effects of patiromer for hyperkalaemia treatment in patients with mild heart failure and diabetic nephropathy on angiotensin-converting enzymes/angiotensin receptor blockers: results from AMETHYST-DN. ESC Heart Fail. 2018;5(4):592-602 - PMID: 29767459 - PMCID: PMC6073017 - DOI: 10.1002/ehf2.12292

  • Newman MA, Ji F, Fischer SEJ, Anselmo A, Sadreyev RI, Ruvkun G The surveillance of pre-mRNA splicing is an early step in C. elegans RNAi of endogenous genes. Genes Dev. 2018;32(9-10):670-681 - PMID: 29739806 - PMCID: PMC6004069 - DOI: 10.1101/gad.311514.118

  • Burke KE, Khalili H, Garber JJ, Haritunians T, McGovern DPB, Xavier RJ, Ananthakrishnan AN Genetic Markers Predict Primary Nonresponse and Durable Response to Anti-Tumor Necrosis Factor Therapy in Ulcerative Colitis. Inflamm Bowel Dis. 2018;24(8):1840-1848 - PMID: 29718226 - PMCID: PMC6128143 - DOI: 10.1093/ibd/izy083

  • Brown EM, Xavier RJ Without Adaptive Immunity, There's a Cost to Responding STAT. Cell Metab. 2018;27(4):705-707 - PMID: 29617636 - DOI: 10.1016/j.cmet.2018.03.011

  • O'Flaherty DK, Kamat NP, Mirza FN, Li L, Prywes N, Szostak JW Copying of mixed sequence RNA templates inside model protocells. J Am Chem Soc. 2018;140(15):5171-5178 - PMID: 29608310 - PMCID: PMC7547884 - DOI: 10.1021/jacs.8b00639

  • Lareau CA, Clement K, Hsu JY, Pattanayak V, Joung JK, Aryee MJ, Pinello L Response to "Unexpected mutations after CRISPR-Cas9 editing in vivo". Nat Methods. 2018;15(4):238-239 - PMID: 29600992 - PMCID: PMC7784551 - DOI: 10.1038/nmeth.4541

  • Mojarro A, Hachey J, Ruvkun G, Zuber MT, Carr CE CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing. BMC Bioinformatics. 2018;19(1):108 - PMID: 29587645 - PMCID: PMC5872496 - DOI: 10.1186/s12859-018-2124-3

  • Kim W, Zhu W, Hendricks GL, Van Tyne D, Steele AD, Keohane CE, Fricke N, Conery AL, Shen S, Pan W, Lee K, Rajamuthiah R, Fuchs BB, Vlahovska PM, Wuest WM, Gilmore MS, Gao H, Ausubel FM, Mylonakis E A new class of synthetic retinoid antibiotics effective against bacterial persisters. Nature. 2018;556(7699):103-107 - PMID: 29590091 - PMCID: PMC6462414 - DOI: 10.1038/nature26157

  • Verma MS, Fink MJ, Salmon GL, Fornelos N, Ohara TE, Ryu SH, Vlamakis H, Xavier RJ, Stappenbeck TS, Whitesides GM A common mechanism links activities of butyrate in the colon. ACS Chem Biol. 2018;13(5):1291-1298 - PMID: 29584955 - DOI: 10.1021/acschembio.8b00073

  • Jin L, Engelhart AE, Adamala KP, Szostak JW Preparation, Purification, and Use of Fatty Acid-containing Liposomes. J Vis Exp. 2018;(132):ePub - PMID: 29553563 - PMCID: PMC5912384 - DOI: 10.3791/57324

  • Clatworthy AE, Romano KP, Hung DT Whole-organism phenotypic screening for anti-infectives promoting host health. Nat Chem Biol. 2018;14(4):331-341 - PMID: 29556098 - DOI: 10.1038/s41589-018-0018-3

  • Haller S, Franchet A, Hakkim A, Chen J, Drenkard E, Yu S, Schirmeier S, Li Z, Martins N, Ausubel FM, Liégeois S, Ferrandon D Quorum-sensing regulator RhlR but not its autoinducer RhlI enablesPseudomonasto evade opsonization. EMBO Rep. 2018;19(5):ePub - PMID: 29523648 - PMCID: PMC5934776 - DOI: 10.15252/embr.201744880

  • Jin L, Kamat NP, Jena S, Szostak JW Fatty Acid/Phospholipid Blended Membranes: A Potential Intermediate State in Protocellular Evolution. Small. 2018;14(15):e1704077 - PMID: 29479815 - PMCID: PMC6278924 - DOI: 10.1002/smll.201704077

  • Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, Sadowsky MJ, Allegretti JR, Smith MB, Xavier RJ, Alm EJ Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation. Cell Host Microbe. 2018;23(2):229-240.e5 - PMID: 29447696 - PMCID: PMC8318347 - DOI: 10.1016/j.chom.2018.01.003

  • Yuen GJ, Ausubel FM Both live and dead Enterococci activate Caenorhabditis elegans host defense via immune and stress pathways. Virulence. 2018;9(1):0 - PMID: 29436902 - PMCID: PMC5955442 - DOI: 10.1080/21505594.2018.1438025

  • Mohanan V, Nakata T, Desch AN, Lévesque C, Boroughs A, Guzman G, Cao Z, Creasey E, Yao J, Boucher G, Charron G, Bhan AK, Schenone M, Carr SA, Reinecker HC, Daly MJ, Rioux JD, Lassen KG, Xavier RJ C1orf106 is a colitis risk gene that regulates stability of epithelial adherens junctions. Science. 2018;359(6380):1161-1166 - PMID: 29420262 - PMCID: PMC6008784 - DOI: 10.1126/science.aan0814

  • Zhang W, Tam CP, Zhou L, Oh SS, Wang J, Szostak JW A structural rationale for the enhanced catalysis of nonenzymatic RNA primer extension by a downstream oligonucleotide. J Am Chem Soc. 2018;140(8):2829-2840 - PMID: 29411978 - PMCID: PMC6326529 - DOI: 10.1021/jacs.7b11750

  • Wellington S, Hung DT The expanding diversity of Mycobacterium tuberculosis drug targets. ACS Infect Dis. 2018;4(5):696-714 - PMID: 29412643 - DOI: 10.1021/acsinfecdis.7b00255

  • Kolde R, Franzosa EA, Rahnavard G, Hall AB, Vlamakis H, Stevens C, Daly MJ, Xavier RJ, Huttenhower C Host genetic variation and its microbiome interactions within the Human Microbiome Project. Genome Med. 2018;10(1):6 - PMID: 29378630 - PMCID: PMC5789541 - DOI: 10.1186/s13073-018-0515-8

  • Luther J, Gala M, Patel SJ, Dave M, Borren N, Xavier RJ, Ananthakrishnan AN Loss of Response to Anti-Tumor Necrosis Factor Alpha Therapy in Crohn's Disease Is Not Associated with Emergence of Novel Inflammatory Pathways. Dig Dis Sci. 2018;63(3):738-745 - PMID: 29372477 - PMCID: PMC6152907 - DOI: 10.1007/s10620-018-4932-8

  • Visschedijk MC, Spekhorst LM, Cheng SC, van Loo ES, Jansen BHD, Blokzijl T, Kil H, de Jong DJ, Pierik M, Maljaars JPWJ, van der Woude CJ, van Bodegraven AA, Oldenburg B, Löwenberg M, Nieuwenhuijs VB, Imhann F, van Sommeren S, Alberts R, Xavier RJ, Dijkstra G, Faber KN, Aldaz CM, Weersma RK, Festen EAM Genomic and expression analyses identify a disease modifying variant for fibrostenotic Crohn's disease. J Crohns Colitis. 2018;12(5):582-588 - PMID: 29361163 - DOI: 10.1093/ecco-jcc/jjy001

  • Datta S, Seed B Influence of multiplicative stochastic variation on translational elongation rates. PLoS One. 2018;13(1):e0191152 - PMID: 29351322 - PMCID: PMC5774726 - DOI: 10.1371/journal.pone.0191152

  • Todd ZR, Fahrenbach AC, Magnani CJ, Ranjan S, Björkbom A, Szostak JW, Sasselov DD Solvated-electron production using cyanocuprates is compatible with the UV-environment on a Hadean-Archaean Earth. Chem Commun (Camb). 2018;54(9):1121-1124 - PMID: 29334083 - DOI: 10.1039/c7cc07748c

  • Dunbar CE, High KA, Joung JK, Kohn DB, Ozawa K, Sadelain M Gene therapy comes of age. Science. 2018;359(6372):ePub - PMID: 29326244 - DOI: 10.1126/science.aan4672

  • Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C Dynamics of metatranscription in the inflammatory bowel disease gut microbiome. Nat Microbiol. 2018;3(3):337-346 - PMID: 29311644 - PMCID: PMC6131705 - DOI: 10.1038/s41564-017-0089-z

  • Tam CP, Zhou L, Fahrenbach AC, Zhang W, Walton T, Szostak JW Synthesis of a nonhydrolyzable nucleotide phosphoroimidazolide analogue that catalyzes nonenzymatic RNA primer extension. J Am Chem Soc. 2018;140(2):783-792 - PMID: 29251930 - PMCID: PMC6326531 - DOI: 10.1021/jacs.7b11623

  • Borren NZ, Conway G, Garber JJ, Khalili H, Budree S, Mallick H, Yajnik V, Xavier RJ, Ananthakrishnan AN Difference in clinical course, genetics, and the microbiome between familial and sporadic inflammatory bowel diseases. J Crohns Colitis. 2018;12(5):525-531 - PMID: 29145572 - PMCID: PMC6018966 - DOI: 10.1093/ecco-jcc/jjx154

  • Kazis LE, Sheridan RL, Shapiro GD, Lee AF, Liang MH, Ryan CM, Schneider JC, Lydon M, Soley-Bori M, Sonis LA, Dore EC, Palmieri T, Herndon D, Meyer W, Warner P, Kagan R, Stoddard FJ, Murphy M, Tompkins RG Development of Clinical Process Measures for Pediatric Burn Care: Understanding Variation in Practice Patterns. J Trauma Acute Care Surg. 2018;84(4):620-627 - PMID: 29140950 - DOI: 10.1097/TA.0000000000001737

  • Lassen KG, Xavier RJ Mechanisms and Function of Autophagy in Intestinal Disease. Autophagy. 2018;14(2):0 - PMID: 29130415 - PMCID: PMC5902220 - DOI: 10.1080/15548627.2017.1389358

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