Publications for All Faculty

  • Stražar M, Temba GS, Vlamakis H, Kullaya VI, Lyamuya F, Mmbaga BT, Joosten LAB, van der Ven AJAM, Netea MG, de Mast Q, Xavier RJ Gut microbiome-mediated metabolism effects on immunity in rural and urban African populations. Nat Commun. 2021;12(1):4845 - PMID: 34381036 - PMCID: PMC8357928

  • Brown EM, Arellano-Santoyo H, Temple ER, Costliow ZA, Pichaud M, Hall AB, Liu K, Durney MA, Gu X, Plichta DR, Clish CA, Porter JA, Vlamakis H, Xavier RJ Gut microbiome ADP-ribosyltransferases are widespread phage-encoded fitness factors. Cell Host Microbe. 2021;29(9):1351-1365.e11 - PMID: 34403684 - PMCID: PMC8429246

  • Sato Y, Atarashi K, Plichta DR, Arai Y, Sasajima S, Kearney SM, Suda W, Takeshita K, Sasaki T, Okamoto S, Skelly AN, Okamura Y, Vlamakis H, Li Y, Tanoue T, Takei H, Nittono H, Narushima S, Irie J, Itoh H, Moriya K, Sugiura Y, Suematsu M, Moritoki N, Shibata S, Littman DR, Fischbach MA, Uwamino Y, Inoue T, Honda A, Hattori M, Murai T, Xavier RJ, Hirose N, Honda K Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians. Nature. 2021;599(7885):458-464 - PMID: 34325466 - DOI: 10.1038/s41586-021-03832-5

  • Liu K, Kong L, Graham DB, Carey KL, Xavier RJ SAC1 regulates autophagosomal phosphatidylinositol-4-phosphate for xenophagy-directed bacterial clearance. Cell Reports. 2021;36(4):109434 - PMID: 34320354 - PMCID: PMC8327279 - DOI: https://doi.org/10.1016/j.celrep.2021.109434

  • Lee JWJ, Plichta D, Hogstrom L, Borren NZ, Lau H, Gregory SM, Tan W, Khalili H, Clish C, Vlamakis H, Xavier RJ, Ananthakrishnan AN Multi-omics reveal microbial determinants impacting responses to biologic therapies in inflammatory bowel disease. Cell Host Microbe. 2021;29(8):1294-1304.e4 - PMID: 34297922 - PMCID: PMC8366279

  • Vadaq N, Schirmer M, Tunjungputri RN, Vlamakis H, Chiriac C, Ardiansyah E, Gasem MH, Joosten L, de Groot PG, Xavier RJ, Netea MG, van der Ven AJAM, de Mast Q Untargeted plasma metabolome and gut microbiome profiling provide novel insights in the regulation of platelet reactivity in healthy individuals. Thromb Haemost. 2021;:ePub - PMID: 34192775 - DOI: 10.1055/a-1541-3706

  • Xie L, McKenzie CI, Qu X, Mu Y, Wang Q, Bing N, Naidoo K, Alam MJ, Yu D, Gong F, Ang C, Robert R, Marques FZ, Furlotte N, Hinds D, Gasser O, 23andMe Research Team, Xavier RJ, Mackay CR pH and Proton Sensor GPR65 Determine Susceptibility to Atopic Dermatitis. J Immunol. 2021;:ePub - PMID: 34135065 - DOI: 10.4049/jimmunol.2001363

  • Arnett A, Moo KG, Flynn KJ, Sundberg TB, Johannessen L, Shamji AF, Gray NS, Decker T, Zheng Y, Gersuk VH, Rahman ZS, Levy DE, Marié IJ, Linsley PS, Xavier RJ, Khor B The CDK8 inhibitor DCA promotes a tolerogenic chemical immunophenotype in CD4+ T cells via a novel CDK8-GATA3-FOXP3 pathway. Mol Cell Biol. 2021;41(9):e0008521 - PMID: 34124936 - PMCID: PMC8384069 - DOI: 10.1128/MCB.00085-21

  • Gligorijević V, Renfrew PD, Kosciolek T, Leman JK, Berenberg D, Vatanen T, Chandler C, Taylor BC, Fisk IM, Vlamakis H, Xavier RJ, Knight R, Cho K, Bonneau R Structure-based protein function prediction using graph convolutional networks. Nat Commun. 2021;12(1):3168 - PMID: 34039967 - PMCID: PMC8155034 - DOI: 10.1038/s41467-021-23303-9

  • Xavier RJ Translating the human microbiome: a path to improving health. Genome Med. 2021;13(1):78 - PMID: 33952319 - PMCID: PMC8097784 - DOI: 10.1186/s13073-021-00896-w

  • 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, Lilley 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 Longitudinal proteomic analysis of plasma from patients with severe COVID-19 reveal patient survival-associated signatures, tissue-specific cell death, and cell-cell interactions. Cell Rep Med. 2021;2(5):100287 - PMID: 33969320 - PMCID: PMC8091031 - DOI: 10.1016/j.xcrm.2021.100287

  • Henke MT, Brown EM, Cassilly CD, Vlamakis H, Xavier RJ, Clardy J Capsular polysaccharide correlates with immune response to the human gut microbe Ruminococcus gnavus. Proc Natl Acad Sci U S A. 2021;118(20):ePub - PMID: 33972416 - PMCID: PMC8157926 - DOI: 10.1073/pnas.2007595118

  • Petri K, Zhang W, Ma J, Schmidts A, Lee H, Horng JE, Kim DY, Kurt IC, Clement K, Hsu JY, Pinello L, Maus MV, Joung JK, Yeh JJ CRISPR prime editing with ribonucleoprotein complexes in zebrafish and primary human cells. Nat Biotechnol. 2021;:ePub - PMID: 33927418 - PMCID: PMC8553808 - DOI: 10.1038/s41587-021-00901-y

  • Penaranda C, Chumbler NM, Hung DT Dual transcriptional analysis reveals adaptation of host and pathogen to intracellular survival of Pseudomonas aeruginosa associated with urinary tract infection. PLoS Pathog. 2021;17(4):e1009534 - PMID: 33901267 - PMCID: PMC8102004 - DOI: 10.1371/journal.ppat.1009534

  • Scheid JF, Barnes CO, Eraslan B, Hudak A, Keeffe JR, Cosimi LA, Brown EM, Muecksch F, Weisblum Y, Zhang S, Delorey T, Woolley AE, Ghantous F, Park SM, Phillips D, Tusi B, Huey-Tubman KE, Cohen AA, Gnanapragasam PNP, Rzasa K, Hatziioanno T, Durney MA, Gu X, Tada T, Landau NR, West AP, Rozenblatt-Rosen O, Seaman MS, Baden LR, Graham DB, Deguine J, Bieniasz PD, Regev A, Hung D, Bjorkman PJ, Xavier RJ B cell genomics behind cross-neutralization of SARS-CoV-2 variants and SARS-CoV. Cell. 2021;184(12):3205-3221.e24 - PMID: 34015271 - PMCID: PMC8064835 - DOI: 10.1016/j.cell.2021.04.032

  • Ma P, He LL, Pironti A, Laibinis HH, Ernst CM, Manson AL, Bhattacharyya RP, Earl AM, Livny J, Hung DT Genetic determinants facilitating the evolution of resistance to carbapenem antibiotics. Elife. 2021;10:ePub - PMID: 33871353 - PMCID: PMC8079144 - DOI: 10.7554/eLife.67310

  • Nasser J, Bergman DT, Fulco CP, Guckelberger P, Doughty BR, Patwardhan TA, Jones TR, Nguyen TH, Ulirsch JC, Lekschas F, Mualim K, Natri HM, Weeks EM, Munson G, Kane M, Kang HY, Cui A, Ray JP, Eisenhaure TM, Collins RL, Dey K, Pfister H, Price AL, Epstein CB, Kundaje A, Xavier RJ, Daly MJ, Huang H, Finucane HK, Hacohen N, Lander ES, Engreitz JM Genome-wide enhancer maps link risk variants to disease genes. Nature. 2021;593(7858):238-243 - PMID: 33828297 - DOI: 10.1038/s41586-021-03446-x

  • Petersen AØ, Jokinen M, Plichta DR, Liebisch G, Gronwald W, Oefner PJ, Vlamakis H, Chung DC, Ranki A, Xavier RJ Cytokine-specific autoantibodies shape the gut microbiome in autoimmune polyendocrine syndrome type 1. J Allergy Clin Immunol. 2021;148(3):876-888 - PMID: 33819509 - PMCID: PMC8429070 - DOI: 10.1016/j.jaci.2021.03.025

  • Jaeger N, Gamini R, Cella M, Schettini JL, Bugatti M, Zhao S, Rosadini CV, Esaulova E, Di Luccia B, Kinnett B, Vermi W, Artyomov MN, Wynn TA, Xavier RJ, Jelinsky SA, Colonna M Single-cell analyses of Crohn's disease tissues reveal intestinal intraepithelial T cells heterogeneity and altered subset distributions. Nat Commun. 2021;12(1):1921 - PMID: 33771991 - PMCID: PMC7997960 - DOI: 10.1038/s41467-021-22164-6

  • Groussin M, Poyet M, Sistiaga A, Kearney SM, Moniz K, Noel M, Hooker J, Gibbons SM, Segurel L, Froment A, Mohamed RS, Fezeu A, Juimo VA, Lafosse S, Tabe FE, Girard C, Iqaluk D, Nguyen LTT, Shapiro BJ, Lehtimäki J, Ruokolainen L, Kettunen PP, Vatanen T, Sigwazi S, Mabulla A, Domínguez-Rodrigo M, Nartey YA, Agyei-Nkansah A, Duah A, Awuku YA, Valles KA, Asibey SO, Afihene MY, Roberts LR, Plymoth A, Onyekwere CA, Summons RE, Xavier RJ, Alm EJ Elevated rates of horizontal gene transfer in the industrialized human microbiome. Cell. 2021;184(8):2053-2067.e18 - PMID: 33794144 - DOI: 10.1016/j.cell.2021.02.052

  • Duzdevich D, Carr CE, Ding D, Zhang SJ, Walton TS, Szostak JW Competition between bridged dinucleotides and activated mononucleotides determines the error frequency of nonenzymatic RNA primer extension. Nucleic Acids Res. 2021;49(7):3681-3691 - PMID: 33744957 - PMCID: PMC8053118 - DOI: 10.1093/nar/gkab173

  • Muus C, Luecken MD, Eraslan G, Sikkema L, Waghray A, Heimberg G, Kobayashi Y, Vaishnav ED, Subramanian A, Smillie C, Jagadeesh KA, Duong ET, Fiskin E, Triglia ET, Ansari M, Cai P, Lin B, Buchanan J, Chen S, Shu J, Haber AL, Chung H, Montoro DT, Adams T, Aliee H, Allon SJ, Andrusivova Z, Angelidis I, Ashenberg O, Bassler K, Bécavin C, Benhar I, Bergenstråhle J, Bergenstråhle L, Bolt L, Braun E, Bui LT, Callori S, Chaffin M, Chichelnitskiy E, Chiou J, Conlon TM, Cuoco MS, Cuomo ASE, Deprez M, Duclos G, Fine D, Fischer DS, Ghazanfar S, Gillich A, Giotti B, Gould J, Guo M, Gutierrez AJ, Habermann AC, Harvey T, He P, Hou X, Hu L, Hu Y, Jaiswal A, Ji L, Jiang P, Kapellos TS, Kuo CS, Larsson L, Leney-Greene MA, Lim K, Litviňuková M, Ludwig LS, Lukassen S, Luo W, Maatz H, Madissoon E, Mamanova L, Manakongtreecheep K, Leroy S, Mayr CH, Mbano IM, McAdams AM, Nabhan AN, Nyquist SK, Penland L, Poirion OB, Poli S, Qi C, Queen R, Reichart D, Rosas I, Schupp JC, Shea CV, Shi X, Sinha R, Sit RV, Slowikowski K, Slyper M, Smith NP, Sountoulidis A, Strunz M, Sullivan TB, Sun D, Talavera-López C, Tan P, Tantivit J, Travaglini KJ, Tucker NR, Vernon KA, Wadsworth MH, Waldman J, Wang X, Xu K, Yan W, Zhao W, Ziegler CGK, NHLBI LungMap Consortium, Human Cell Atlas Lung Biological Network Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nat Med. 2021;27(3):546-559 - PMID: 33654293 - DOI: 10.1038/s41591-020-01227-z

  • Sullivan ZA, Khoury-Hanold W, Lim J, Smillie C, Biton M, Reis BS, Zwick RK, Pope SD, Israni-Winger K, Parsa R, Philip NH, Rashed S, Palm N, Wang A, Mucida D, Regev A, Medzhitov R γδ T cells regulate the intestinal response to nutrient sensing. Science. 2021;371(6535):ePub - PMID: 33737460 - DOI: 10.1126/science.aba8310

  • Plichta DR, Somani J, Pichaud M, Wallace ZS, Fernandes AD, Perugino CA, Lähdesmäki H, Stone JH, Vlamakis H, Chung DC, Khanna D, Pillai S, Xavier RJ Congruent microbiome signatures in fibrosis-prone autoimmune diseases: IgG4-related disease and systemic sclerosis. Genome Med. 2021;13(1):35 - PMID: 33648559 - PMCID: PMC7919092 - DOI: 10.1186/s13073-021-00853-7

  • Kim SC, O'Flaherty DK, Giurgiu C, Zhou L, Szostak JW The Emergence of RNA from the Heterogeneous Products of Prebiotic Nucleotide Synthesis. J Am Chem Soc. 2021;143(9):3267-3279 - PMID: 33636080 - DOI: 10.1021/jacs.0c12955

  • Annas GJ, Beisel CL, Clement K, Crisanti A, Francis S, Galardini M, Galizi R, Grünewald J, Immobile G, Khalil AS, Müller R, Pattanayak V, Petri K, Paul L, Pinello L, Simoni A, Taxiarchi C, Joung JK A Code of Ethics for Gene Drive Research. CRISPR J. 2021;4(1):19-24 - PMID: 33571044 - PMCID: PMC7898401 - DOI: 10.1089/crispr.2020.0096

  • Mojarro A, Jin L, Szostak JW, Head JW, Zuber MT In search of the RNA world on Mars. Geobiology. 2021;19(3):307-321 - PMID: 33565260 - PMCID: PMC8248371 - DOI: 10.1111/gbi.12433

  • Radakovic A, Wright TH, Lelyveld VS, Szostak JW A Potential Role for Aminoacylation in Primordial RNA Copying Chemistry. Biochemistry. 2021;60(6):477-488 - PMID: 33523633 - DOI: 10.1021/acs.biochem.0c00943

  • You K, Wang L, Chou CH, Liu K, Nakata T, Jaiswal A, Yao J, Lefkovith A, Omar A, Perrigoue JG, Towne JE, Regev A, Graham DB, Xavier RJ QRICH1 dictates the outcome of ER stress through transcriptional control of proteostasis. Science. 2021;371(6524):ePub - PMID: 33384352 - PMCID: PMC8315080 - DOI: 10.1126/science.abb6896

  • Warnhoff K, Hercher TW, Mendel RR, Ruvkun G Protein-bound molybdenum cofactor is bioavailable and rescues molybdenum cofactor-deficient C. elegans. Genes Dev. 2021;35(3-4):212-217 - PMID: 33446569 - PMCID: PMC7849362 - DOI: 10.1101/gad.345579.120

  • Zabaleta N, Dai W, Bhatt U, Chichester JA, Estelien R, Sanmiguel J, Michalson KT, Diop C, Maciorowski D, Qi W, Hudspeth E, Cucalon A, Dyer CD, Pampena MB, Knox JJ, LaRocque RC, Charles RC, Li D, Kim M, Sheridan A, Storm N, Johnson RI, Feldman J, Hauser BM, Ryan A, Kobayashi DT, Chauhan R, McGlynn M, Ryan ET, Schmidt AG, Price B, Honko A, Griffiths A, Yaghmour S, Hodge R, Betts MR, Freeman MW, Wilson JM, Vandenberghe LH Immunogenicity of an AAV-based, room-temperature stable, single dose COVID-19 vaccine in mice and non-human primates. bioRxiv. 2021;:ePub - PMID: 33442684 - PMCID: PMC7805441 - DOI: 10.1101/2021.01.05.422952

  • Tanes C, Bittinger K, Gao Y, Friedman ES, Nessel L, Paladhi UR, Chau L, Panfen E, Fischbach MA, Braun J, Xavier RJ, Clish CB, Li H, Bushman FD, Lewis JD, Wu GD Role of dietary fiber in the recovery of the human gut microbiome and its metabolome. Cell Host Microbe. 2021;29(3):394-407.e5 - PMID: 33440171 - PMCID: PMC8022197 - DOI: 10.1016/j.chom.2020.12.012

  • 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

  • Dong X, Yang Y, Zou Z, Zhao Y, Ci B, Zhong L, Bhave M, Wang L, Kuo YC, Zang X, Zhong R, Aguilera ER, Richardson RB, Simonetti B, Schoggins JW, Pfeiffer JK, Yu L, Zhang X, Xie Y, Schmid SL, Xiao G, Gleeson PA, Ktistakis NT, Cullen PJ, Xavier RJ, Levine B Sorting nexin 5 mediates virus-induced autophagy and immunity. Nature. 2021;589(7842):456-461 - PMID: 33328639 - PMCID: PMC7856200 - DOI: 10.1038/s41586-020-03056-z

  • Zhang W, Kim SC, Tam CP, Lelyveld VS, Bala S, Chaput JC, Szostak JW Structural interpretation of the effects of threo-nucleotides on nonenzymatic template-directed polymerization. Nucleic Acids Res. 2021;49(2):646-656 - PMID: 33347562 - PMCID: PMC7826252 - DOI: 10.1093/nar/gkaa1215

  • 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

  • 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

  • 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

  • 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

  • Efron PA, Darden DB, Wang Z, Nacionales DC, Lopez MC, Hawkins RB, Cox MC, Rincon JC, Ungaro R, Dirain ML, Ghita GL, Chen T, Billiar TR, Delano MJ, Leeuwenburgh C, Bihorac A, Brakenridge SC, Moore FA, Mohr AM, Tompkins RG, Brumback BA, Baker HV, Upchurch GR, Moldawer LL Transcriptomic responses from improved murine sepsis models can better mimic human surgical sepsis. FASEB J. 2021;35(2):e21156 - PMID: 33140449 - PMCID: PMC7855423 - DOI: 10.1096/fj.202002150R

  • 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

  • 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

  • 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

  • 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

  • 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

  • Zhou L, Ding D, Szostak JW The Virtual Circular Genome Model for Primordial RNA Replication. RNA. 2021;27(1):1-11 - PMID: 33028653 - PMCID: PMC7749632 - DOI: 10.1261/rna.077693.120

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • 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

  • Kurt IC, Zhou R, Iyer S, Garcia SP, Miller BR, Langner LM, Grünewald J, Joung JK CRISPR C-to-G base editors for inducing targeted DNA transversions in human cells. Nat Biotechnol. 2021;39(1):41-46 - PMID: 32690971 - PMCID: PMC7854778 - DOI: 10.1038/s41587-020-0609-x

  • Hu S, Vich Vila A, Gacesa R, Collij V, Stevens C, Fu JM, Wong I, Talkowski ME, Rivas MA, Imhann F, Bolte L, van Dullemen H, Dijkstra G, Visschedijk MC, Festen EA, Xavier RJ, Fu J, Daly MJ, Wijmenga C, Zhernakova A, Kurilshikov A, Weersma RK Whole exome sequencing analyses reveal gene-microbiota interactions in the context of IBD. Gut. 2021;70(2):285-296 - PMID: 32651235 - PMCID: PMC7815889 - DOI: 10.1136/gutjnl-2019-319706

  • 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

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

  • 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

  • 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

  • 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

  • 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

  • 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

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  • Xavier RJ, Rioux JD Genome-wide association studies: a new window into immune-mediated diseases. Nat Rev Immunol. 2008;8(8):631-43 - PMID: 18654571 - PMCID: PMC2750781 - DOI: 10.1038/nri2361

  • Xavier RJ, Rioux JD Genome-wide association studies: a new window into immune-mediated diseases. Nat Rev Immunol. 2008;8(8):631-43 - PMID: 18654571 - PMCID: PMC2750781 - DOI: 10.1038/nri2361

  • Labbé C, Goyette P, Lefebvre C, Stevens C, Green T, Tello-Ruiz MK, Cao Z, Landry AL, Stempak J, Annese V, Latiano A, Brant SR, Duerr RH, Taylor KD, Cho JH, Steinhart AH, Daly MJ, Silverberg MS, Xavier RJ, Rioux JD MAST3: a novel IBD risk factor that modulates TLR4 signaling. Genes Immun. 2008;9(7):602-12 - PMID: 18650832 - PMCID: PMC2574831 - DOI: 10.1038/gene.2008.57

  • Fujiki K, Duerr EM, Kikuchi H, Ng A, Xavier RJ, Mizukami Y, Imamura T, Kulke MH, Chung DC Hoxc6 is overexpressed in gastrointestinal carcinoids and interacts with JunD to regulate tumor growth. Gastroenterology. 2008;135(3):907-16, 916.e1-2 - PMID: 18655788 - PMCID: PMC3777410 - DOI: 10.1053/j.gastro.2008.06.034

  • Upadhyay G, Goessling W, North TE, Xavier R, Zon LI, Yajnik V Molecular association between beta-catenin degradation complex and Rac guanine exchange factor DOCK4 is essential for Wnt/beta-catenin signaling. Oncogene. 2008;27(44):5845-55 - PMID: 18641688 - PMCID: PMC4774646 - DOI: 10.1038/onc.2008.202

  • Friedman CS, O'Donnell MA, Legarda-Addison D, Ng A, Cárdenas WB, Yount JS, Moran TM, Basler CF, Komuro A, Horvath CM, Xavier R, Ting AT The tumour suppressor CYLD is a negative regulator of RIG-I-mediated antiviral response. EMBO Rep. 2008;9(9):930-6 - PMID: 18636086 - PMCID: PMC2529351 - DOI: 10.1038/embor.2008.136

  • Maheswaran S, Sequist LV, Nagrath S, Ulkus L, Brannigan B, Collura CV, Inserra E, Diederichs S, Iafrate AJ, Bell DW, Digumarthy S, Muzikansky A, Irimia D, Settleman J, Tompkins RG, Lynch TJ, Toner M, Haber DA Detection of mutations in EGFR in circulating lung-cancer cells. N Engl J Med. 2008;359(4):366-77 - PMID: 18596266 - PMCID: PMC3551471 - DOI: 10.1056/NEJMoa0800668

  • Adonizio A, Leal SM, Ausubel FM, Mathee K Attenuation of Pseudomonas aeruginosa virulence by medicinal plants in a Caenorhabditis elegans model system. J Med Microbiol. 2008;57(Pt 7):809-813 - PMID: 18566137 - DOI: 10.1099/jmm.0.47802-0

  • Shan L, He P, Li J, Heese A, Peck SC, Nürnberger T, Martin GB, Sheen J Bacterial effectors target the common signaling partner BAK1 to disrupt multiple MAMP receptor-signaling complexes and impede plant immunity. Cell Host Microbe. 2008;4(1):17-27 - PMID: 18621007 - PMCID: PMC2830012 - DOI: 10.1016/j.chom.2008.05.017

  • Maeder ML, Thibodeau-Beganny S, Osiak A, Wright DA, Anthony RM, Eichtinger M, Jiang T, Foley JE, Winfrey RJ, Townsend JA, Unger-Wallace E, Sander JD, Müller-Lerch F, Fu F, Pearlberg J, Göbel C, Dassie JP, Pruett-Miller SM, Porteus MH, Sgroi DC, Iafrate AJ, Dobbs D, McCray PB, Cathomen T, Voytas DF, Joung JK Rapid open-source engineering of customized zinc-finger nucleases for highly efficient gene modification. Mol Cell. 2008;31(2):294-301 - PMID: 18657511 - PMCID: PMC2535758 - DOI: 10.1016/j.molcel.2008.06.016

  • Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, , Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E, , , Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwilliam R, Tremelling M, Deloukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet. 2008;40(8):955-62 - PMID: 18587394 - PMCID: PMC2574810 - DOI: 10.1038/ng.175

  • Sena MJ, Utter GH, Cuschieri J, Maier RV, Tompkins RG, Harbrecht BG, Moore EE, O'Keefe GE Early supplemental parenteral nutrition is associated with increased infectious complications in critically ill trauma patients. J Am Coll Surg. 2008;207(4):459-67 - PMID: 18926446 - PMCID: PMC4002002 - DOI: 10.1016/j.jamcollsurg.2008.04.028

  • Ruvkun G Tiny RNA: Where do we come from? What are we? Where are we going?. Trends Plant Sci. 2008;13(7):313-6 - PMID: 18562240 - DOI: 10.1016/j.tplants.2008.05.005

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  • Lemaitre B, Ausubel FM Animal models for host-pathogen interactions. Curr Opin Microbiol. 2008;11(3):249-50 - PMID: 18539076 - DOI: 10.1016/j.mib.2008.05.002

  • Mansy SS, Schrum JP, Krishnamurthy M, Tobé S, Treco DA, Szostak JW Template-directed synthesis of a genetic polymer in a model protocell. Nature. 2008;454(7200):122-5 - PMID: 18528332 - PMCID: PMC2743009 - DOI: 10.1038/nature07018

  • Samuelson AV, Klimczak RR, Thompson DB, Carr CE, Ruvkun G Identification of Caenorhabditis elegans genes regulating longevity using enhanced RNAi-sensitive strains. Cold Spring Harb Symp Quant Biol. 2008;72:489-97 - PMID: 18419309 - DOI: 10.1101/sqb.2007.72.068

  • Ketteler R, Seed B Quantitation of autophagy by luciferase release assay. Autophagy. 2008;4(6):801-6 - PMID: 18641457 - PMCID: PMC2910585 - DOI: 10.4161/auto.6401

  • Tzika AA, Astrakas LG, Cao H, Mintzopoulos D, Zhang Q, Padfield K, Yu H, Mindrinos MN, Rahme LG, Tompkins RG Murine intramyocellular lipids quantified by NMR act as metabolic biomarkers in burn trauma. Int J Mol Med. 2008;21(6):825-32 - PMID: 18506378

  • Freeman RM, Wu M, Cordonnier-Pratt MM, Pratt LH, Gruber CE, Smith M, Lander ES, Stange-Thomann N, Lowe CJ, Gerhart J, Kirschner M cDNA sequences for transcription factors and signaling proteins of the hemichordate Saccoglossus kowalevskii: efficacy of the expressed sequence tag (EST) approach for evolutionary and developmental studies of a new organism. Biol Bull. 2008;214(3):284-302 - PMID: 18574105 - DOI: 10.2307/25470670

  • Denoux C, Galletti R, Mammarella N, Gopalan S, Werck D, De Lorenzo G, Ferrari S, Ausubel FM, Dewdney J Activation of defense response pathways by OGs and Flg22 elicitors in Arabidopsis seedlings. Mol Plant. 2008;1(3):423-45 - PMID: 19825551 - PMCID: PMC2954645 - DOI: 10.1093/mp/ssn019

  • Patel DS, Fang LL, Svy DK, Ruvkun G, Li W Genetic identification of HSD-1, a conserved steroidogenic enzyme that directs larval development in Caenorhabditis elegans. Development. 2008;135(13):2239-49 - PMID: 18495818 - DOI: 10.1242/dev.016972

  • Tamehiro N, Zhou S, Okuhira K, Benita Y, Brown CE, Zhuang DZ, Latz E, Hornemann T, von Eckardstein A, Xavier RJ, Freeman MW, Fitzgerald ML SPTLC1 binds ABCA1 to negatively regulate trafficking and cholesterol efflux activity of the transporter. Biochemistry. 2008;47(23):6138-47 - PMID: 18484747 - PMCID: PMC2504083 - DOI: 10.1021/bi800182t

  • Huett A, Xavier RJ Neither hide nor hair: the difficulty of identifying useful disease biomarkers. Gastroenterology. 2008;134(7):2164-8 - PMID: 18486617 - DOI: 10.1053/j.gastro.2008.04.013

  • Karve A, Rauh BL, Xia X, Kandasamy M, Meagher RB, Sheen J, Moore BD Expression and evolutionary features of the hexokinase gene family in Arabidopsis. Planta. 2008;228(3):411-25 - PMID: 18481082 - PMCID: PMC2953952 - DOI: 10.1007/s00425-008-0746-9

  • Müller B, Sheen J Cytokinin and auxin interaction in root stem-cell specification during early embryogenesis. Nature. 2008;453(7198):1094-7 - PMID: 18463635 - PMCID: PMC2601652 - DOI: 10.1038/nature06943

  • Simon DJ, Madison JM, Conery AL, Thompson-Peer KL, Soskis M, Ruvkun GB, Kaplan JM, Kim JK The microRNA miR-1 regulates a MEF-2-dependent retrograde signal at neuromuscular junctions. Cell. 2008;133(5):903-15 - PMID: 18510933 - PMCID: PMC2553566 - DOI: 10.1016/j.cell.2008.04.035

  • Ramirez CL, Foley JE, Wright DA, Müller-Lerch F, Rahman SH, Cornu TI, Winfrey RJ, Sander JD, Fu F, Townsend JA, Cathomen T, Voytas DF, Joung JK Unexpected failure rates for modular assembly of engineered zinc fingers. Nat Methods. 2008;5(5):374-5 - PMID: 18446154 - PMCID: PMC7880305 - DOI: 10.1038/nmeth0508-374

  • Cabral CB, Bullock KH, Bischoff DJ, Tompkins RG, Yu YM, Kelleher JK Estimating glutathione synthesis with deuterated water: a model for peptide biosynthesis. Anal Biochem. 2008;379(1):40-4 - PMID: 18486587 - PMCID: PMC4065382 - DOI: 10.1016/j.ab.2008.04.042

  • Gabel HW, Ruvkun G The exonuclease ERI-1 has a conserved dual role in 5.8S rRNA processing and RNAi. Nat Struct Mol Biol. 2008;15(5):531-3 - PMID: 18438419 - PMCID: PMC2910399 - DOI: 10.1038/nsmb.1411

  • Seed B, Xavier R Spinophilin and the immune synapse. J Cell Biol. 2008;181(2):181-3 - PMID: 18411314 - PMCID: PMC2315665 - DOI: 10.1083/jcb.200803120

  • Subtelny AO, Hartman MC, Szostak JW Ribosomal synthesis of N-methyl peptides. J Am Chem Soc. 2008;130(19):6131-6 - PMID: 18402453 - PMCID: PMC2728122 - DOI: 10.1021/ja710016v

  • Liberati NT, Urbach JM, Thurber TK, Wu G, Ausubel FM Comparing insertion libraries in two Pseudomonas aeruginosa strains to assess gene essentiality. Methods Mol Biol. 2008;416:153-69 - PMID: 18392966 - DOI: 10.1007/978-1-59745-321-9_10

  • Zhang Q, Ma B, Fischman AJ, Tompkins RG, Carter EA Increased uncoupling protein 1 mRNA expression in mice brown adipose tissue after burn injury. J Burn Care Res. 2008;29(2):358-62 - PMID: 18354294 - DOI: 10.1097/BCR.0b013e318166739c

  • Zhang Q, Carter EA, Ma B, Fischman AJ, Tompkins RG Burn-related metabolic and signaling changes in rat brain. J Burn Care Res. 2008;29(2):346-52 - PMID: 18354292 - DOI: 10.1097/BCR.0b013e3181667387

  • Ketteler R, Sun Z, Kovacs KF, He WW, Seed B A pathway sensor for genome-wide screens of intracellular proteolytic cleavage. Genome Biol. 2008;9(4):R64 - PMID: 18387192 - PMCID: PMC2643935 - DOI: 10.1186/gb-2008-9-4-r64

  • Russom A, Sethu P, Irimia D, Mindrinos MN, Calvano SE, Garcia I, Finnerty C, Tannahill C, Abouhamze A, Wilhelmy J, López MC, Baker HV, Herndon DN, Lowry SF, Maier RV, Davis RW, Moldawer LL, Tompkins RG, Toner M, Microfluidic leukocyte isolation for gene expression analysis in critically ill hospitalized patients. Clin Chem. 2008;54(5):891-900 - PMID: 18375483 - PMCID: PMC4011019 - DOI: 10.1373/clinchem.2007.099150

  • Powell JR, Ausubel FM Models of Caenorhabditis elegans infection by bacterial and fungal pathogens. Methods Mol Biol. 2008;415:403-27 - PMID: 18370168 - DOI: 10.1007/978-1-59745-570-1_24

  • Schöbel S, Neumann S, Hertweck M, Dislich B, Kuhn PH, Kremmer E, Seed B, Baumeister R, Haass C, Lichtenthaler SF A novel sorting nexin modulates endocytic trafficking and alpha-secretase cleavage of the amyloid precursor protein. J Biol Chem. 2008;283(21):14257-68 - PMID: 18353773 - DOI: 10.1074/jbc.M801531200

  • Pruett-Miller SM, Connelly JP, Maeder ML, Joung JK, Porteus MH Comparison of zinc finger nucleases for use in gene targeting in mammalian cells. Mol Ther. 2008;16(4):707-17 - PMID: 18334988 - DOI: 10.1038/mt.2008.20

  • Thibodeau-Beganny S, Joung JK Engineering Cys2His2 zinc finger domains using a bacterial cell-based two-hybrid selection system. Methods Mol Biol. 2008;408:317-34 - PMID: 18314590 - DOI: 10.1007/978-1-59745-547-3_17

  • Duerr EM, Mizukami Y, Ng A, Xavier RJ, Kikuchi H, Deshpande V, Warshaw AL, Glickman J, Kulke MH, Chung DC Defining molecular classifications and targets in gastroenteropancreatic neuroendocrine tumors through DNA microarray analysis. Endocr Relat Cancer. 2008;15(1):243-56 - PMID: 18310291 - DOI: 10.1677/ERC-07-0194

  • Sims KB, Pastores GM, Weinreb NJ, Barranger J, Rosenbloom BE, Packman S, Kaplan P, Mankin H, Xavier R, Angell J, Fitzpatrick MA, Rosenthal D Improvement of bone disease by imiglucerase (Cerezyme) therapy in patients with skeletal manifestations of type 1 Gaucher disease: results of a 48-month longitudinal cohort study. Clin Genet. 2008;73(5):430-40 - PMID: 18312448 - PMCID: PMC2440418 - DOI: 10.1111/j.1399-0004.2008.00978.x

  • Di Carlo D, Edd JF, Irimia D, Tompkins RG, Toner M Equilibrium separation and filtration of particles using differential inertial focusing. Anal Chem. 2008;80(6):2204-11 - PMID: 18275222 - DOI: 10.1021/ac702283m

  • Xavier RJ, Huett A, Rioux JD Autophagy as an important process in gut homeostasis and Crohn's disease pathogenesis. Gut. 2008;57(6):717-20 - PMID: 18272545 - PMCID: PMC2735854 - DOI: 10.1136/gut.2007.134254

  • Monnard PA, Szostak JW Metal-ion catalyzed polymerization in the eutectic phase in water-ice: a possible approach to template-directed RNA polymerization. J Inorg Biochem. 2008;102(5-6):1104-11 - PMID: 18329104 - DOI: 10.1016/j.jinorgbio.2008.01.026

  • Miyata S, Begun J, Troemel ER, Ausubel FM DAF-16-dependent suppression of immunity during reproduction in Caenorhabditis elegans. Genetics. 2008;178(2):903-18 - PMID: 18245330 - PMCID: PMC2248360 - DOI: 10.1534/genetics.107.083923

  • Toner M, Tompkins RG Invention, innovation, entrepreneurship in academic medical centers. Surgery. 2008;143(2):168-71 - PMID: 18242329 - PMCID: PMC2408552 - DOI: 10.1016/j.surg.2007.11.004

  • Stuart LM, Ezekowitz RA Phagocytosis and comparative innate immunity: learning on the fly. Nat Rev Immunol. 2008;8(2):131-41 - PMID: 18219310 - DOI: 10.1038/nri2240

  • Tzika AA, Mintzopoulos D, Padfield K, Wilhelmy J, Mindrinos MN, Yu H, Cao H, Zhang Q, Astrakas LG, Zhang J, Yu YM, Rahme LG, Tompkins RG Reduced rate of adenosine triphosphate synthesis by in vivo 31P nuclear magnetic resonance spectroscopy and downregulation of PGC-1beta in distal skeletal muscle following burn. Int J Mol Med. 2008;21(2):201-8 - PMID: 18204786

  • Sugimoto K, Ogawa A, Mizoguchi E, Shimomura Y, Andoh A, Bhan AK, Blumberg RS, Xavier RJ, Mizoguchi A IL-22 ameliorates intestinal inflammation in a mouse model of ulcerative colitis. J Clin Invest. 2008;118(2):534-44 - PMID: 18172556 - PMCID: PMC2157567 - DOI: 10.1172/JCI33194

  • Yoo SD, Cho YH, Tena G, Xiong Y, Sheen J Dual control of nuclear EIN3 by bifurcate MAPK cascades in C2H4 signalling. Nature. 2008;451(7180):789-95 - PMID: 18273012 - PMCID: PMC3488589 - DOI: 10.1038/nature06543

  • Gavi S, Qurashi S, Stuart LM, Lau R, Melendez MM, Mynarcik DC, McNurlan MA, Gelato MC Influence of age on the association of retinol-binding protein 4 with metabolic syndrome. Obesity (Silver Spring). 2008;16(4):893-5 - PMID: 18239568 - DOI: 10.1038/oby.2007.138

  • Goyette P, Lefebvre C, Ng A, Brant SR, Cho JH, Duerr RH, Silverberg MS, Taylor KD, Latiano A, Aumais G, Deslandres C, Jobin G, Annese V, Daly MJ, Xavier RJ, Rioux JD Gene-centric association mapping of chromosome 3p implicates MST1 in IBD pathogenesis. Mucosal Immunol. 2008;1(2):131-8 - PMID: 19079170 - PMCID: PMC4550306 - DOI: 10.1038/mi.2007.15

  • Yagi T, Giallourakis C, Mohanty S, Scheidig C, Shen J, Zheng H, Xavier RJ, Shaw AC Defective signal transduction in B lymphocytes lacking presenilin proteins. Proc Natl Acad Sci U S A. 2008;105(3):979-84 - PMID: 18195359 - PMCID: PMC2242696 - DOI: 10.1073/pnas.0707755105

  • Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, Xavier RJ, Lieberman J, Elledge SJ Identification of host proteins required for HIV infection through a functional genomic screen. Science. 2008;319(5865):921-6 - PMID: 18187620 - DOI: 10.1126/science.1152725

  • Pierce ML, Weston MD, Fritzsch B, Gabel HW, Ruvkun G, Soukup GA MicroRNA-183 family conservation and ciliated neurosensory organ expression. Evol Dev. 2008;10(1):106-13 - PMID: 18184361 - PMCID: PMC2637451 - DOI: 10.1111/j.1525-142X.2007.00217.x

  • Ip WK, Takahashi K, Moore KJ, Stuart LM, Ezekowitz RA Mannose-binding lectin enhances Toll-like receptors 2 and 6 signaling from the phagosome. J Exp Med. 2008;205(1):169-81 - PMID: 18180310 - PMCID: PMC2234382 - DOI: 10.1084/jem.20071164

  • Huett A, Xavier R SNPping away at the pathogenesis of Crohn's disease. Inflamm Bowel Dis. 2008;14(1):136-7 - PMID: 17941076 - DOI: 10.1002/ibd.20306

  • Apidianakis Y, Mindrinos MN, Xiao W, Tegos GP, Papisov MI, Hamblin MR, Davis RW, Tompkins RG, Rahme LG Involvement of skeletal muscle gene regulatory network in susceptibility to wound infection following trauma. PLoS One. 2007;2(12):e1356 - PMID: 18159239 - PMCID: PMC2131783 - DOI: 10.1371/journal.pone.0001356

  • Isenbarger TA, Finney M, Ríos-Velázquez C, Handelsman J, Ruvkun G Miniprimer PCR, a new lens for viewing the microbial world. Appl Environ Microbiol. 2008;74(3):840-9 - PMID: 18083877 - PMCID: PMC2227730 - DOI: 10.1128/AEM.01933-07

  • Greenhalgh DG, Saffle JR, Holmes JH, Gamelli RL, Palmieri TL, Horton JW, Tompkins RG, Traber DL, Mozingo DW, Deitch EA, Goodwin CW, Herndon DN, Gallagher JJ, Sanford AP, Jeng JC, Ahrenholz DH, Neely AN, O'Mara MS, Wolf SE, Purdue GF, Garner WL, Yowler CJ, Latenser BA, American Burn Association consensus conference to define sepsis and infection in burns. J Burn Care Res. 2007;28(6):776-90 - PMID: 17925660 - DOI: 10.1097/BCR.0b013e3181599bc9

  • Chen Z, Agnew JL, Cohen JD, He P, Shan L, Sheen J, Kunkel BN Pseudomonas syringae type III effector AvrRpt2 alters Arabidopsis thaliana auxin physiology. Proc Natl Acad Sci U S A. 2007;104(50):20131-6 - PMID: 18056646 - PMCID: PMC2148434 - DOI: 10.1073/pnas.0704901104

  • Nagrath S, Sequist LV, Maheswaran S, Bell DW, Irimia D, Ulkus L, Smith MR, Kwak EL, Digumarthy S, Muzikansky A, Ryan P, Balis UJ, Tompkins RG, Haber DA, Toner M Isolation of rare circulating tumour cells in cancer patients by microchip technology. Nature. 2007;450(7173):1235-9 - PMID: 18097410 - PMCID: PMC3090667 - DOI: 10.1038/nature06385

  • Leb VM, Jahn-Schmid B, Schmetterer KG, Kueng HJ, Haiderer D, Neunkirchner A, Fischer GF, Nissler K, Hartl A, Thalhamer J, Bohle B, Seed B, Pickl WF Molecular and functional analysis of the antigen receptor of Art v 1-specific helper T lymphocytes. J Allergy Clin Immunol. 2008;121(1):64-71 - PMID: 18037161 - DOI: 10.1016/j.jaci.2007.10.006

  • Cornu TI, Thibodeau-Beganny S, Guhl E, Alwin S, Eichtinger M, Joung JK, Joung JK, Cathomen T DNA-binding specificity is a major determinant of the activity and toxicity of zinc-finger nucleases. Mol Ther. 2008;16(2):352-8 - PMID: 18026168 - DOI: 10.1038/sj.mt.6300357

  • Parry DH, Xu J, Ruvkun G A whole-genome RNAi Screen for C. elegans miRNA pathway genes. Curr Biol. 2007;17(23):2013-22 - PMID: 18023351 - PMCID: PMC2211719 - DOI: 10.1016/j.cub.2007.10.058

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  • Yokoyama T, Banta S, Berthiaume F, Nagrath D, Tompkins RG, Yarmush ML Evolution of intrahepatic carbon, nitrogen, and energy metabolism in a D-galactosamine-induced rat liver failure model. Metab Eng. 2005;7(2):88-103 - PMID: 15781418 - DOI: 10.1016/j.ymben.2004.09.003

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  • Rolland F, Sheen J Sugar sensing and signalling networks in plants. Biochem Soc Trans. 2005;33(Pt 1):269-71 - PMID: 15667323 - DOI: 10.1042/BST0330269

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  • Irimia D, Tompkins RG, Toner M Single-cell chemical lysis in picoliter-scale closed volumes using a microfabricated device. Anal Chem. 2004;76(20):6137-43 - PMID: 15481964 - DOI: 10.1021/ac0497508

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  • Duda DG, Fukumura D, Munn LL, Booth MF, Brown EB, Huang P, Seed B, Jain RK Differential transplantability of tumor-associated stromal cells. Cancer Res. 2004;64(17):5920-4 - PMID: 15342367 - DOI: 10.1158/0008-5472.CAN-04-1268

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