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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 - DOI: 10.1016/j.chom.2021.07.011
Tak YE, Horng JE, Perry NT, Schultz HT, Iyer S, Yao Q, Zou LS, Aryee MJ, Pinello L, Joung JK

Augmenting and directing long-range CRISPR-mediated activation in human cells.

Nat Methods. 2021;18(9):1075-1081 - PMID: 34354266 - PMCID: PMC8446310 - DOI: 10.1038/s41592-021-01224-1
Li L, Liu KH, Sheen J

Dynamic Nutrient Signaling Networks in Plants.

Annu Rev Cell Dev Biol. 2021;37:341-367 - PMID: 34351784 - PMCID: PMC8497281 - DOI: 10.1146/annurev-cellbio-010521-015047
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 - DOI: 10.1016/j.chom.2021.06.019
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;122(4):529-539 - 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;207(1):101-109 - PMID: 34135065 - PMCID: PMC8674371 - 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;40(2):189-193 - 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 - PMCID: PMC9153265 - 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 - PMCID: PMC9469728 - 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 - PMCID: PMC11617329 - 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
Total: 2459