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Hsu CT, Yuan YH, Lin YC, Lin S, Cheng QW, Wu FH, Sheen J, Shih MC, Lin CS

Efficient and Economical Targeted Insertion in Plant Genomes via Protoplast Regeneration.
CRISPR J. 2021;4(5):752-760 - PMID: 34569819 - PMCID: PMC9639242 - DOI: 10.1089/crispr.2021.0045

Charlesworth AG, Seroussi U, Lehrbach NJ, Renaud MS, Sundby AE, Molnar RI, Lao RX, Willis AR, Woock JR, Aber MJ, Diao AJ, Reinke AW, Ruvkun G, Claycomb JM

Two isoforms of the essential C. elegans Argonaute CSR-1 differentially regulate sperm and oocyte fertility.
Nucleic Acids Res. 2021;49(15):8836-8865 - PMID: 34329465 - PMCID: PMC8421154 - DOI: 10.1093/nar/gkab619

Pelka K, Hofree M, Chen JH, Sarkizova S, Pirl JD, Jorgji V, Bejnood A, Dionne D, Ge WH, Xu KH, Chao SX, Zollinger DR, Lieb DJ, Reeves JW, Fuhrman CA, Hoang ML, Delorey T, Nguyen LT, Waldman J, Klapholz M, Wakiro I, Cohen O, Albers J, Smillie CS, Cuoco MS, Wu J, Su MJ, Yeung J, Vijaykumar B, Magnuson AM, Asinovski N, Moll T, Goder-Reiser MN, Applebaum AS, Brais LK, DelloStritto LK, Denning SL, Phillips ST, Hill EK, Meehan JK, Frederick DT, Sharova T, Kanodia A, Todres EZ, Jané-Valbuena J, Biton M, Izar B, Lambden CD, Clancy TE, Bleday R, Melnitchouk N, Irani J, Kunitake H, Berger DL, Srivastava A, Hornick JL, Ogino S, Rotem A, Vigneau S, Johnson BE, Corcoran RB, Sharpe AH, Kuchroo VK, Ng K, Giannakis M, Nieman LT, Boland GM, Aguirre AJ, Anderson AC, Rozenblatt-Rosen O, Regev A, Hacohen N

Spatially organized multicellular immune hubs in human colorectal cancer.
Cell. 2021;184(18):4734-4752.e20 - PMID: 34450029 - PMCID: PMC8772395 - DOI: 10.1016/j.cell.2021.08.003

Subramanian S, Xavier RJ

Tuning in to inflammation: A path forward for precise and efficacious microbiome medicines?
Med (N Y). 2021;2(8):892-894 - PMID: 35590164 - DOI: 10.1016/j.medj.2021.07.006

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 - DOI: 10.1038/s41467-021-25213-2

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
Total: 2489