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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

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 - PMCID: PMC9634692 - DOI: 10.1021/acs.biochem.0c00943

Todd ZR, Szostak JW, Sasselov DD

Shielding from UV Photodamage: Implications for Surficial Origins of Life Chemistry on the Early Earth.
ACS Earth Space Chem. 2021;5(2):239-246 - PMID: 36317066 - PMCID: PMC9616438 - DOI: 10.1021/acsearthspacechem.0c00270

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
Total: 2498