Publications for All Faculty

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Slyper M, Porter CBM, Ashenberg O, Waldman J, Drokhlyansky E, Wakiro I, Smillie C, Smith-Rosario G, Wu J, Dionne D, Vigneau S, Jané-Valbuena J, Tickle TL, Napolitano S, Su MJ, Patel AG, Karlstrom A, Gritsch S, Nomura M, Waghray A, Gohil SH, Tsankov AM, Jerby-Arnon L, Cohen O, Klughammer J, Rosen Y, Gould J, Nguyen L, Hofree M, Tramontozzi PJ, Li B, Wu CJ, Izar B, Haq R, Hodi FS, Yoon CH, Hata AN, Baker SJ, Suvà ML, Bueno R, Stover EH, Clay MR, Dyer MA, Collins NB, Matulonis UA, Wagle N, Johnson BE, Rotem A, Rozenblatt-Rosen O, Regev A

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors.
Nat Med. 2020;26(5):792-802 - PMID: 32405060 - PMCID: PMC7220853 - DOI: 10.1038/s41591-020-0844-1

Duzdevich D, Carr CE, Szostak JW

Deep sequencing of non-enzymatic RNA primer extension.
Nucleic Acids Res. 2020;48(12):e70 - PMID: 32427335 - PMCID: PMC7337528 - DOI: 10.1093/nar/gkaa400

Ernst CM, Braxton JR, Rodriguez-Osorio CA, Zagieboylo AP, Li L, Pironti A, Manson AL, Nair AV, Benson M, Cummins K, Clatworthy AE, Earl AM, Cosimi LA, Hung DT

Adaptive evolution of virulence and persistence in carbapenem-resistant Klebsiella pneumoniae.
Nat Med. 2020;26(5):705-711 - PMID: 32284589 - PMCID: PMC9194776 - DOI: 10.1038/s41591-020-0825-4

Todd ZR, Fahrenbach AC, Ranjan S, Magnani CJ, Szostak JW, Sasselov DD

Ultraviolet-Driven Deamination of Cytidine Ribonucleotides Under Planetary Conditions.
Astrobiology. 2020;20(7):878-888 - PMID: 32267736 - PMCID: PMC9634989 - DOI: 10.1089/ast.2019.2182

Ackerman CM, Myhrvold C, Thakku SG, Freije CA, Metsky HC, Yang DK, Ye SH, Boehm CK, Kosoko-Thoroddsen TF, Kehe J, Nguyen TG, Carter A, Kulesa A, Barnes JR, Dugan VG, Hung DT, Blainey PC, Sabeti PC

Massively multiplexed nucleic acid detection with Cas13.
Nature. 2020;582(7811):277-282 - PMID: 32349121 - PMCID: PMC7332423 - DOI: 10.1038/s41586-020-2279-8

Lelyveld VS, Zhang W, Szostak JW

Synthesis of phosphoramidate-linked DNA by a modified DNA polymerase.
Proc Natl Acad Sci U S A. 2020;117(13):7276-7283 - PMID: 32188786 - PMCID: PMC7132125 - DOI: 10.1073/pnas.1922400117

Borren NZ, Plichta D, Joshi AD, Bonilla G, Peng V, Colizzo FP, Luther J, Khalili H, Garber JJ, van der Woude CJ, Sadreyev R, Vlamakis H, Xavier RJ, Ananthakrishnan AN

Alterations in Fecal Microbiomes and Serum Metabolomes of Fatigued Patients With Quiescent Inflammatory Bowel Diseases.
Clin Gastroenterol Hepatol. 2021;19(3):519-527.e5 - PMID: 32184182 - DOI: 10.1016/j.cgh.2020.03.013

Frydman GH, Tessier SN, Wong KHK, Vanderburg CR, Fox JG, Toner M, Tompkins RG, Irimia D

Megakaryocytes contain extranuclear histones and may be a source of platelet-associated histones during sepsis.
Sci Rep. 2020;10(1):4621 - PMID: 32165642 - PMCID: PMC7067782 - DOI: 10.1038/s41598-020-61309-3

Netea MG, Domínguez-Andrés J, Barreiro LB, Chavakis T, Divangahi M, Fuchs E, Joosten LAB, van der Meer JWM, Mhlanga MM, Mulder WJM, Riksen NP, Schlitzer A, Schultze JL, Stabell Benn C, Sun JC, Xavier RJ, Latz E

Defining trained immunity and its role in health and disease.
Nat Rev Immunol. 2020;20(6):375-388 - PMID: 32132681 - PMCID: PMC7186935 - DOI: 10.1038/s41577-020-0285-6

Fischer SEJ, Ruvkun G

Caenorhabditis elegans ADAR editing and the ERI-6/7/MOV10 RNAi pathway silence endogenous viral elements and LTR retrotransposons.
Proc Natl Acad Sci U S A. 2020;117(11):5987-5996 - PMID: 32123111 - PMCID: PMC7084138 - DOI: 10.1073/pnas.1919028117

Walton T, DasGupta S, Duzdevich D, Oh SS, Szostak JW

In vitro selection of ribozyme ligases that use prebiotically plausible 2-aminoimidazole-activated substrates.
Proc Natl Acad Sci U S A. 2020;117(11):5741-5748 - PMID: 32123094 - PMCID: PMC7084097 - DOI: 10.1073/pnas.1914367117

Graham DB, Xavier RJ

Pathway paradigms revealed from the genetics of inflammatory bowel disease.
Nature. 2020;578(7796):527-539 - PMID: 32103191 - PMCID: PMC7871366 - DOI: 10.1038/s41586-020-2025-2

Quinn RA, Melnik AV, Vrbanac A, Fu T, Patras KA, Christy MP, Bodai Z, Belda-Ferre P, Tripathi A, Chung LK, Downes M, Welch RD, Quinn M, Humphrey G, Panitchpakdi M, Weldon KC, Aksenov A, da Silva R, Avila-Pacheco J, Clish C, Bae S, Mallick H, Franzosa EA, Lloyd-Price J, Bussell R, Thron T, Nelson AT, Wang M, Leszczynski E, Vargas F, Gauglitz JM, Meehan MJ, Gentry E, Arthur TD, Komor AC, Poulsen O, Boland BS, Chang JT, Sandborn WJ, Lim M, Garg N, Lumeng JC, Xavier RJ, Kazmierczak BI, Jain R, Egan M, Rhee KE, Ferguson D, Raffatellu M, Vlamakis H, Haddad GG, Siegel D, Huttenhower C, Mazmanian SK, Evans RM, Nizet V, Knight R, Dorrestein PC

Global chemical effects of the microbiome include new bile-acid conjugations.
Nature. 2020;579(7797):123-129 - PMID: 32103176 - PMCID: PMC7252668 - DOI: 10.1038/s41586-020-2047-9

Reyes M, Filbin MR, Bhattacharyya RP, Billman K, Eisenhaure T, Hung DT, Levy BD, Baron RM, Blainey PC, Goldberg MB, Hacohen N

An immune-cell signature of bacterial sepsis.
Nat Med. 2020;26(3):333-340 - PMID: 32066974 - PMCID: PMC7235950 - DOI: 10.1038/s41591-020-0752-4

Liu KH, Diener A, Lin Z, Liu C, Sheen J

Primary nitrate responses via calcium signalling and diverse protein phosphorylation.
J Exp Bot. 2020;71(15):4428-4441 - PMID: 31985788 - PMCID: PMC7382375 - DOI: 10.1093/jxb/eraa047

Ennamorati M, Vasudevan C, Clerkin K, Halvorsen S, Verma S, Ibrahim S, Prosper S, Porter C, Yeliseyev V, Kim M, Gardecki J, Sassi S, Tearney G, Cherayil BJ, Bry L, Seed B, Jain N

Intestinal microbes influence development of thymic lymphocytes in early life.
Proc Natl Acad Sci U S A. 2020;117(5):2570-2578 - PMID: 31964813 - PMCID: PMC7007548 - DOI: 10.1073/pnas.1915047117

Fornelos N, Franzosa EA, Bishai J, Annand JW, Oka A, Lloyd-Price J, Arthur TD, Garner A, Avila-Pacheco J, Haiser HJ, Tolonen AC, Porter JA, Clish CB, Sartor RB, Huttenhower C, Vlamakis H, Xavier RJ

Growth effects of N-acylethanolamines on gut bacteria reflect altered bacterial abundances in inflammatory bowel disease.
Nat Microbiol. 2020;5(3):486-497 - PMID: 31959971 - PMCID: PMC7047597 - DOI: 10.1038/s41564-019-0655-7

Brady KJS, Ni P, Grant GG, Thorpe CR, Nadler D, Lee A, Shapiro G, Kogosov A, Palmieri TL, Tompkins RG, Schneider JC, Kazis LE, Ryan CM

Translation and Cross-Cultural Validation of the English Young Adult Burn Outcome Questionnaire (YABOQ) in Spanish.
J Burn Care Res. 2020;41(3):640-646 - PMID: 31930334 - PMCID: PMC9834989 - DOI: 10.1093/jbcr/iraa011

Kim SC, Zhou L, Zhang W, O'Flaherty DK, Rondo-Brovetto V, Szostak JW

A model for the emergence of RNA from a prebiotically plausible mixture of ribonucleotides, arabinonucleotides and 2'-deoxynucleotides.
J Am Chem Soc. 2020;142(5):2317-2326 - PMID: 31913615 - PMCID: PMC7577264 - DOI: 10.1021/jacs.9b11239

Chizzolini F, Passalacqua LFM, Oumais M, Dingilian AI, Szostak JW, Lupták A

Large phenotypic enhancement of structured random RNA pools.
J Am Chem Soc. 2020;142(4):1941-1951 - PMID: 31887027 - DOI: 10.1021/jacs.9b11396

Betin V, Penaranda C, Bandyopadhyay N, Yang R, Abitua A, Bhattacharyya RP, Fan A, Avraham R, Livny J, Shoresh N, Hung DT

Hybridization-based capture of pathogen mRNA enables paired host-pathogen transcriptional analysis.
Sci Rep. 2019;9(1):19244 - PMID: 31848386 - PMCID: PMC6917760 - DOI: 10.1038/s41598-019-55633-6

Dreckmann SC, Amini-Nik S, Tompkins RG, Vojvodic M, Jeschke MG

Genome-wide comparisons of gene expression in adult versus elderly burn patients.
PLoS One. 2019;14(12):e0226425 - PMID: 31834907 - PMCID: PMC6910697 - DOI: 10.1371/journal.pone.0226425

Jiang X, Hall AB, Xavier RJ, Alm EJ

Comprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools.
PLoS One. 2019;14(12):e0223680 - PMID: 31830054 - PMCID: PMC6907783 - DOI: 10.1371/journal.pone.0223680

Vasquez-Rifo A, Veksler-Lublinsky I, Cheng Z, Ausubel FM, Ambros V

The Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans.
Genome Biol. 2019;20(1):270 - PMID: 31823826 - PMCID: PMC6902481 - DOI: 10.1186/s13059-019-1890-1

Bhattacharyya RP, Bandyopadhyay N, Ma P, Son SS, Liu J, He LL, Wu L, Khafizov R, Boykin R, Cerqueira GC, Pironti A, Rudy RF, Patel MM, Yang R, Skerry J, Nazarian E, Musser KA, Taylor J, Pierce VM, Earl AM, Cosimi LA, Shoresh N, Beechem J, Livny J, Hung DT

Simultaneous detection of genotype and phenotype enables rapid and accurate antibiotic susceptibility determination.
Nat Med. 2019;25(12):1858-1864 - PMID: 31768064 - PMCID: PMC6930013 - DOI: 10.1038/s41591-019-0650-9
Total: 2489