Publications for All Faculty

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Datta S, Seed B

Influence of multiplicative stochastic variation on translational elongation rates.

PLoS One. 2018;13(1):e0191152 - PMID: 29351322 - PMCID: PMC5774726 - DOI: 10.1371/journal.pone.0191152
Visschedijk MC, Spekhorst LM, Cheng SC, van Loo ES, Jansen BHD, Blokzijl T, Kil H, de Jong DJ, Pierik M, Maljaars JPWJ, van der Woude CJ, van Bodegraven AA, Oldenburg B, Löwenberg M, Nieuwenhuijs VB, Imhann F, van Sommeren S, Alberts R, Xavier RJ, Dijkstra G, Faber KN, Aldaz CM, Weersma RK, Festen EAM

Genomic and expression analyses identify a disease modifying variant for fibrostenotic Crohn's disease.

J Crohns Colitis. 2018;12(5):582-588 - PMID: 29361163 - DOI: 10.1093/ecco-jcc/jjy001
Todd ZR, Fahrenbach AC, Magnani CJ, Ranjan S, Björkbom A, Szostak JW, Sasselov DD

Solvated-electron production using cyanocuprates is compatible with the UV-environment on a Hadean-Archaean Earth.

Chem Commun (Camb). 2018;54(9):1121-1124 - PMID: 29334083 - PMCID: PMC9631354 - DOI: 10.1039/c7cc07748c
Schirmer M, Franzosa EA, Lloyd-Price J, McIver LJ, Schwager R, Poon TW, Ananthakrishnan AN, Andrews E, Barron G, Lake K, Prasad M, Sauk J, Stevens B, Wilson RG, Braun J, Denson LA, Kugathasan S, McGovern DPB, Vlamakis H, Xavier RJ, Huttenhower C

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.

Nat Microbiol. 2018;3(3):337-346 - PMID: 29311644 - PMCID: PMC6131705 - DOI: 10.1038/s41564-017-0089-z
Dunbar CE, High KA, Joung JK, Kohn DB, Ozawa K, Sadelain M

Gene therapy comes of age.

Science. 2018;359(6372):ePub - PMID: 29326244 - DOI: 10.1126/science.aan4672
Tam CP, Zhou L, Fahrenbach AC, Zhang W, Walton T, Szostak JW

Synthesis of a nonhydrolyzable nucleotide phosphoroimidazolide analogue that catalyzes nonenzymatic RNA primer extension.

J Am Chem Soc. 2018;140(2):783-792 - PMID: 29251930 - PMCID: PMC6326531 - DOI: 10.1021/jacs.7b11623
Graham DB, Lefkovith A, Deelen P, de Klein N, Varma M, Boroughs A, Desch AN, Ng ACY, Guzman G, Schenone M, Petersen CP, Bhan AK, Rivas MA, Daly MJ, Carr SA, Wijmenga C, Xavier RJ

TMEM258 Is a Component of the Oligosaccharyltransferase Complex Controlling ER Stress and Intestinal Inflammation

Cell Rep. 2016;17(11):2955-2965 - PMID: 27974209 - PMCID: PMC5661940 - DOI: 10.1016/j.celrep.2016.11.042
Rogers KW, Lord ND, Gagnon JA, Pauli A, Zimmerman S, Aksel DC, Reyon D, Tsai SQ, Joung JK, Schier AF

Nodal patterning without Lefty inhibitory feedback is functional but fragile.

Elife. 2017;6:ePub - PMID: 29215332 - PMCID: PMC5720593 - DOI: 10.7554/eLife.28785
Hall AB, Yassour M, Sauk J, Garner A, Jiang X, Arthur T, Lagoudas GK, Vatanen T, Fornelos N, Wilson R, Bertha M, Cohen M, Garber J, Khalili H, Gevers D, Ananthakrishnan AN, Kugathasan S, Lander ES, Blainey P, Vlamakis H, Xavier RJ, Huttenhower C

A novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients.

Genome Med. 2017;9(1):103 - PMID: 29183332 - PMCID: PMC5704459 - DOI: 10.1186/s13073-017-0490-5
Li Z, Zhang D, Xiong X, Yan B, Xie W, Sheen J, Li JF

A potent Cas9-derived gene activator for plant and mammalian cells.

Nat Plants. 2017;3(12):930-936 - PMID: 29158545 - PMCID: PMC5894343 - DOI: 10.1038/s41477-017-0046-0
Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y, Tirosh I, Beyaz S, Dionne D, Zhang M, Raychowdhury R, Garrett WS, Rozenblatt-Rosen O, Shi HN, Yilmaz O, Xavier RJ, Regev A

A single-cell survey of the small intestinal epithelium

Nature. 2017;:ePub
Borren NZ, Conway G, Garber JJ, Khalili H, Budree S, Mallick H, Yajnik V, Xavier RJ, Ananthakrishnan AN

Difference in clinical course, genetics, and the microbiome between familial and sporadic inflammatory bowel diseases.

J Crohns Colitis. 2018;12(5):525-531 - PMID: 29145572 - PMCID: PMC6018966 - DOI: 10.1093/ecco-jcc/jjx154
Kazis LE, Sheridan RL, Shapiro GD, Lee AF, Liang MH, Ryan CM, Schneider JC, Lydon M, Soley-Bori M, Sonis LA, Dore EC, Palmieri T, Herndon D, Meyer W, Warner P, Kagan R, Stoddard FJ, Murphy M, Tompkins RG

Development of Clinical Process Measures for Pediatric Burn Care: Understanding Variation in Practice Patterns.

J Trauma Acute Care Surg. 2018;84(4):620-627 - PMID: 29140950 - DOI: 10.1097/TA.0000000000001737
Lassen KG, Xavier RJ

Mechanisms and Function of Autophagy in Intestinal Disease.

Autophagy. 2018;14(2):0 - PMID: 29130415 - PMCID: PMC5902220 - DOI: 10.1080/15548627.2017.1389358
Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y, Tirosh I, Beyaz S, Dionne D, Zhang M, Raychowdhury R, Garrett WS, Rozenblatt-Rosen O, Shi HN, Yilmaz O, Xavier RJ, Regev A

A single-cell survey of the small intestinal epithelium.

Nature. 2017;551(7680):333-339 - PMID: 29144463 - PMCID: PMC6022292 - DOI: 10.1038/nature24489
Haber AL, Biton M, Rogel N, Herbst RH, Shekhar K, Smillie C, Burgin G, Delorey TM, Howitt MR, Katz Y, Tirosh I, Beyaz S, Dionne D, Zhang M, Raychowdhury R, Garrett WS, Rozenblatt-Rosen O, Shi HN, Yilmaz O, Xavier RJ, Regev A

A single-cell survey of the small intestinal epithelium.

Nature. 2017;551(7680):333-339 - PMID: 29144463 - PMCID: PMC6022292 - DOI: 10.1038/nature24489
Giurgiu C, Li L, O'Flaherty DK, Tam CP, Szostak JW

A Mechanistic Explanation for the Regioselectivity of Nonenzymatic RNA Primer Extension.

J Am Chem Soc. 2017;139(46):16741-16747 - PMID: 29112424 - PMCID: PMC6326530 - DOI: 10.1021/jacs.7b08784
Jia TZ, Fahrenbach AC, Kamat NP, Adamala KP, Szostak JW

Retraction: Oligoarginine peptides slow strand annealing and assist non-enzymatic RNA replication.

Nat Chem. 2017;9(12):1286 - PMID: 29168488 - PMCID: PMC7412977 - DOI: 10.1038/nchem.2885
Ni J, Shen TD, Chen EZ, Bittinger K, Bailey A, Roggiani M, Sirota-Madi A, Friedman ES, Chau L, Lin A, Nissim I, Scott J, Lauder A, Hoffmann C, Rivas G, Albenberg L, Baldassano RN, Braun J, Xavier RJ, Clish CB, Yudkoff M, Li H, Goulian M, Bushman FD, Lewis JD, Wu GD

A role for bacterial urease in gut dysbiosis and Crohn's disease.

Sci Transl Med. 2017;9(416):ePub - PMID: 29141885 - PMCID: PMC5808452 - DOI: 10.1126/scitranslmed.aah6888
Haney CH, Wiesmann CL, Shapiro LR, O'Sullivan LR, Khorasani S, Melnyk RA, Xiao L, Han J, Bush J, Carrillo J, Pierce NE, Ausubel FM

Rhizosphere-associated Pseudomonas induce systemic resistance to herbivores at the cost of susceptibility to bacterial pathogens.

Mol Ecol. 2018;27(8):1833-1847 - PMID: 29087012 - DOI: 10.1111/mec.14400
Tak YE, Kleinstiver BP, Nuñez JK, Hsu JY, Horng JE, Gong J, Weissman JS, Joung JK

Inducible and multiplex gene regulation using CRISPR-Cpf1-based transcription factors.

Nat Methods. 2017;14(12):1163-1166 - PMID: 29083402 - PMCID: PMC5909187 - DOI: 10.1038/nmeth.4483
Avital G, Avraham R, Fan A, Hashimshony T, Hung DT, Yanai I

scDual-Seq: mapping the gene regulatory program of Salmonella infection by host and pathogen single-cell RNA-sequencing.

Genome Biol. 2017;18(1):200 - PMID: 29073931 - PMCID: PMC5658913 - DOI: 10.1186/s13059-017-1340-x
Murano T, Najibi M, Paulus GLC, Adiliaghdam F, Valencia-Guerrero A, Selig M, Wang X, Jeffrey K, Xavier RJ, Lassen KG, Irazoqui JE

Transcription factor TFEB cell-autonomously modulates susceptibility to intestinal epithelial cell injury in vivo.

Sci Rep. 2017;7(1):13938 - PMID: 29066772 - PMCID: PMC5655326 - DOI: 10.1038/s41598-017-14370-4
Walton T, Szostak JW

A kinetic model of nonenzymatic RNA polymerization by cytidine-5'-phosphoro-2-aminoimidazolide.

Biochemistry. 2017;56(43):5739-5747 - PMID: 29022704 - PMCID: PMC6340129 - DOI: 10.1021/acs.biochem.7b00792
Li Y, Lv M, Su C, Long S, Zhang W, Conway KL, Li W, Xavier RJ, Shi HN

p40 (phox) -Deficient Mice Exhibit Impaired Bacterial Clearance and Enhanced Pro-inflammatory Responses during Salmonella enterica serovar Typhimurium Infection.

Front Immunol. 2017;8:1270 - PMID: 29062317 - PMCID: PMC5640886 - DOI: 10.3389/fimmu.2017.01270
Total: 2466