Publications for All Faculty

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Verma MS, Fink MJ, Salmon GL, Fornelos N, Ohara TE, Ryu SH, Vlamakis H, Xavier RJ, Stappenbeck TS, Whitesides GM

A common mechanism links activities of butyrate in the colon.
ACS Chem Biol. 2018;13(5):1291-1298 - PMID: 29584955 - DOI: 10.1021/acschembio.8b00073

Mojarro A, Hachey J, Ruvkun G, Zuber MT, Carr CE

CarrierSeq: a sequence analysis workflow for low-input nanopore sequencing.
BMC Bioinformatics. 2018;19(1):108 - PMID: 29587645 - PMCID: PMC5872496 - DOI: 10.1186/s12859-018-2124-3

Clatworthy AE, Romano KP, Hung DT

Whole-organism phenotypic screening for anti-infectives promoting host health.
Nat Chem Biol. 2018;14(4):331-341 - PMID: 29556098 - PMCID: PMC9843822 - DOI: 10.1038/s41589-018-0018-3

Johns NI, Gomes ALC, Yim SS, Yang A, Blazejewski T, Smillie CS, Smith MB, Alm EJ, Kosuri S, Wang HH

Metagenomic mining of regulatory elements enables programmable species-selective gene expression.
Nat Methods. 2018;15(5):323-329 - PMID: 30052624 - PMCID: PMC6065261 - DOI: 10.1038/nmeth.4633

Haller S, Franchet A, Hakkim A, Chen J, Drenkard E, Yu S, Schirmeier S, Li Z, Martins N, Ausubel FM, Liégeois S, Ferrandon D

Quorum-sensing regulator RhlR but not its autoinducer RhlI enablesPseudomonasto evade opsonization.
EMBO Rep. 2018;19(5):ePub - PMID: 29523648 - PMCID: PMC5934776 - DOI: 10.15252/embr.201744880

Jin L, Kamat NP, Jena S, Szostak JW

Fatty Acid/Phospholipid Blended Membranes: A Potential Intermediate State in Protocellular Evolution.
Small. 2018;14(15):e1704077 - PMID: 29479815 - PMCID: PMC6278924 - DOI: 10.1002/smll.201704077

Yuen GJ, Ausubel FM

Both live and dead Enterococci activate Caenorhabditis elegans host defense via immune and stress pathways.
Virulence. 2018;9(1):0 - PMID: 29436902 - PMCID: PMC5955442 - DOI: 10.1080/21505594.2018.1438025

Jin L, Engelhart AE, Adamala KP, Szostak JW

Preparation, Purification, and Use of Fatty Acid-containing Liposomes.
J Vis Exp. 2018;(132):ePub - PMID: 29553563 - PMCID: PMC5912384 - DOI: 10.3791/57324

Wellington S, Hung DT

The expanding diversity of Mycobacterium tuberculosis drug targets.
ACS Infect Dis. 2018;4(5):696-714 - PMID: 29412643 - DOI: 10.1021/acsinfecdis.7b00255

Zhang W, Tam CP, Zhou L, Oh SS, Wang J, Szostak JW

A structural rationale for the enhanced catalysis of nonenzymatic RNA primer extension by a downstream oligonucleotide.
J Am Chem Soc. 2018;140(8):2829-2840 - PMID: 29411978 - PMCID: PMC6326529 - DOI: 10.1021/jacs.7b11750

Mohanan V, Nakata T, Desch AN, Lévesque C, Boroughs A, Guzman G, Cao Z, Creasey E, Yao J, Boucher G, Charron G, Bhan AK, Schenone M, Carr SA, Reinecker HC, Daly MJ, Rioux JD, Lassen KG, Xavier RJ

C1orf106 is a colitis risk gene that regulates stability of epithelial adherens junctions.
Science. 2018;359(6380):1161-1166 - PMID: 29420262 - PMCID: PMC6008784 - DOI: 10.1126/science.aan0814

Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, Sadowsky MJ, Allegretti JR, Smith MB, Xavier RJ, Alm EJ

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation.
Cell Host Microbe. 2018;23(2):229-240.e5 - PMID: 29447696 - PMCID: PMC8318347 - DOI: 10.1016/j.chom.2018.01.003

Smillie CS, Sauk J, Gevers D, Friedman J, Sung J, Youngster I, Hohmann EL, Staley C, Khoruts A, Sadowsky MJ, Allegretti JR, Smith MB, Xavier RJ, Alm EJ

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation.
Cell Host Microbe. 2018;23(2):229-240.e5 - PMID: 29447696 - PMCID: PMC8318347 - DOI: 10.1016/j.chom.2018.01.003

Kolde R, Franzosa EA, Rahnavard G, Hall AB, Vlamakis H, Stevens C, Daly MJ, Xavier RJ, Huttenhower C

Host genetic variation and its microbiome interactions within the Human Microbiome Project.
Genome Med. 2018;10(1):6 - PMID: 29378630 - PMCID: PMC5789541 - DOI: 10.1186/s13073-018-0515-8

Luther J, Gala M, Patel SJ, Dave M, Borren N, Xavier RJ, Ananthakrishnan AN

Loss of Response to Anti-Tumor Necrosis Factor Alpha Therapy in Crohn's Disease Is Not Associated with Emergence of Novel Inflammatory Pathways.
Dig Dis Sci. 2018;63(3):738-745 - PMID: 29372477 - PMCID: PMC6152907 - DOI: 10.1007/s10620-018-4932-8

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
Total: 2481