Publications for All Faculty

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Tanoue T, Morita S, Plichta DR, Skelly AN, Suda W, Sugiura Y, Narushima S, Vlamakis H, Motoo I, Sugita K, Shiota A, Takeshita K, Yasuma-Mitobe K, Riethmacher D, Kaisho T, Norman JM, Mucida D, Suematsu M, Yaguchi T, Bucci V, Inoue T, Kawakami Y, Olle B, Roberts B, Hattori M, Xavier RJ, Atarashi K, Honda K

A defined commensal consortium elicits CD8 T cells and anti-cancer immunity.

Nature. 2019;565(7741):600-605 - PMID: 30675064 - DOI: 10.1038/s41586-019-0878-z
Strecker J, Jones S, Koopal B, Schmid-Burgk J, Zetsche B, Gao L, Makarova KS, Koonin EV, Zhang F

Engineering of CRISPR-Cas12b for human genome editing.

Nat Commun. 2019;10(1):212 - PMID: 30670702 - PMCID: PMC6342934 - DOI: 10.1038/s41467-018-08224-4
Lavoie S, Conway KL, Lassen KG, Jijon HB, Pan H, Chun E, Michaud M, Lang JK, Gallini Comeau CA, Dreyfuss JM, Glickman JN, Vlamakis H, Ananthakrishnan A, Kostic A, Garrett WS, Xavier RJ

The Crohn's disease polymorphism, ATG16L1 T300A, alters the gut microbiota and enhances the local Th1/Th17 response.

Elife. 2019;8:ePub - PMID: 30666959 - PMCID: PMC6342529 - DOI: 10.7554/eLife.39982
Jia M, Liu X, Xue H, Wu Y, Shi L, Wang R, Chen Y, Xu N, Zhao J, Shao J, Qi Y, An L, Sheen J, Yu F

Noncanonical ATG8-ABS3 interaction controls senescence in plants.

Nat Plants. 2019;5(2):212-224 - PMID: 30664732 - PMCID: PMC6368864 - DOI: 10.1038/s41477-018-0348-x
Nakazawa H, Ikeda K, Shinozaki S, Yasuhara S, Yu YM, Martyn JAJ, Tompkins RG, Yorozu T, Inoue S, Kaneki M

Coenzyme Q10 protects against burn-induced mitochondrial dysfunction and impaired insulin signaling in mouse skeletal muscle.

FEBS Open Bio. 2019;9(2):348-363 - PMID: 30761259 - PMCID: PMC6356165 - DOI: 10.1002/2211-5463.12580
Xiaofang Jiang, A. Brantley Hall, Timothy D. Arthur, Damian R. Plichta, Christian T. Covington, Mathilde Poyet, Jessica Crothers, Peter L. Moses, Andrew C. Tolonen, Hera Vlamakis, Eric J. Alm, Ramnik J. Xavier

Invertible promoters mediate bacterial phase variation, antibiotic resistance, and host adaptation in the gut

Science. 2019;363, Issue 6423:181-187 - PMID: 30630933 - PMCID: PMC6543533 - DOI: 10.1126/science.aau5238
Wang A, Chan Miller C, Szostak JW

Core-Shell Modeling of Light Scattering by Vesicles: Effect of Size, Contents, and Lamellarity.

Biophys J. 2019;116(4):659-669 - PMID: 30686489 - PMCID: PMC6382849 - DOI: 10.1016/j.bpj.2019.01.006
Haberman Y, Karns R, Dexheimer PJ, Schirmer M, Somekh J, Jurickova I, Braun T, Novak E, Bauman L, Collins MH, Mo A, Rosen MJ, Bonkowski E, Gotman N, Marquis A, Nistel M, Rufo PA, Baker SS, Sauer CG, Markowitz J, Pfefferkorn MD, Rosh JR, Boyle BM, Mack DR, Baldassano RN, Shah S, Leleiko NS, Heyman MB, Grifiths AM, Patel AS, Noe JD, Aronow BJ, Kugathasan S, Walters TD, Gibson G, Thomas SD, Mollen K, Shen-Orr S, Huttenhower C, Xavier RJ, Hyams JS, Denson LA

Ulcerative colitis mucosal transcriptomes reveal mitochondriopathy and personalized mechanisms underlying disease severity and treatment response.

Nat Commun. 2019;10(1):38 - PMID: 30604764 - PMCID: PMC6318335 - DOI: 10.1038/s41467-018-07841-3
Walton T, Pazienza L, Szostak JW

Template-directed catalysis of a multi-step reaction pathway for nonenzymatic RNA primer extension.

Biochemistry. 2019;58(6):755-762 - PMID: 30566332 - PMCID: PMC7547881 - DOI: 10.1021/acs.biochem.8b01156
Vatanen T, Plichta DR, Somani J, Münch PC, Arthur TD, Hall AB, Rudolf S, Oakeley EJ, Ke X, Young RA, Haiser HJ, Kolde R, Yassour M, Luopajärvi K, Siljander H, Virtanen SM, Ilonen J, Uibo R, Tillmann V, Mokurov S, Dorshakova N, Porter JA, McHardy AC, Lähdesmäki H, Vlamakis H, Huttenhower C, Knip M, Xavier RJ

Genomic variation and strain-specific functional adaptation in the human gut microbiome during early life.

Nat Microbiol. 2019;4(3):470-479 - PMID: 30559407 - PMCID: PMC6384140 - DOI: 10.1038/s41564-018-0321-5
Lee H, Jun YS, Cha OK, Sheen J

Mitogen-activated protein kinases MPK3 and MPK6 are required for stem cell maintenance in the Arabidopsis shoot apical meristem.

Plant Cell Rep. 2019;38(3):311-319 - PMID: 30552452 - PMCID: PMC6573032 - DOI: 10.1007/s00299-018-2367-5
Haberman Y, Schirmer M, Dexheimer PJ, Karns R, Braun T, Kim MO, Walters TD, Baldassano RN, Noe JD, Rosh J, Markowitz J, Crandall WV, Mack DR, Griffiths AM, Heyman MB, Baker SS, Kellermayer R, Moulton D, Patel AS, Gulati AS, Steiner SJ, LeLeiko N, Otley A, Oliva-Hemker M, Ziring D, Kirschner BS, Keljo DJ, Guthery SL, Cohen SA, Snapper S, Evans J, Dubinsky M, Aronow B, Hyams JS, Kugathasan S, Huttenhower C, Xavier RJ, Denson LA

Age-of-diagnosis dependent ileal immune intensification and reduced alpha-defensin in older versus younger pediatric Crohn Disease patients despite already established dysbiosis.

Mucosal Immunol. 2019;12(2):491-502 - PMID: 30542108 - PMCID: PMC6375755 - DOI: 10.1038/s41385-018-0114-4
Franzosa EA, Sirota-Madi A, Avila-Pacheco J, Fornelos N, Haiser HJ, Reinker S, Vatanen T, Hall AB, Mallick H, McIver LJ, Sauk JS, Wilson RG, Stevens BW, Scott JM, Pierce K, Deik AA, Bullock K, Imhann F, Porter JA, Zhernakova A, Fu J, Weersma RK, Wijmenga C, Clish CB, Vlamakis H, Huttenhower C, Xavier RJ

Gut microbiome structure and metabolic activity in inflammatory bowel disease.

Nat Microbiol. 2019;4(2):293-305 - PMID: 30531976 - PMCID: PMC6342642 - DOI: 10.1038/s41564-018-0306-4
Kim SC, O'Flaherty DK, Zhou L, Lelyveld VS, Szostak JW

Inosine, but none of the 8-oxo-purines, is a plausible component of a primordial version of RNA.

Proc Natl Acad Sci U S A. 2018;115(52):13318-13323 - PMID: 30509978 - PMCID: PMC6310819 - DOI: 10.1073/pnas.1814367115
Hsu JY, Fulco CP, Cole MA, Canver MC, Pellin D, Sher F, Farouni R, Clement K, Guo JA, Biasco L, Orkin SH, Engreitz JM, Lander ES, Joung JK, Bauer DE, Pinello L

CRISPR-SURF: discovering regulatory elements by deconvolution of CRISPR tiling screen data.

Nat Methods. 2018;15(12):992-993 - PMID: 30504875 - PMCID: PMC6620603 - DOI: 10.1038/s41592-018-0225-6
Vich Vila A, Imhann F, Collij V, Jankipersadsing SA, Gurry T, Mujagic Z, Kurilshikov A, Bonder MJ, Jiang X, Tigchelaar EF, Dekens J, Peters V, Voskuil MD, Visschedijk MC, van Dullemen HM, Keszthelyi D, Swertz MA, Franke L, Alberts R, Festen EAM, Dijkstra G, Masclee AAM, Hofker MH, Xavier RJ, Alm EJ, Fu J, Wijmenga C, Jonkers DMAE, Zhernakova A, Weersma RK

Gut microbiota composition and functional changes in inflammatory bowel disease and irritable bowel syndrome.

Sci Transl Med. 2018;10(472):ePub - PMID: 30567928 - DOI: 10.1126/scitranslmed.aap8914
Chen GH, Liu MJ, Xiong Y, Sheen J, Wu SH

TOR and RPS6 transmit light signals to enhance protein translation in deetiolating Arabidopsis seedlings.

Proc Natl Acad Sci U S A. 2018;115(50):12823-12828 - PMID: 30482859 - PMCID: PMC6294885 - DOI: 10.1073/pnas.1809526115
Tan JMJ, Mellouk N, Osborne SE, Ammendolia DA, Dyer DN, Li R, Brunen D, van Rijn JM, Huang J, Czuczman MA, Cemma MA, Won AM, Yip CM, Xavier RJ, MacDuff DA, Reggiori F, Debnath J, Yoshimori T, Kim PK, Fairn GD, Coyaud E, Raught B, Muise AM, Higgins DE, Brumell JH

An ATG16L1-dependent pathway promotes plasma membrane repair and limits Listeria monocytogenes cell-to-cell spread.

Nat Microbiol. 2018;3(12):1472-1485 - PMID: 30478389 - DOI: 10.1038/s41564-018-0293-5
Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, Zhang M, Tirosh I, Dionne D, Nguyen LT, Xifaras ME, Shalek AK, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz OH, Regev A, Xavier RJ

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.

Cell. 2018;175(5):1307-1320.e22 - PMID: 30392957 - PMCID: PMC6239889 - DOI: 10.1016/j.cell.2018.10.008
Uniken Venema WT, Voskuil MD, Vich Vila A, van der Vries G, Jansen BH, Jabri B, Faber KN, Dijkstra G, Xavier RJ, Wijmenga C, Graham DB, Weersma RK, Festen EA

Single-cell RNA Sequencing of Blood and Ileal T cells From Patients With Crohn's Disease Reveals Tissue-specific Characteristics and Drug Targets.

Gastroenterology. 2019;156(3):812-815.e22 - PMID: 30391472 - PMCID: PMC6759855 - DOI: 10.1053/j.gastro.2018.10.046
Biton M, Haber AL, Rogel N, Burgin G, Beyaz S, Schnell A, Ashenberg O, Su CW, Smillie C, Shekhar K, Chen Z, Wu C, Ordovas-Montanes J, Alvarez D, Herbst RH, Zhang M, Tirosh I, Dionne D, Nguyen LT, Xifaras ME, Shalek AK, von Andrian UH, Graham DB, Rozenblatt-Rosen O, Shi HN, Kuchroo V, Yilmaz OH, Regev A, Xavier RJ

T Helper Cell Cytokines Modulate Intestinal Stem Cell Renewal and Differentiation.

Cell. 2018;175(5):1307-1320.e22 - PMID: 30392957 - PMCID: PMC6239889 - DOI: 10.1016/j.cell.2018.10.008
Stewart CJ, Ajami NJ, O'Brien JL, Hutchinson DS, Smith DP, Wong MC, Ross MC, Lloyd RE, Doddapaneni H, Metcalf GA, Muzny D, Gibbs RA, Vatanen T, Huttenhower C, Xavier RJ, Rewers M, Hagopian W, Toppari J, Ziegler AG, She JX, Akolkar B, Lernmark A, Hyoty H, Vehik K, Krischer JP, Petrosino JF

Temporal development of the gut microbiome in early childhood from the TEDDY study.

Nature. 2018;562(7728):583-588 - PMID: 30356187 - PMCID: PMC6415775 - DOI: 10.1038/s41586-018-0617-x
Vatanen T, Franzosa EA, Schwager R, Tripathi S, Arthur TD, Vehik K, Lernmark Å, Hagopian WA, Rewers MJ, She JX, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Stewart CJ, Ajami NJ, Petrosino JF, Gevers D, Lähdesmäki H, Vlamakis H, Huttenhower C, Xavier RJ

The human gut microbiome in early-onset type 1 diabetes from the TEDDY study.

Nature. 2018;562(7728):589-594 - PMID: 30356183 - PMCID: PMC6296767 - DOI: 10.1038/s41586-018-0620-2
Lin XX, Sen I, Janssens GE, Zhou X, Fonslow BR, Edgar D, Stroustrup N, Swoboda P, Yates JR, Ruvkun G, Riedel CG

DAF-16/FOXO and HLH-30/TFEB function as combinatorial transcription factors to promote stress resistance and longevity.

Nat Commun. 2018;9(1):4400 - PMID: 30353013 - PMCID: PMC6199276 - DOI: 10.1038/s41467-018-06624-0
Graham DB, Luo C, O'Connell DJ, Lefkovith A, Brown EM, Yassour M, Varma M, Abelin JG, Conway KL, Jasso GJ, Matar CG, Carr SA, Xavier RJ

Antigen discovery and specification of immunodominance hierarchies for MHCII-restricted epitopes.

Nat Med. 2018;24(11):1762-1772 - PMID: 30349087 - PMCID: PMC6312190 - DOI: 10.1038/s41591-018-0203-7
Total: 2466