Value of the history and stool occult blood test in selection of patients for upper endoscopy in Zimbabwe.

Xavier RJ, Stein CM, Kiire CF, Arrow J, Kitai I
East Afr Med J. 1992;69(5):268-71 - PMID: 1644046

Peroxynitrite-induced rat colitis--a new model of colonic inflammation.

Rachmilewitz D, Stamler JS, Karmeli F, Mullins ME, Singel DJ, Loscalzo J, Xavier RJ, Podolsky DK
Gastroenterology. 1993;105(6):1681-8 - PMID: 8253344

Nonreceptor tyrosine kinases in aggregation-mediated cell activation.

Seed B, Kolanus W, Romeo C, Xavier R
Adv Exp Med Biol. 1995;365:111-9 - PMID: 7887297

Malignant epithelioid hemangioendothelioma of the tibia associated with a bone infarct in a patient who had Gaucher disease. A case report.

Pins MR, Mankin HJ, Xavier RJ, Rosenthal DI, Dickersin GR, Rosenberg AE
J Bone Joint Surg Am. 1995;77(5):777-81 - PMID: 7744904

Enzyme replacement therapy for Gaucher disease: skeletal responses to macrophage-targeted glucocerebrosidase.

Rosenthal DI, Doppelt SH, Mankin HJ, Dambrosia JM, Xavier RJ, McKusick KA, Rosen BR, Baker J, Niklason LT, Hill SC
Pediatrics. 1995;96(4 Pt 1):629-37 - PMID: 7567322

Atheroembolic renal failure after invasive procedures. Natural history based on 52 histologically proven cases.

Thadhani RI, Camargo CA, Xavier RJ, Fang LS, Bazari H
Medicine (Baltimore). 1995;74(6):350-8 - PMID: 7500898

Clustered syk tyrosine kinase domains trigger phagocytosis.

Greenberg S, Chang P, Wang DC, Xavier R, Seed B
Proc Natl Acad Sci U S A. 1996;93(3):1103-7 - PMID: 8577722 - PMCID: PMC40038

Transgenic expression of tpr-met oncogene leads to development of mammary hyperplasia and tumors.

Liang TJ, Reid AE, Xavier R, Cardiff RD, Wang TC
J Clin Invest. 1996;97(12):2872-7 - PMID: 8675700 - PMCID: PMC507382 - DOI: 10.1172/JCI118744

Paracoccidioidomycosis of bones and joints. A clinical, radiologic, and pathologic study of 9 cases.

Amstalden EM, Xavier R, Kattapuram SV, Bertolo MB, Swartz MN, Rosenberg AE
Medicine (Baltimore). 1996;75(4):213-25 - PMID: 8699961

SEK1/MKK4 is required for maintenance of a normal peripheral lymphoid compartment but not for lymphocyte development.

Swat W, Fujikawa K, Ganiatsas S, Yang D, Xavier RJ, Harris NL, Davidson L, Ferrini R, Davis RJ, Labow MA, Flavell RA, Zon LI, Alt FW
Immunity. 1998;8(5):625-34 - PMID: 9620683

Membrane compartmentation is required for efficient T cell activation.

Xavier R, Brennan T, Li Q, McCormack C, Seed B
Immunity. 1998;8(6):723-32 - PMID: 9655486

Tumor induction of VEGF promoter activity in stromal cells.

Fukumura D, Xavier R, Sugiura T, Chen Y, Park EC, Lu N, Selig M, Nielsen G, Taksir T, Jain RK, Seed B
Cell. 1998;94(6):715-25 - PMID: 9753319

Health information in the developing world.

Lown B, Bukachi F, Xavier R
Lancet. 1998;352 Suppl 2:SII34-8 - PMID: 9798645

Membrane compartmentation and the response to antigen.

Xavier R, Seed B
Curr Opin Immunol. 1999;11(3):265-9 - PMID: 10375560

A paradoxical reduction in susceptibility to colonic injury upon targeted transgenic ablation of goblet cells.

Itoh H, Beck PL, Inoue N, Xavier R, Podolsky DK
J Clin Invest. 1999;104(11):1539-47 - PMID: 10587517 - PMCID: PMC409855 - DOI: 10.1172/JCI6211

Fractalkine is an epithelial and endothelial cell-derived chemoattractant for intraepithelial lymphocytes in the small intestinal mucosa.

Muehlhoefer A, Saubermann LJ, Gu X, Luedtke-Heckenkamp K, Xavier R, Blumberg RS, Podolsky DK, MacDermott RP, Reinecker HC
J Immunol. 2000;164(6):3368-76 - PMID: 10706732

Microbiology. How to get along--friendly microbes in a hostile world.

Xavier RJ, Podolsky DK
Science. 2000;289(5484):1483-4 - PMID: 10991734

Mechanisms of NSAID-induced gastrointestinal injury defined using mutant mice.

Beck PL, Xavier R, Lu N, Nanda NN, Dinauer M, Podolsky DK, Seed B
Gastroenterology. 2000;119(3):699-705 - PMID: 10982764

TBX1 is responsible for cardiovascular defects in velo-cardio-facial/DiGeorge syndrome.

Merscher S, Funke B, Epstein JA, Heyer J, Puech A, Lu MM, Xavier RJ, Demay MB, Russell RG, Factor S, Tokooya K, Jore BS, Lopez M, Pandita RK, Lia M, Carrion D, Xu H, Schorle H, Kobler JB, Scambler P, Wynshaw-Boris A, Skoultchi AI, Morrow BE, Kucherlapati R
Cell. 2001;104(4):619-29 - PMID: 11239417

Gaucher disease. New approaches to an ancient disease.

Mankin HJ, Rosenthal DI, Xavier R
J Bone Joint Surg Am. 2001;83-A(5):748-62 - PMID: 11379747

Hepatitis C virus replication is directly inhibited by IFN-alpha in a full-length binary expression system.

Chung RT, He W, Saquib A, Contreras AM, Xavier RJ, Chawla A, Wang TC, Schmidt EV
Proc Natl Acad Sci U S A. 2001;98(17):9847-52 - PMID: 11493707 - PMCID: PMC55541 - DOI: 10.1073/pnas.171319698

L-histidine decarboxylase decreases its own transcription through downregulation of ERK activity.

Colucci R, Fleming JV, Xavier R, Wang TC
Am J Physiol Gastrointest Liver Physiol. 2001;281(4):G1081-91 - PMID: 11557529 - DOI: 10.1152/ajpgi.2001.281.4.G1081

Role of tumor necrosis factor receptor 2 (TNFR2) in colonic epithelial hyperplasia and chronic intestinal inflammation in mice.

Mizoguchi E, Mizoguchi A, Takedatsu H, Cario E, de Jong YP, Ooi CJ, Xavier RJ, Terhorst C, Podolsky DK, Bhan AK
Gastroenterology. 2002;122(1):134-44 - PMID: 11781288

Identification of a novel Ras-regulated proapoptotic pathway.

Khokhlatchev A, Rabizadeh S, Xavier R, Nedwidek M, Chen T, Zhang XF, Seed B, Avruch J
Curr Biol. 2002;12(4):253-65 - PMID: 11864565

Decreased bone density in splenectomized Gaucher patients receiving enzyme replacement therapy.

Schiffmann R, Mankin H, Dambrosia JM, Xavier RJ, Kreps C, Hill SC, Barton NW, Rosenthal DI
Blood Cells Mol Dis. 2002;28(2):288-96 - PMID: 12064924

Transforming growth factor-beta mediates intestinal healing and susceptibility to injury in vitro and in vivo through epithelial cells.

Beck PL, Rosenberg IM, Xavier RJ, Koh T, Wong JF, Podolsky DK
Am J Pathol. 2003;162(2):597-608 - PMID: 12547717 - PMCID: PMC1851153

Essential role for Vav1 in activation, but not development, of gammadelta T cells.

Swat W, Xavier R, Mizoguchi A, Mizoguchi E, Fredericks J, Fujikawa K, Bhan AK, Alt FW
Int Immunol. 2003;15(2):215-21 - PMID: 12578851

Colonic epithelial functional phenotype varies with type and phase of experimental colitis.

Mizoguchi E, Xavier RJ, Reinecker HC, Uchino H, Bhan AK, Podolsky DK, Mizoguchi A
Gastroenterology. 2003;125(1):148-61 - PMID: 12851880

Homer-3 regulates activation of serum response element in T cells via its EVH1 domain.

Ishiguro K, Xavier R
Blood. 2003;103(6):2248-56 - PMID: 14645007 - DOI: 10.1182/blood-2003-08-2671

Paradoxical roles of different nitric oxide synthase isoforms in colonic injury.

Beck PL, Xavier R, Wong J, Ezedi I, Mashimo H, Mizoguchi A, Mizoguchi E, Bhan AK, Podolsky DK
Am J Physiol Gastrointest Liver Physiol. 2004;286(1):G137-47 - PMID: 14665440 - DOI: 10.1152/ajpgi.00309.2003

Chemotherapy- and radiotherapy-induced intestinal damage is regulated by intestinal trefoil factor.

Beck PL, Wong JF, Li Y, Swaminathan S, Xavier RJ, Devaney KL, Podolsky DK
Gastroenterology. 2004;126(3):796-808 - PMID: 14988834

The scaffold protein CNK1 interacts with the tumor suppressor RASSF1A and augments RASSF1A-induced cell death.

Rabizadeh S, Xavier RJ, Ishiguro K, Bernabeortiz J, Lopez-Ilasaca M, Khokhlatchev A, Mollahan P, Pfeifer GP, Avruch J, Seed B
J Biol Chem. 2004;279(28):29247-54 - PMID: 15075335 - DOI: 10.1074/jbc.M401699200

Discs large (Dlg1) complexes in lymphocyte activation.

Xavier R, Rabizadeh S, Ishiguro K, Andre N, Ortiz JB, Wachtel H, Morris DG, Lopez-Ilasaca M, Shaw AC, Swat W, Seed B
J Cell Biol. 2004;166(2):173-8 - PMID: 15263016 - PMCID: PMC2172307 - DOI: 10.1083/jcb.200309044

Wave2 activates serum response element via its VCA region and functions downstream of Rac.

Ishiguro K, Cao Z, Ilasca ML, Ando T, Xavier R
Exp Cell Res. 2004;301(2):331-7 - PMID: 15530867 - DOI: 10.1016/j.yexcr.2004.09.003

Bioluminescence resonance energy transfer identify scaffold protein CNK1 interactions in intact cells.

Lopez-Ilasaca MA, Bernabe-Ortiz JC, Na SY, Dzau VJ, Xavier RJ
FEBS Lett. 2005;579(3):648-54 - PMID: 15670823 - DOI: 10.1016/j.febslet.2004.12.039

GRIM-19 interacts with nucleotide oligomerization domain 2 and serves as downstream effector of anti-bacterial function in intestinal epithelial cells.

Barnich N, Hisamatsu T, Aguirre JE, Xavier R, Reinecker HC, Podolsky DK
J Biol Chem. 2005;280(19):19021-6 - PMID: 15753091 - DOI: 10.1074/jbc.M413776200

Commensal flora: wolf in sheep's clothing.

Xavier R, Podolsky DK
Gastroenterology. 2005;128(4):1122-6 - PMID: 15825094

PDZ domains and the politics of polarity in lymphocytes.

Xavier R, Seed B
Immunity. 2005;22(6):655-6 - PMID: 15963778 - DOI: 10.1016/j.immuni.2005.06.003

Membrane recruitment of NOD2 in intestinal epithelial cells is essential for nuclear factor-{kappa}B activation in muramyl dipeptide recognition.

Barnich N, Aguirre JE, Reinecker HC, Xavier R, Podolsky DK
J Cell Biol. 2005;170(1):21-6 - PMID: 15998797 - PMCID: PMC2171381 - DOI: 10.1083/jcb.200502153

Large-scale screens for cDNAs with in vivo activity.

Ting A, Lichtenthaler S, Xavier R, Na SY, Rabizadeh S, Holmes T, Seed B
Novartis Found Symp. 2005;267:219-29; discussion 229-30 - PMID: 15999809

Nore1B regulates TCR signaling via Ras and Carma1.

Ishiguro K, Avruch J, Landry A, Qin S, Ando T, Goto H, Xavier R
Cell Signal. 2006;18(10):1647-54 - PMID: 16520020 - PMCID: PMC3204664 - DOI: 10.1016/j.cellsig.2006.01.015

CARMA1 is critical for the development of allergic airway inflammation in a murine model of asthma.

Medoff BD, Seed B, Jackobek R, Zora J, Yang Y, Luster AD, Xavier R
J Immunol. 2006;176(12):7272-7 - PMID: 16751370

Immune cell transcriptome datasets reveal novel leukocyte subset-specific genes and genes associated with allergic processes.

Liu SM, Xavier R, Good KL, Chtanova T, Newton R, Sisavanh M, Zimmer S, Deng C, Silva DG, Frost MJ, Tangye SG, Rolph MS, Mackay CR
J Allergy Clin Immunol. 2006;118(2):496-503 - PMID: 16890777 - DOI: 10.1016/j.jaci.2006.04.040

Isolation and analysis of lipid rafts in cell-cell interactions.

Landry A, Xavier R
Methods Mol Biol. 2006;341:251-82 - PMID: 16799204 - DOI: 10.1385/1-59745-113-4:251

Ca2+/calmodulin-dependent protein kinase II is a modulator of CARMA1-mediated NF-kappaB activation.

Ishiguro K, Green T, Rapley J, Wachtel H, Giallourakis C, Landry A, Cao Z, Lu N, Takafumi A, Goto H, Daly MJ, Xavier RJ
Mol Cell Biol. 2006;26(14):5497-508 - PMID: 16809782 - PMCID: PMC1592706 - DOI: 10.1128/MCB.02469-05

A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands.

Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R
Genome Res. 2006;16(8):1056-72 - PMID: 16825666 - PMCID: PMC1524865 - DOI: 10.1101/gr.5285206

Paeonol attenuates TNBS-induced colitis by inhibiting NF-kappaB and STAT1 transactivation.

Ishiguro K, Ando T, Maeda O, Hasegawa M, Kadomatsu K, Ohmiya N, Niwa Y, Xavier R, Goto H
Toxicol Appl Pharmacol. 2006;217(1):35-42 - PMID: 16928387 - DOI: 10.1016/j.taap.2006.07.002

Centaurin beta1 down-regulates nucleotide-binding oligomerization domains 1- and 2-dependent NF-kappaB activation.

Yamamoto-Furusho JK, Barnich N, Xavier R, Hisamatsu T, Podolsky DK
J Biol Chem. 2006;281(47):36060-70 - PMID: 17005562 - DOI: 10.1074/jbc.M602383200

Bcl10 is phosphorylated on Ser138 by Ca2+/calmodulin-dependent protein kinase II.

Ishiguro K, Ando T, Goto H, Xavier R
Mol Immunol. 2006;44(8):2095-100 - PMID: 17052756 - DOI: 10.1016/j.molimm.2006.09.012

ABCA3 inactivation in mice causes respiratory failure, loss of pulmonary surfactant, and depletion of lung phosphatidylglycerol.

Fitzgerald ML, Xavier R, Haley KJ, Welti R, Goss JL, Brown CE, Zhuang DZ, Bell SA, Lu N, McKee M, Seed B, Freeman MW
J Lipid Res. 2006;48(3):621-32 - PMID: 17142808 - DOI: 10.1194/jlr.M600449-JLR200

Vav proteins control MyD88-dependent oxidative burst.

Miletic AV, Graham DB, Montgrain V, Fujikawa K, Kloeppel T, Brim K, Weaver B, Schreiber R, Xavier R, Swat W
Blood. 2006;109(8):3360-8 - PMID: 17158234 - PMCID: PMC1852252 - DOI: 10.1182/blood-2006-07-033662

Discs-large homolog 1 regulates smooth muscle orientation in the mouse ureter.

Mahoney ZX, Sammut B, Xavier RJ, Cunningham J, Go G, Brim KL, Stappenbeck TS, Miner JH, Swat W
Proc Natl Acad Sci U S A. 2006;103(52):19872-7 - PMID: 17172448 - PMCID: PMC1750896 - DOI: 10.1073/pnas.0609326103

Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis.

Rioux JD, Xavier RJ, Taylor KD, Silverberg MS, Goyette P, Huett A, Green T, Kuballa P, Barmada MM, Datta LW, Shugart YY, Griffiths AM, Targan SR, Ippoliti AF, Bernard EJ, Mei L, Nicolae DL, Regueiro M, Schumm LP, Steinhart AH, Rotter JI, Duerr RH, Cho JH, Daly MJ, Brant SR
Nat Genet. 2007;39(5):596-604 - PMID: 17435756 - PMCID: PMC2757939 - DOI: 10.1038/ng2032

Molecular pathogenesis of inflammatory bowel disease: genotypes, phenotypes and personalized medicine.

Goyette P, Labbé C, Trinh TT, Xavier RJ, Rioux JD
Ann Med. 2007;39(3):177-99 - PMID: 17457716 - DOI: 10.1080/07853890701197615

Unravelling the pathogenesis of inflammatory bowel disease.

Xavier RJ, Podolsky DK
Nature. 2007;448(7152):427-34 - PMID: 17653185 - DOI: 10.1038/nature06005

DLGH1 is a negative regulator of T-lymphocyte proliferation.

Stephenson LM, Sammut B, Graham DB, Chan-Wang J, Brim KL, Huett AS, Miletic AV, Kloeppel T, Landry A, Xavier R, Swat W
Mol Cell Biol. 2007;27(21):7574-81 - PMID: 17724087 - PMCID: PMC2169038 - DOI: 10.1128/MCB.00439-07

DLG1 is an anchor for the E3 ligase MARCH2 at sites of cell-cell contact.

Cao Z, Huett A, Kuballa P, Giallourakis C, Xavier RJ
Cell Signal. 2007;20(1):73-82 - PMID: 17980554 - PMCID: PMC2257480 - DOI: 10.1016/j.cellsig.2007.08.019

Wiskott Aldrich syndrome protein (WASP) and N-WASP are critical for T cell development.

Cotta-de-Almeida V, Westerberg L, Maillard MH, Onaldi D, Wachtel H, Meelu P, Chung UI, Xavier R, Alt FW, Snapper SB
Proc Natl Acad Sci U S A. 2007;104(39):15424-9 - PMID: 17878299 - PMCID: PMC2000553 - DOI: 10.1073/pnas.0706881104

AKAP13, a RhoA GTPase-specific guanine exchange factor, is a novel regulator of TLR2 signaling.

Shibolet O, Giallourakis C, Rosenberg I, Mueller T, Xavier RJ, Podolsky DK
J Biol Chem. 2007;282(48):35308-17 - PMID: 17878165 - DOI: 10.1074/jbc.M704426200

SNPping away at the pathogenesis of Crohn's disease.

Huett A, Xavier R
Inflamm Bowel Dis. 2008;14(1):136-7 - PMID: 17941076 - DOI: 10.1002/ibd.20306

Identification of host proteins required for HIV infection through a functional genomic screen.

Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, Xavier RJ, Lieberman J, Elledge SJ
Science. 2008;319(5865):921-6 - PMID: 18187620 - DOI: 10.1126/science.1152725

Defective signal transduction in B lymphocytes lacking presenilin proteins.

Yagi T, Giallourakis C, Mohanty S, Scheidig C, Shen J, Zheng H, Xavier RJ, Shaw AC
Proc Natl Acad Sci U S A. 2008;105(3):979-84 - PMID: 18195359 - PMCID: PMC2242696 - DOI: 10.1073/pnas.0707755105

Gene-centric association mapping of chromosome 3p implicates MST1 in IBD pathogenesis.

Goyette P, Lefebvre C, Ng A, Brant SR, Cho JH, Duerr RH, Silverberg MS, Taylor KD, Latiano A, Aumais G, Deslandres C, Jobin G, Annese V, Daly MJ, Xavier RJ, Rioux JD
Mucosal Immunol. 2008;1(2):131-8 - PMID: 19079170 - PMCID: PMC4550306 - DOI: 10.1038/mi.2007.15

IL-22 ameliorates intestinal inflammation in a mouse model of ulcerative colitis.

Sugimoto K, Ogawa A, Mizoguchi E, Shimomura Y, Andoh A, Bhan AK, Blumberg RS, Xavier RJ, Mizoguchi A
J Clin Invest. 2008;118(2):534-44 - PMID: 18172556 - PMCID: PMC2157567 - DOI: 10.1172/JCI33194

Autophagy as an important process in gut homeostasis and Crohn's disease pathogenesis.

Xavier RJ, Huett A, Rioux JD
Gut. 2008;57(6):717-20 - PMID: 18272545 - PMCID: PMC2735854 - DOI: 10.1136/gut.2007.134254

Improvement of bone disease by imiglucerase (Cerezyme) therapy in patients with skeletal manifestations of type 1 Gaucher disease: results of a 48-month longitudinal cohort study.

Sims KB, Pastores GM, Weinreb NJ, Barranger J, Rosenbloom BE, Packman S, Kaplan P, Mankin H, Xavier R, Angell J, Fitzpatrick MA, Rosenthal D
Clin Genet. 2008;73(5):430-40 - PMID: 18312448 - PMCID: PMC2440418 - DOI: 10.1111/j.1399-0004.2008.00978.x

Defining molecular classifications and targets in gastroenteropancreatic neuroendocrine tumors through DNA microarray analysis.

Duerr EM, Mizukami Y, Ng A, Xavier RJ, Kikuchi H, Deshpande V, Warshaw AL, Glickman J, Kulke MH, Chung DC
Endocr Relat Cancer. 2008;15(1):243-56 - PMID: 18310291 - DOI: 10.1677/ERC-07-0194

Spinophilin and the immune synapse.

Seed B, Xavier R
J Cell Biol. 2008;181(2):181-3 - PMID: 18411314 - PMCID: PMC2315665 - DOI: 10.1083/jcb.200803120

Neither hide nor hair: the difficulty of identifying useful disease biomarkers.

Huett A, Xavier RJ
Gastroenterology. 2008;134(7):2164-8 - PMID: 18486617 - DOI: 10.1053/j.gastro.2008.04.013

SPTLC1 binds ABCA1 to negatively regulate trafficking and cholesterol efflux activity of the transporter.

Tamehiro N, Zhou S, Okuhira K, Benita Y, Brown CE, Zhuang DZ, Latz E, Hornemann T, von Eckardstein A, Xavier RJ, Freeman MW, Fitzgerald ML
Biochemistry. 2008;47(23):6138-47 - PMID: 18484747 - PMCID: PMC2504083 - DOI: 10.1021/bi800182t

Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease.

Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmada MM, Bitton A, Dassopoulos T, Datta LW, Green T, Griffiths AM, Kistner EO, Murtha MT, Regueiro MD, Rotter JI, Schumm LP, Steinhart AH, Targan SR, Xavier RJ, , Libioulle C, Sandor C, Lathrop M, Belaiche J, Dewit O, Gut I, Heath S, Laukens D, Mni M, Rutgeerts P, Van Gossum A, Zelenika D, Franchimont D, Hugot JP, de Vos M, Vermeire S, Louis E, , , Cardon LR, Anderson CA, Drummond H, Nimm ...
Nat Genet. 2008;40(8):955-62 - PMID: 18587394 - PMCID: PMC2574810 - DOI: 10.1038/ng.175

The tumour suppressor CYLD is a negative regulator of RIG-I-mediated antiviral response.

Friedman CS, O'Donnell MA, Legarda-Addison D, Ng A, Cárdenas WB, Yount JS, Moran TM, Basler CF, Komuro A, Horvath CM, Xavier R, Ting AT
EMBO Rep. 2008;9(9):930-6 - PMID: 18636086 - PMCID: PMC2529351 - DOI: 10.1038/embor.2008.136

Molecular association between beta-catenin degradation complex and Rac guanine exchange factor DOCK4 is essential for Wnt/beta-catenin signaling.

Upadhyay G, Goessling W, North TE, Xavier R, Zon LI, Yajnik V
Oncogene. 2008;27(44):5845-55 - PMID: 18641688 - PMCID: PMC4774646 - DOI: 10.1038/onc.2008.202

Hoxc6 is overexpressed in gastrointestinal carcinoids and interacts with JunD to regulate tumor growth.

Fujiki K, Duerr EM, Kikuchi H, Ng A, Xavier RJ, Mizukami Y, Imamura T, Kulke MH, Chung DC
Gastroenterology. 2008;135(3):907-16, 916.e1-2 - PMID: 18655788 - PMCID: PMC3777410 - DOI: 10.1053/j.gastro.2008.06.034

MAST3: a novel IBD risk factor that modulates TLR4 signaling.

Labbé C, Goyette P, Lefebvre C, Stevens C, Green T, Tello-Ruiz MK, Cao Z, Landry AL, Stempak J, Annese V, Latiano A, Brant SR, Duerr RH, Taylor KD, Cho JH, Steinhart AH, Daly MJ, Silverberg MS, Xavier RJ, Rioux JD
Genes Immun. 2008;9(7):602-12 - PMID: 18650832 - PMCID: PMC2574831 - DOI: 10.1038/gene.2008.57

Genome-wide association studies: a new window into immune-mediated diseases.

Xavier RJ, Rioux JD
Nat Rev Immunol. 2008;8(8):631-43 - PMID: 18654571 - PMCID: PMC2750781 - DOI: 10.1038/nri2361

Genome-wide association studies: a new window into immune-mediated diseases.

Xavier RJ, Rioux JD
Nat Rev Immunol. 2008;8(8):631-43 - PMID: 18654571 - PMCID: PMC2750781 - DOI: 10.1038/nri2361

CARMA3 mediates lysophosphatidic acid-stimulated cytokine secretion by bronchial epithelial cells.

Medoff BD, Landry AL, Wittbold KA, Sandall BP, Derby MC, Cao Z, Adams JC, Xavier RJ
Am J Respir Cell Mol Biol. 2008;40(3):286-94 - PMID: 18757306 - PMCID: PMC2645526 - DOI: 10.1165/rcmb.2008-0129OC

RNA interference screen for human genes associated with West Nile virus infection.

Krishnan MN, Ng A, Sukumaran B, Gilfoy FD, Uchil PD, Sultana H, Brass AL, Adametz R, Tsui M, Qian F, Montgomery RR, Lev S, Mason PW, Koski RA, Elledge SJ, Xavier RJ, Agaisse H, Fikrig E
Nature. 2008;455(7210):242-5 - PMID: 18690214 - PMCID: PMC3136529 - DOI: 10.1038/nature07207

Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease.

McCarroll SA, Huett A, Kuballa P, Chilewski SD, Landry A, Goyette P, Zody MC, Hall JL, Brant SR, Cho JH, Duerr RH, Silverberg MS, Taylor KD, Rioux JD, Altshuler D, Daly MJ, Xavier RJ
Nat Genet. 2008;40(9):1107-12 - PMID: 19165925 - PMCID: PMC2731799 - DOI: 10.1038/ng.215

A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells.

Cadwell K, Liu JY, Brown SL, Miyoshi H, Loh J, Lennerz JK, Kishi C, Kc W, Carrero JA, Hunt S, Stone CD, Brunt EM, Xavier RJ, Sleckman BP, Li E, Mizushima N, Stappenbeck TS, Virgin HW
Nature. 2008;456(7219):259-63 - PMID: 18849966 - PMCID: PMC2695978 - DOI: 10.1038/nature07416

Impaired autophagy of an intracellular pathogen induced by a Crohn's disease associated ATG16L1 variant.

Kuballa P, Huett A, Rioux JD, Daly MJ, Xavier RJ
PLoS One. 2008;3(10):e3391 - PMID: 18852889 - PMCID: PMC2566595 - DOI: 10.1371/journal.pone.0003391

Role for beta-catenin and HOX transcription factors in Caenorhabditis elegans and mammalian host epithelial-pathogen interactions.

Irazoqui JE, Ng A, Xavier RJ, Ausubel FM
Proc Natl Acad Sci U S A. 2008;105(45):17469-74 - PMID: 18981407 - PMCID: PMC2582251 - DOI: 10.1073/pnas.0809527105

Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway.

Hitomi J, Christofferson DE, Ng A, Yao J, Degterev A, Xavier RJ, Yuan J
Cell. 2008;135(7):1311-23 - PMID: 19109899 - PMCID: PMC2621059 - DOI: 10.1016/j.cell.2008.10.044

The Nore1B/Mst1 complex restrains antigen receptor-induced proliferation of naïve T cells.

Zhou D, Medoff BD, Chen L, Li L, Zhang XF, Praskova M, Liu M, Landry A, Blumberg RS, Boussiotis VA, Xavier R, Avruch J
Proc Natl Acad Sci U S A. 2008;105(51):20321-6 - PMID: 19073936 - PMCID: PMC2600581 - DOI: 10.1073/pnas.0810773105

Rassf family of tumor suppressor polypeptides.

Avruch J, Xavier R, Bardeesy N, Zhang XF, Praskova M, Zhou D, Xia F
J Biol Chem. 2008;284(17):11001-5 - PMID: 19091744 - PMCID: PMC2670104 - DOI: 10.1074/jbc.R800073200

Differential requirement for CARMA1 in agonist-selected T-cell development.

Medoff BD, Sandall BP, Landry A, Nagahama K, Mizoguchi A, Luster AD, Xavier RJ
Eur J Immunol. 2009;39(1):78-84 - PMID: 19130560 - PMCID: PMC2747028 - DOI: 10.1002/eji.200838734

On the level: IRGM gene function is all about expression.

Huett A, McCarroll SA, Daly MJ, Xavier RJ
Autophagy. 2009;5(1):96-9 - PMID: 19029815 - PMCID: PMC3204672

HIF-1alpha and HIF-2alpha have divergent roles in colon cancer.

Imamura T, Kikuchi H, Herraiz MT, Park DY, Mizukami Y, Mino-Kenduson M, Lynch MP, Rueda BR, Benita Y, Xavier RJ, Chung DC
Int J Cancer. 2009;124(4):763-71 - PMID: 19030186 - PMCID: PMC2682346 - DOI: 10.1002/ijc.24032

Genetic variants in the region harbouring IL2/IL21 associated with ulcerative colitis.

Festen EA, Goyette P, Scott R, Annese V, Zhernakova A, Lian J, Lefèbvre C, Brant SR, Cho JH, Silverberg MS, Taylor KD, de Jong DJ, Stokkers PC, Mcgovern D, Palmieri O, Achkar JP, Xavier RJ, Daly MJ, Duerr RH, Wijmenga C, Weersma RK, Rioux JD
Gut. 2009;58(6):799-804 - PMID: 19201773 - PMCID: PMC2757103 - DOI: 10.1136/gut.2008.166918

A functional genomic screen identifies cellular cofactors of hepatitis C virus replication.

Tai AW, Benita Y, Peng LF, Kim SS, Sakamoto N, Xavier RJ, Chung RT
Cell Host Microbe. 2009;5(3):298-307 - PMID: 19286138 - PMCID: PMC2756022 - DOI: 10.1016/j.chom.2009.02.001

Selective activation of nuclear factor kappa B in the cochlea by sensory and inflammatory stress.

Adams JC, Seed B, Lu N, Landry A, Xavier RJ
Neuroscience. 2009;160(2):530-9 - PMID: 19285117 - PMCID: PMC2673023 - DOI: 10.1016/j.neuroscience.2009.02.073

Selective activation of nuclear factor kappa B in the cochlea by sensory and inflammatory stress.

Adams JC, Seed B, Lu N, Landry A, Xavier RJ
Neuroscience. 2009;160(2):530-9 - PMID: 19285117 - PMCID: PMC2673023 - DOI: 10.1016/j.neuroscience.2009.02.073

A novel hybrid yeast-human network analysis reveals an essential role for FNBP1L in antibacterial autophagy.

Huett A, Ng A, Cao Z, Kuballa P, Komatsu M, Daly MJ, Podolsky DK, Xavier RJ
J Immunol. 2009;182(8):4917-30 - PMID: 19342671 - PMCID: PMC2752416 - DOI: 10.4049/jimmunol.0803050

The cytoskeletal scaffold Shank3 is recruited to pathogen-induced actin rearrangements.

Huett A, Leong JM, Podolsky DK, Xavier RJ
Exp Cell Res. 2009;315(12):2001-11 - PMID: 19371741 - PMCID: PMC2693461 - DOI: 10.1016/j.yexcr.2009.04.003

An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia.

Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung DC, Xavier RJ
Nucleic Acids Res. 2009;37(14):4587-602 - PMID: 19491311 - PMCID: PMC2724271 - DOI: 10.1093/nar/gkp425

Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions.

Raychaudhuri S, Plenge RM, Rossin EJ, Ng AC, , Purcell SM, Sklar P, Scolnick EM, Xavier RJ, Altshuler D, Daly MJ
PLoS Genet. 2009;5(6):e1000534 - PMID: 19557189 - PMCID: PMC2694358 - DOI: 10.1371/journal.pgen.1000534

Identification of Atg5-dependent transcriptional changes and increases in mitochondrial mass in Atg5-deficient T lymphocytes.

Stephenson LM, Miller BC, Ng A, Eisenberg J, Zhao Z, Cadwell K, Graham DB, Mizushima NN, Xavier R, Virgin HW, Swat W
Autophagy. 2009;5(5):625-35 - PMID: 19276668 - PMCID: PMC3737142

Building complex biological networks based upon model organisms: mapping the human autophagy interactome via a hybrid yeast-human protein interaction network.

Huett A, Xavier R
Autophagy. 2009;5(6):884-6 - PMID: 19535904

A genome-wide genetic screen for host factors required for hepatitis C virus propagation.

Li Q, Brass AL, Ng A, Hu Z, Xavier RJ, Liang TJ, Elledge SJ
Proc Natl Acad Sci U S A. 2009;106(38):16410-5 - PMID: 19717417 - PMCID: PMC2752535 - DOI: 10.1073/pnas.0907439106

Crohn's disease-associated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly.

Lapaquette P, Glasser AL, Huett A, Xavier RJ, Darfeuille-Michaud A
Cell Microbiol. 2009;12(1):99-113 - PMID: 19747213 - PMCID: PMC3743084 - DOI: 10.1111/j.1462-5822.2009.01381.x

Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43.

Maslowski KM, Vieira AT, Ng A, Kranich J, Sierro F, Yu D, Schilter HC, Rolph MS, Mackay F, Artis D, Xavier RJ, Teixeira MM, Mackay CR
Nature. 2009;461(7268):1282-6 - PMID: 19865172 - PMCID: PMC3256734 - DOI: 10.1038/nature08530

Autophagy, immunity and human disease.

Heath RJ, Xavier RJ
Curr Opin Gastroenterol. 2009;25(6):512-20 - PMID: 19826372 - PMCID: PMC2849745 - DOI: 10.1097/MOG.0b013e32833104f1

Common variants at five new loci associated with early-onset inflammatory bowel disease.

Imielinski M, Baldassano RN, Griffiths A, Russell RK, Annese V, Dubinsky M, Kugathasan S, Bradfield JP, Walters TD, Sleiman P, Kim CE, Muise A, Wang K, Glessner JT, Saeed S, Zhang H, Frackelton EC, Hou C, Flory JH, Otieno G, Chiavacci RM, Grundmeier R, Castro M, Latiano A, Dallapiccola B, Stempak J, Abrams DJ, Taylor K, McGovern D, , Silber G, Wrobel I, Quiros A, , Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmuda MM, Bitton A, Dasso ...
Nat Genet. 2009;41(12):1335-40 - PMID: 19915574 - PMCID: PMC3267927 - DOI: 10.1038/ng.489

The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus.

Brass AL, Huang IC, Benita Y, John SP, Krishnan MN, Feeley EM, Ryan BJ, Weyer JL, van der Weyden L, Fikrig E, Adams DJ, Xavier RJ, Farzan M, Elledge SJ
Cell. 2009;139(7):1243-54 - PMID: 20064371 - PMCID: PMC2824905 - DOI: 10.1016/j.cell.2009.12.017

Autophagy at the gut interface: mucosal responses to stress and the consequences for inflammatory bowel diseases.

Huett A, Xavier RJ
Inflamm Bowel Dis. 2010;16(1):152-74 - PMID: 19575363 - PMCID: PMC3954538 - DOI: 10.1002/ibd.20991

Genome-wide association identifies multiple ulcerative colitis susceptibility loci.

McGovern DP, Gardet A, Törkvist L, Goyette P, Essers J, Taylor KD, Neale BM, Ong RT, Lagacé C, Li C, Green T, Stevens CR, Beauchamp C, Fleshner PR, Carlson M, D'Amato M, Halfvarson J, Hibberd ML, Lördal M, Padyukov L, Andriulli A, Colombo E, Latiano A, Palmieri O, Bernard EJ, Deslandres C, Hommes DW, de Jong DJ, Stokkers PC, Weersma RK, , Sharma Y, Silverberg MS, Cho JH, Wu J, Roeder K, Brant SR, Schumm LP, Duerr RH, Dubinsky MC, Glazer NL, Haritunians T, Ippoliti A, Melmed GY, Siscovick DS ...
Nat Genet. 2010;42(4):332-7 - PMID: 20228799 - PMCID: PMC3087600 - DOI: 10.1038/ng.549

Exploring the interplay of barrier function and leukocyte recruitment in intestinal inflammation by targeting fucosyltransferase VII and trefoil factor 3.

Beck PL, Ihara E, Hirota SA, MacDonald JA, Meng D, Nanthakumar NN, Podolsky DK, Xavier RJ
Am J Physiol Gastrointest Liver Physiol. 2010;299(1):G43-53 - PMID: 20299601 - PMCID: PMC2904110 - DOI: 10.1152/ajpgi.00228.2009

Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor.

Benita Y, Cao Z, Giallourakis C, Li C, Gardet A, Xavier RJ
Blood. 2010;115(26):5376-84 - PMID: 20410506 - PMCID: PMC2902135 - DOI: 10.1182/blood-2010-01-263855

Differential expression of microRNA (miRNA) in chordoma reveals a role for miRNA-1 in Met expression.

Duan Z, Choy E, Nielsen GP, Rosenberg A, Iafrate J, Yang C, Schwab J, Mankin H, Xavier R, Hornicek FJ
J Orthop Res. 2010;28(6):746-52 - PMID: 20041488 - DOI: 10.1002/jor.21055

Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine.

Cadwell K, Patel KK, Maloney NS, Liu TC, Ng AC, Storer CE, Head RD, Xavier R, Stappenbeck TS, Virgin HW
Cell. 2010;141(7):1135-45 - PMID: 20602997 - PMCID: PMC2908380 - DOI: 10.1016/j.cell.2010.05.009

Characterization and analysis of human chordoma cell lines.

Yang C, Hornicek FJ, Wood KB, Schwab JH, Choy E, Iafrate J, Rosenberg A, Nielsen GP, Xavier RJ, Mankin H, Duan Z
Spine (Phila Pa 1976). 2010;35(13):1257-64 - PMID: 20461036 - PMCID: PMC3769690 - DOI: 10.1097/BRS.0b013e3181c2a8b0

A genome-wide siRNA screen reveals multiple mTORC1 independent signaling pathways regulating autophagy under normal nutritional conditions.

Lipinski MM, Hoffman G, Ng A, Zhou W, Py BF, Hsu E, Liu X, Eisenberg J, Liu J, Blenis J, Xavier RJ, Yuan J
Dev Cell. 2010;18(6):1041-52 - PMID: 20627085 - PMCID: PMC2935848 - DOI: 10.1016/j.devcel.2010.05.005

Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity.

Ng AC, Eisenberg JM, Heath RJ, Huett A, Robinson CM, Nau GJ, Xavier RJ
Proc Natl Acad Sci U S A. 2010;108 Suppl 1:4631-8 - PMID: 20616063 - PMCID: PMC3063585 - DOI: 10.1073/pnas.1000093107

A systems biology viewpoint on autophagy in health and disease.

Huett A, Goel G, Xavier RJ
Curr Opin Gastroenterol. 2010;26(4):302-9 - PMID: 20571384 - DOI: 10.1097/MOG.0b013e32833ae2ed

Wnt signaling regulates mitochondrial physiology and insulin sensitivity.

Yoon JC, Ng A, Kim BH, Bianco A, Xavier RJ, Elledge SJ
Genes Dev. 2010;24(14):1507-18 - PMID: 20634317 - PMCID: PMC2904941 - DOI: 10.1101/gad.1924910

Genome-wide analysis reveals mechanisms modulating autophagy in normal brain aging and in Alzheimer's disease.

Lipinski MM, Zheng B, Lu T, Yan Z, Py BF, Ng A, Xavier RJ, Li C, Yankner BA, Scherzer CR, Yuan J
Proc Natl Acad Sci U S A. 2010;107(32):14164-9 - PMID: 20660724 - PMCID: PMC2922576 - DOI: 10.1073/pnas.1009485107

Human IRGM gene "to be or not to be".

Bekpen C, Xavier RJ, Eichler EE
Semin Immunopathol. 2010;32(4):437-44 - PMID: 20737271 - DOI: 10.1007/s00281-010-0224-x

NLRP3 inflammasome plays a key role in the regulation of intestinal homeostasis.

Hirota SA, Ng J, Lueng A, Khajah M, Parhar K, Li Y, Lam V, Potentier MS, Ng K, Bawa M, McCafferty DM, Rioux KP, Ghosh S, Xavier RJ, Colgan SP, Tschopp J, Muruve D, MacDonald JA, Beck PL
Inflamm Bowel Dis. 2010;17(6):1359-72 - PMID: 20872834 - PMCID: PMC3026862 - DOI: 10.1002/ibd.21478

LRRK2 is involved in the IFN-gamma response and host response to pathogens.

Gardet A, Benita Y, Li C, Sands BE, Ballester I, Stevens C, Korzenik JR, Rioux JD, Daly MJ, Xavier RJ, Podolsky DK
J Immunol. 2010;185(9):5577-85 - PMID: 20921534 - PMCID: PMC3156100 - DOI: 10.4049/jimmunol.1000548

Ubiquitin accumulation in autophagy-deficient mice is dependent on the Nrf2-mediated stress response pathway: a potential role for protein aggregation in autophagic substrate selection.

Riley BE, Kaiser SE, Shaler TA, Ng AC, Hara T, Hipp MS, Lage K, Xavier RJ, Ryu KY, Taguchi K, Yamamoto M, Tanaka K, Mizushima N, Komatsu M, Kopito RR
J Cell Biol. 2010;191(3):537-52 - PMID: 21041446 - PMCID: PMC3003313 - DOI: 10.1083/jcb.201005012

Failure and exploitation of autophagy in human pathologies-cellular integrity between inflammation, infection, and cell survival.

Kuballa P, Xavier RJ
Semin Immunopathol. 2010;32(4):319-22 - PMID: 21107575 - DOI: 10.1007/s00281-010-0229-5

Control and manipulation of pathogens with an optical trap for live cell imaging of intercellular interactions.

Tam JM, Castro CE, Heath RJ, Cardenas ML, Xavier RJ, Lang MJ, Vyas JM
PLoS One. 2010;5(12):e15215 - PMID: 21217821 - PMCID: PMC3013098 - DOI: 10.1371/journal.pone.0015215

Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology.

Rossin EJ, Lage K, Raychaudhuri S, Xavier RJ, Tatar D, Benita Y, , Cotsapas C, Daly MJ
PLoS Genet. 2011;7(1):e1001273 - PMID: 21249183 - PMCID: PMC3020935 - DOI: 10.1371/journal.pgen.1001273

Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47.

Anderson CA, Boucher G, Lees CW, Franke A, D'Amato M, Taylor KD, Lee JC, Goyette P, Imielinski M, Latiano A, Lagacé C, Scott R, Amininejad L, Bumpstead S, Baidoo L, Baldassano RN, Barclay M, Bayless TM, Brand S, Büning C, Colombel JF, Denson LA, De Vos M, Dubinsky M, Edwards C, Ellinghaus D, Fehrmann RS, Floyd JA, Florin T, Franchimont D, Franke L, Georges M, Glas J, Glazer NL, Guthery SL, Haritunians T, Hayward NK, Hugot JP, Jobin G, Laukens D, Lawrance I, Lémann M, Levine A, Libioulle C, L ...
Nat Genet. 2011;43(3):246-52 - PMID: 21297633 - PMCID: PMC3084597 - DOI: 10.1038/ng.764

Crohn disease: a current perspective on genetics, autophagy and immunity.

Stappenbeck TS, Rioux JD, Mizoguchi A, Saitoh T, Huett A, Darfeuille-Michaud A, Wileman T, Mizushima N, Carding S, Akira S, Parkes M, Xavier RJ
Autophagy. 2011;7(4):355-74 - PMID: 20729636 - PMCID: PMC3842289 - DOI: 10.4161/auto.7.2.13074

Bacterial and host determinants of MAL activation upon EPEC infection: the roles of Tir, ABRA, and FLRT3.

Heath RJ, Leong JM, Visegrády B, Machesky LM, Xavier RJ
PLoS Pathog. 2011;7(4):e1001332 - PMID: 21490959 - PMCID: PMC3072376 - DOI: 10.1371/journal.ppat.1001332

Recurrent chromosomal copy number alterations in sporadic chordomas.

Le LP, Nielsen GP, Rosenberg AE, Thomas D, Batten JM, Deshpande V, Schwab J, Duan Z, Xavier RJ, Hornicek FJ, Iafrate AJ
PLoS One. 2011;6(5):e18846 - PMID: 21602918 - PMCID: PMC3094331 - DOI: 10.1371/journal.pone.0018846

MyD88-dependent TLR1/2 signals educate dendritic cells with gut-specific imprinting properties.

Wang S, Villablanca EJ, De Calisto J, Gomes DC, Nguyen DD, Mizoguchi E, Kagan JC, Reinecker HC, Hacohen N, Nagler C, Xavier RJ, Rossi-Bergmann B, Chen YB, Blomhoff R, Snapper SB, Mora JR
J Immunol. 2011;187(1):141-50 - PMID: 21646294 - PMCID: PMC3119749 - DOI: 10.4049/jimmunol.1003740

A Francisella tularensis locus required for spermine responsiveness is necessary for virulence.

Russo BC, Horzempa J, O'Dee DM, Schmitt DM, Brown MJ, Carlson PE, Xavier RJ, Nau GJ
Infect Immun. 2011;79(9):3665-76 - PMID: 21670171 - PMCID: PMC3165480 - DOI: 10.1128/IAI.00135-11

Genetics and pathogenesis of inflammatory bowel disease.

Khor B, Gardet A, Xavier RJ
Nature. 2011;474(7351):307-17 - PMID: 21677747 - PMCID: PMC3204665 - DOI: 10.1038/nature10209

Use of an optical trap for study of host-pathogen interactions for dynamic live cell imaging.

Tam JM, Castro CE, Heath RJ, Mansour MK, Cardenas ML, Xavier RJ, Lang MJ, Vyas JM
J Vis Exp. 2011;(53):ePub - PMID: 21841755 - PMCID: PMC3197446 - DOI: 10.3791/3123

Control of NOD2 and Rip2-dependent innate immune activation by GEF-H1.

Zhao Y, Alonso C, Ballester I, Song JH, Chang SY, Guleng B, Arihiro S, Murray PJ, Xavier R, Kobayashi KS, Reinecker HC
Inflamm Bowel Dis. 2011;18(4):603-12 - PMID: 21887730 - PMCID: PMC3594873 - DOI: 10.1002/ibd.21851

Leucine-rich repeat (LRR) proteins: integrators of pattern recognition and signaling in immunity.

Ng A, Xavier RJ
Autophagy. 2011;7(9):1082-4 - PMID: 21606681 - PMCID: PMC3901792

Phosphoprotein associated with glycosphingolipid-enriched microdomains differentially modulates SRC kinase activity in brain maturation.

Lindquist S, Karitkina D, Langnaese K, Posevitz-Fejfar A, Schraven B, Xavier R, Seed B, Lindquist JA
PLoS One. 2011;6(9):e23978 - PMID: 21915273 - PMCID: PMC3167820 - DOI: 10.1371/journal.pone.0023978

HCV causes chronic endoplasmic reticulum stress leading to adaptation and interference with the unfolded protein response.

Merquiol E, Uzi D, Mueller T, Goldenberg D, Nahmias Y, Xavier RJ, Tirosh B, Shibolet O
PLoS One. 2011;6(9):e24660 - PMID: 21949742 - PMCID: PMC3176279 - DOI: 10.1371/journal.pone.0024660

Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease.

Rivas MA, Beaudoin M, Gardet A, Stevens C, Sharma Y, Zhang CK, Boucher G, Ripke S, Ellinghaus D, Burtt N, Fennell T, Kirby A, Latiano A, Goyette P, Green T, Halfvarson J, Haritunians T, Korn JM, Kuruvilla F, Lagacé C, Neale B, Lo KS, Schumm P, Törkvist L, , , , Dubinsky MC, Brant SR, Silverberg MS, Duerr RH, Altshuler D, Gabriel S, Lettre G, Franke A, D'Amato M, McGovern DP, Cho JH, Rioux JD, Xavier RJ, Daly MJ
Nat Genet. 2011;43(11):1066-73 - PMID: 21983784 - PMCID: PMC3378381 - DOI: 10.1038/ng.952

Genome-wide expression profiling implicates a MAST3-regulated gene set in colonic mucosal inflammation of ulcerative colitis patients.

Labbé C, Boucher G, Foisy S, Alikashani A, Nkwimi H, David G, Beaudoin M, Goyette P, Charron G, Xavier RJ, Rioux JD
Inflamm Bowel Dis. 2011;18(6):1072-80 - PMID: 21994190 - PMCID: PMC3269563 - DOI: 10.1002/ibd.21887

Caspase 8 inhibits programmed necrosis by processing CYLD.

O'Donnell MA, Perez-Jimenez E, Oberst A, Ng A, Massoumi R, Xavier R, Green DR, Ting AT
Nat Cell Biol. 2011;13(12):1437-42 - PMID: 22037414 - PMCID: PMC3229661 - DOI: 10.1038/ncb2362

CARMA1 is necessary for optimal T cell responses in a murine model of allergic asthma.

Ramadas RA, Roche MI, Moon JJ, Ludwig T, Xavier RJ, Medoff BD
J Immunol. 2011;187(12):6197-207 - PMID: 22075698 - PMCID: PMC3237896 - DOI: 10.4049/jimmunol.1101348

Image-based genome-wide siRNA screen identifies selective autophagy factors.

Orvedahl A, Sumpter R, Xiao G, Ng A, Zou Z, Tang Y, Narimatsu M, Gilpin C, Sun Q, Roth M, Forst CV, Wrana JL, Zhang YE, Luby-Phelps K, Xavier RJ, Xie Y, Levine B
Nature. 2011;480(7375):113-7 - PMID: 22020285 - PMCID: PMC3229641 - DOI: 10.1038/nature10546

Autophagy suppresses interleukin-1? (IL-1?) signaling by activation of p62 degradation via lysosomal and proteasomal pathways.

Lee J, Kim HR, Quinley C, Kim J, Gonzalez-Navajas J, Xavier R, Raz E
J Biol Chem. 2011;287(6):4033-40 - PMID: 22167182 - PMCID: PMC3281713 - DOI: 10.1074/jbc.M111.280065

Genome-wide siRNA screen for mediators of NF-?B activation.

Gewurz BE, Towfic F, Mar JC, Shinners NP, Takasaki K, Zhao B, Cahir-McFarland ED, Quackenbush J, Xavier RJ, Kieff E
Proc Natl Acad Sci U S A. 2012;109(7):2467-72 - PMID: 22308454 - PMCID: PMC3289371 - DOI: 10.1073/pnas.1120542109

Tribbles 2 (Trib2) is a novel regulator of toll-like receptor 5 signaling.

Wei SC, Rosenberg IM, Cao Z, Huett AS, Xavier RJ, Podolsky DK
Inflamm Bowel Dis. 2012;18(5):877-88 - PMID: 22271508 - PMCID: PMC3881418 - DOI: 10.1002/ibd.22883


Duerr EM, Mizukami Y, Moriichi K, Gala M, Jo WS, Kikuchi H, Xavier RJ, Chung DC
Am J Physiol Gastrointest Liver Physiol. 2012;302(10):G1223-30 - PMID: 22383492 - PMCID: PMC3362092 - DOI: 10.1152/ajpgi.00047.2011

Guidelines for the use and interpretation of assays for monitoring autophagy.

Klionsky DJ, Abdalla FC, Abeliovich H, Abraham RT, Acevedo-Arozena A, Adeli K, Agholme L, Agnello M, Agostinis P, Aguirre-Ghiso JA, Ahn HJ, Ait-Mohamed O, Ait-Si-Ali S, Akematsu T, Akira S, Al-Younes HM, Al-Zeer MA, Albert ML, Albin RL, Alegre-Abarrategui J, Aleo MF, Alirezaei M, Almasan A, Almonte-Becerril M, Amano A, Amaravadi R, Amarnath S, Amer AO, Andrieu-Abadie N, Anantharam V, Ann DK, Anoopkumar-Dukie S, Aoki H, Apostolova N, Auberger P, Baba M, Backues SK, Baehrecke EH, Bahr BA, Bai ...
Autophagy. 2012;8(4):445-544 - PMID: 22966490 - PMCID: PMC3404883

Nondegradative Role of Atg5-Atg12/ Atg16L1 Autophagy Protein Complex in Antiviral Activity of Interferon Gamma.

Hwang S, Maloney NS, Bruinsma MW, Goel G, Duan E, Zhang L, Shrestha B, Diamond MS, Dani A, Sosnovtsev SV, Green KY, Lopez-Otin C, Xavier RJ, Thackray LB, Virgin HW
Cell Host Microbe. 2012;11(4):397-409 - PMID: 22520467 - PMCID: PMC3348177 - DOI: 10.1016/j.chom.2012.03.002

Autophagy and the immune system.

Kuballa P, Nolte WM, Castoreno AB, Xavier RJ
Annu Rev Immunol. 2012;30:611-46 - PMID: 22449030 - DOI: 10.1146/annurev-immunol-020711-074948

Regulation of monocyte functional heterogeneity by miR-146a and Relb.

Etzrodt M, Cortez-Retamozo V, Newton A, Zhao J, Ng A, Wildgruber M, Romero P, Wurdinger T, Xavier R, Geissmann F, Meylan E, Nahrendorf M, Swirski FK, Baltimore D, Weissleder R, Pittet MJ
Cell Rep. 2012;1(4):317-324 - PMID: 22545247 - PMCID: PMC3334310 - DOI: 10.1016/j.celrep.2012.02.009

Establishment and characterization of a novel chordoma cell line: CH22.

Liu X, Nielsen GP, Rosenberg AE, Waterman PR, Yang W, Choy E, Sassi S, Yang S, Harmon DC, Yang C, Schwab JH, Kobayashi E, Mankin HJ, Xavier R, Weissleder R, Duan Z, Hornicek FJ
J Orthop Res. 2012;30(10):1666-73 - PMID: 22504929 - DOI: 10.1002/jor.22113

Helminth Infection Impairs Autophagy-Mediated Killing of Bacterial Enteropathogens by Macrophages.

Su CW, Cao Y, Zhang M, Kaplan J, Su L, Fu Y, Walker WA, Xavier R, Cherayil BJ, Shi HN
J Immunol. 2012;189(3):1459-66 - PMID: 22732589 - PMCID: PMC3423331 - DOI: 10.4049/jimmunol.1200484

Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease.

Papa E, Docktor M, Smillie C, Weber S, Preheim SP, Gevers D, Giannoukos G, Ciulla D, Tabbaa D, Ingram J, Schauer DB, Ward DV, Korzenik JR, Xavier RJ, Bousvaros A, Alm EJ
PLoS One. 2012;7(6):e39242 - PMID: 22768065 - PMCID: PMC3387146 - DOI: 10.1371/journal.pone.0039242

Case 23-2012.

Xavier RJ, Gala MK, Bronzo BK, Kelly PJ
N Engl J Med. 2012;367(4):363-73 - PMID: 22830467 - DOI: 10.1056/NEJMcpc1109275

Candida albicans Infection Affords Protection against Reinfection via Functional Reprogramming of Monocytes.

Quintin J, Saeed S, Martens JH, Giamarellos-Bourboulis EJ, Ifrim DC, Logie C, Jacobs L, Jansen T, Kullberg BJ, Wijmenga C, Joosten LA, Xavier RJ, van der Meer JW, Stunnenberg HG, Netea MG
Cell Host Microbe. 2012;12(2):223-32 - PMID: 22901542 - PMCID: PMC3864037 - DOI: 10.1016/j.chom.2012.06.006

Enhanced Tim3 activity improves survival after influenza infection.

Cho JL, Roche MI, Sandall B, Brass AL, Seed B, Xavier RJ, Medoff BD
J Immunol. 2012;189(6):2879-89 - PMID: 22875804 - PMCID: PMC3436990 - DOI: 10.4049/jimmunol.1102483

Enhanced Tim3 Activity Improves Survival after Influenza Infection.

Cho JL, Roche MI, Sandall B, Brass AL, Seed B, Xavier RJ, Medoff BD
J Immunol. 2012;189(6):2879-89 - PMID: 22875804 - PMCID: PMC3436990 - DOI: 10.4049/jimmunol.1102483

p40phox Expression Regulates Neutrophil Recruitment and Function during the Resolution Phase of Intestinal Inflammation.

Conway KL, Goel G, Sokol H, Manocha M, Mizoguchi E, Terhorst C, Bhan AK, Gardet A, Xavier RJ
J Immunol. 2012;189(7):3631-40 - PMID: 22914050 - PMCID: PMC3780969 - DOI: 10.4049/jimmunol.1103746

Essential cell autonomous role for interferon regulatory factor 1 in interferon-?-mediated inhibition of norovirus replication in macrophages.

Maloney NS, Thackray LB, Goel G, Hwang S, Duan E, Vachharajani P, Xavier R, Virgin HW
J Virol. 2012;86(23):12655-64 - PMID: 22973039 - PMCID: PMC3497668 - DOI: 10.1128/JVI.01564-12

Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes.

Kleinnijenhuis J, Quintin J, Preijers F, Joosten LA, Ifrim DC, Saeed S, Jacobs C, van Loenhout J, de Jong D, Stunnenberg HG, Xavier RJ, van der Meer JW, van Crevel R, Netea MG
Proc Natl Acad Sci U S A. 2012;109(43):17537-42 - PMID: 22988082 - PMCID: PMC3491454 - DOI: 10.1073/pnas.1202870109

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment.

Morgan XC, Tickle TL, Sokol H, Gevers D, Devaney KL, Ward DV, Reyes JA, Shah SA, Leleiko N, Snapper SB, Bousvaros A, Korzenik J, Sands BE, Xavier RJ, Huttenhower C
Genome Biol. 2012;13(9):R79 - PMID: 23013615 - PMCID: PMC3506950 - DOI: 10.1186/gb-2012-13-9-r79

Common alleles that influence autophagy and the risk for inflammatory bowel disease.

Gardet A, Xavier RJ
Curr Opin Immunol. 2012;24(5):522-9 - PMID: 23041451 - DOI: 10.1016/j.coi.2012.08.001

Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease.

Jostins L, Ripke S, Weersma RK, Duerr RH, McGovern DP, Hui KY, Lee JC, Schumm LP, Sharma Y, Anderson CA, Essers J, Mitrovic M, Ning K, Cleynen I, Theatre E, Spain SL, Raychaudhuri S, Goyette P, Wei Z, Abraham C, Achkar JP, Ahmad T, Amininejad L, Ananthakrishnan AN, Andersen V, Andrews JM, Baidoo L, Balschun T, Bampton PA, Bitton A, Boucher G, Brand S, Büning C, Cohain A, Cichon S, D'Amato M, De Jong D, Devaney KL, Dubinsky M, Edwards C, Ellinghaus D, Ferguson LR, Franchimont D, Fransen K, Ge ...
Nature. 2012;491(7422):119-24 - PMID: 23128233 - PMCID: PMC3491803 - DOI: 10.1038/nature11582

The LRR and RING Domain Protein LRSAM1 Is an E3 Ligase Crucial for Ubiquitin-Dependent Autophagy of Intracellular Salmonella Typhimurium.

Huett A, Heath RJ, Begun J, Sassi SO, Baxt LA, Vyas JM, Goldberg MB, Xavier RJ
Cell Host Microbe. 2012;12(6):778-90 - PMID: 23245322 - PMCID: PMC3785244 - DOI: 10.1016/j.chom.2012.10.019

Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans.

Smeekens SP, Ng A, Kumar V, Johnson MD, Plantinga TS, van Diemen C, Arts P, Verwiel ET, Gresnigt MS, Fransen K, van Sommeren S, Oosting M, Cheng SC, Joosten LA, Hoischen A, Kullberg BJ, Scott WK, Perfect JR, van der Meer JW, Wijmenga C, Netea MG, Xavier RJ
Nat Commun. 2013;4:1342 - PMID: 23299892 - PMCID: PMC3625375 - DOI: 10.1038/ncomms2343

Angiotensin II Drives the Production of Tumor-Promoting Macrophages.

Cortez-Retamozo V, Etzrodt M, Newton A, Ryan R, Pucci F, Sio SW, Kuswanto W, Rauch PJ, Chudnovskiy A, Iwamoto Y, Kohler R, Marinelli B, Gorbatov R, Wojtkiewicz G, Panizzi P, Mino-Kenudson M, Forghani R, Figueiredo JL, Chen JW, Xavier R, Swirski FK, Nahrendorf M, Weissleder R, Pittet MJ
Immunity. 2013;38(2):296-308 - PMID: 23333075 - PMCID: PMC3582771 - DOI: 10.1016/j.immuni.2012.10.015

ATG5 regulates plasma cell differentiation.

Conway KL, Kuballa P, Khor B, Zhang M, Shi HN, Virgin HW, Xavier RJ
Autophagy. 2013;9(4):528-37 - PMID: 23327930 - PMCID: PMC3627668 - DOI: 10.4161/auto.23484

Identification of a candidate therapeutic autophagy-inducing peptide.

Shoji-Kawata S, Sumpter R, Leveno M, Campbell GR, Zou Z, Kinch L, Wilkins AD, Sun Q, Pallauf K, MacDuff D, Huerta C, Virgin HW, Helms JB, Eerland R, Tooze SA, Xavier R, Lenschow DJ, Yamamoto A, King D, Lichtarge O, Grishin NV, Spector SA, Kaloyanova DV, Levine B
Nature. 2013;494(7436):201-6 - PMID: 23364696 - PMCID: PMC3788641 - DOI: 10.1038/nature11866

Autophagy modulates Borrelia burgdorferi-induced production of interleukin-1? (IL-1?).

Buffen K, Oosting M, Mennens S, Anand PK, Plantinga TS, Sturm P, van de Veerdonk FL, van der Meer JW, Xavier RJ, Kannegati TD, Netea MG, Joosten LA
J Biol Chem. 2013;288(12):8658-66 - PMID: 23386602 - PMCID: PMC3605684 - DOI: 10.1074/jbc.M112.412841

?-6 Polyunsaturated fatty acids extend life span through the activation of autophagy.

O'Rourke EJ, Kuballa P, Xavier R, Ruvkun G
Genes Dev. 2013;27(4):429-40 - PMID: 23392608 - PMCID: PMC3589559 - DOI: 10.1101/gad.205294.112

Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing.

Kirby A, Gnirke A, Jaffe DB, Barešová V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, Defelice M, H?lková H, Sovová J, Vylet'al P, Antignac C, Guttman M, Handsaker RE, Perrin D, Steelman S, Sigurdsson S, Scheinman SJ, Sougnez C, Cibulskis K, Parkin M, Green T, Rossin E, Zody MC, Xavier RJ, Pollak MR, Alper SL, Lindblad-Toh K, Gabriel S, Hart PS, Regev A, Nusbaum C, Kmoch S, Bleyer AJ, Lander ES, Daly MJ
Nat Genet. 2013;45(3):299-303 - PMID: 23396133 - PMCID: PMC3901305 - DOI: 10.1038/ng.2543

Development of a Colon Cancer GEMM-Derived Orthotopic Transplant Model for Drug Discovery and Validation.

Martin ES, Belmont PJ, Sinnamon MJ, Georgeon Richard L, Yuan J, Coffee EM, Roper J, Lee L, Heidari P, Lunt SY, Goel G, Ji C, Xie J, Xie T, Lamb J, Weinrich S, Vanarsdale TL, Bronson RT, Xavier RJ, Vander Heiden M, Kan JL, Mahmood U, Hung KE
Clin Cancer Res. 2013;19(11):2929-40 - PMID: 23403635 - PMCID: PMC3951107 - DOI: 10.1158/1078-0432.CCR-12-2307

Cutting Edge: cell-autonomous control of IL-7 response revealed in a novel stage of precursor B cells.

Sandoval GJ, Graham DB, Bhattacharya D, Sleckman BP, Xavier RJ, Swat W
J Immunol. 2013;190(6):2485-9 - PMID: 23420891 - PMCID: PMC3649847 - DOI: 10.4049/jimmunol.1203208

Polarity gene discs large homolog 1 regulates the generation of memory T cells.

Gmyrek GB, Graham DB, Sandoval G, Blaufuss GS, Akilesh HM, Fujikawa K, Xavier RJ, Swat W
Eur J Immunol. 2013;43(5):1185-94 - PMID: 23436244 - PMCID: PMC3894631 - DOI: 10.1002/eji.201142362

Receptor interacting protein kinase 2-mediated mitophagy regulates inflammasome activation during virus infection.

Lupfer C, Thomas PG, Anand PK, Vogel P, Milasta S, Martinez J, Huang G, Green M, Kundu M, Chi H, Xavier RJ, Green DR, Lamkanfi M, Dinarello CA, Doherty PC, Kanneganti TD
Nat Immunol. 2013;14(5):480-8 - PMID: 23525089 - PMCID: PMC3631456 - DOI: 10.1038/ni.2563

Succinate is an inflammatory signal that induces IL-1? through HIF-1?.

Tannahill GM, Curtis AM, Adamik J, Palsson-McDermott EM, McGettrick AF, Goel G, Frezza C, Bernard NJ, Kelly B, Foley NH, Zheng L, Gardet A, Tong Z, Jany SS, Corr SC, Haneklaus M, Caffrey BE, Pierce K, Walmsley S, Beasley FC, Cummins E, Nizet V, Whyte M, Taylor CT, Lin H, Masters SL, Gottlieb E, Kelly VP, Clish C, Auron PE, Xavier RJ, O'Neill LA
Nature. 2013;496(7444):238-42 - PMID: 23535595 - PMCID: PMC4031686 - DOI: 10.1038/nature11986

Genome-wide Analysis of Immune System Genes by Expressed Sequence Tag Profiling.

Giallourakis CC, Benita Y, Molinie B, Cao Z, Despo O, Pratt HE, Zukerberg LR, Daly MJ, Rioux JD, Xavier RJ
J Immunol. 2013;190(11):5578-5587 - PMID: 23616578 - PMCID: PMC3703829 - DOI: 10.4049/jimmunol.1203471

From genetics of inflammatory bowel disease towards mechanistic insights.

Graham DB, Xavier RJ
Trends Immunol. 2013;34(8):371-8 - PMID: 23639549 - PMCID: PMC3735683 - DOI: 10.1016/

Concomitant BRAF and PI3K/mTOR Blockade Is Required for Effective Treatment of BRAFV600E Colorectal Cancer.

Coffee EM, Faber AC, Roper J, Sinnamon MJ, Goel G, Keung L, Wang WV, Vecchione L, de Vriendt V, Weinstein BJ, Bronson RT, Tejpar S, Xavier RJ, Engelman JA, Martin ES, Hung KE
Clin Cancer Res. 2013;19(10):2688-98 - PMID: 23549875 - PMCID: PMC3815598 - DOI: 10.1158/1078-0432.CCR-12-2556

How Does Genotype Influence Disease Phenotype in Inflammatory Bowel Disease?

Ananthakrishnan AN, Xavier RJ
Inflamm Bowel Dis. 2013;19(9):2021-30 - PMID: 23644824 - PMCID: PMC3720704 - DOI: 10.1097/MIB.0b013e318281f5c5

Conformational stability, vibrational spectra, HOMO-LUMO and NBO analysis of 1,3,4-thiadiazolidine-2,5-dithione with experimental (FT-IR and FT-Raman) techniques and scaled quantum mechanical calculations.

Xavier RJ, Dinesh P
Spectrochim Acta A Mol Biomol Spectrosc. 2013;113C:171-181 - PMID: 23727670 - DOI: 10.1016/j.saa.2013.04.108

Card9 Mediates Intestinal Epithelial Cell Restitution, T-helper 17 Responses, and Control of Bacterial Infection in Mice.

Sokol H, Conway KL, Zhang M, Choi M, Morin B, Cao Z, Villablanca EJ, Li C, Wijmenga C, Yun SH, Shi HN, Xavier RJ
Gastroenterology. 2013;145(3):591-601.e3 - PMID: 23732773 - PMCID: PMC3781941 - DOI: 10.1053/j.gastro.2013.05.047

Skin Microbiome Imbalance in Patients with STAT1/STAT3 Defects Impairs Innate Host Defense Responses.

Smeekens SP, Huttenhower C, Riza A, van de Veerdonk FL, Zeeuwen PL, Schalkwijk J, van der Meer JW, Xavier RJ, Netea MG, Gevers D
J Innate Immun. 2013;6(3):253-62 - PMID: 23796786 - PMCID: PMC4045018 - DOI: 10.1159/000351912

Genetic risk factors for Clostridium difficile infection in ulcerative colitis.

Ananthakrishnan AN, Oxford EC, Nguyen DD, Sauk J, Yajnik V, Xavier RJ
Aliment Pharmacol Ther. 2013;38(5):522-30 - PMID: 23848254 - PMCID: PMC3755009 - DOI: 10.1111/apt.12425

Functional profiling of the gut microbiome in disease-associated inflammation.

Börnigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower C
Genome Med. 2013;5(7):65 - PMID: 23906180 - PMCID: PMC3978847 - DOI: 10.1186/gm469

Beclin 2 Functions in Autophagy, Degradation of G Protein-Coupled Receptors, and Metabolism.

He C, Wei Y, Sun K, Li B, Dong X, Zou Z, Liu Y, Kinch LN, Khan S, Sinha S, Xavier RJ, Grishin NV, Xiao G, Eskelinen EL, Scherer PE, Whistler JL, Levine B
Cell. 2013;154(5):1085-99 - PMID: 23954414 - PMCID: PMC4231430 - DOI: 10.1016/j.cell.2013.07.035

Atg16l1 is Required for Autophagy in Intestinal Epithelial Cells and Protection of Mice from Salmonella Infection.

Conway KL, Kuballa P, Song JH, Patel KK, Castoreno AB, Yilmaz OH, Jijon HB, Zhang M, Aldrich LN, Villablanca EJ, Peloquin JM, Goel G, Lee IA, Mizoguchi E, Shi HN, Bhan AK, Shaw SY, Schreiber SL, Virgin HW, Shamji AF, Stappenbeck TS, Reinecker HC, Xavier RJ
Gastroenterology. 2013;145(6):1347-57 - PMID: 23973919 - PMCID: PMC3840157 - DOI: 10.1053/j.gastro.2013.08.035

Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis.

Beaudoin M, Goyette P, Boucher G, Lo KS, Rivas MA, Stevens C, Alikashani A, Ladouceur M, Ellinghaus D, Törkvist L, Goel G, Lagacé C, Annese V, Bitton A, Begun J, Brant SR, Bresso F, Cho JH, Duerr RH, Halfvarson J, McGovern DP, Radford-Smith G, Schreiber S, Schumm PL, Sharma Y, Silverberg MS, Weersma RK, , , , D'Amato M, Vermeire S, Franke A, Lettre G, Xavier RJ, Daly MJ, Rioux JD
PLoS Genet. 2013;9(9):e1003723 - PMID: 24068945 - PMCID: PMC3772057 - DOI: 10.1371/journal.pgen.1003723

Genetic Variants Synthesize to Produce Paneth Cell Phenotypes that Define Subtypes of Crohn's Disease.

Vandussen KL, Liu TC, Li D, Towfic F, Modiano N, Winter R, Haritunians T, Taylor KD, Dhall D, Targan SR, Xavier RJ, McGovern DP, Stappenbeck TS
Gastroenterology. 2013;146(1):200-9 - PMID: 24076061 - PMCID: PMC3899786 - DOI: 10.1053/j.gastro.2013.09.048

Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome.

Knights D, Lassen KG, Xavier RJ
Gut. 2013;62(10):1505-10 - PMID: 24037875 - PMCID: PMC3822528 - DOI: 10.1136/gutjnl-2012-303954

Novel Mechanism of Tumor Suppression by Polarity Gene Discs Large 1 (DLG1) Revealed in a Murine Model of Pediatric B-ALL.

Sandoval GJ, Graham DB, Gmyrek GB, Akilesh HM, Fujikawa K, Sammut B, Bhattacharya D, Srivatsan S, Kim A, Shaw AS, Yang-Iott K, Bassing CH, Duncavage E, Xavier RJ, Swat W
Cancer Immunol Res. 2013;1(6):426-37 - PMID: 24778134 - PMCID: PMC4006353 - DOI: 10.1158/2326-6066.CIR-13-0065

Selective Modulation of Autophagy, Innate Immunity, and Adaptive Immunity by Small Molecules.

Shaw SY, Tran K, Castoreno AB, Peloquin JM, Lassen KG, Khor B, Aldrich LN, Tan PH, Graham DB, Kuballa P, Goel G, Daly MJ, Shamji AF, Schreiber SL, Xavier RJ
ACS Chem Biol. 2013;8(12):2724-33 - PMID: 24168452 - PMCID: PMC3951132 - DOI: 10.1021/cb400352d

Long-Lasting Effects of BCG Vaccination on Both Heterologous Th1/Th17 Responses and Innate Trained Immunity.

Kleinnijenhuis J, Quintin J, Preijers F, Benn CS, Joosten LA, Jacobs C, van Loenhout J, Xavier RJ, Aaby P, van der Meer JW, van Crevel R, Netea MG
J Innate Immun. 2013;6(2):152-8 - PMID: 24192057 - PMCID: PMC3944069 - DOI: 10.1159/000355628

Autophagy at the crossroads of metabolism and cellular defense.

Begun J, Xavier RJ
Curr Opin Gastroenterol. 2013;29(6):588-596 - PMID: 24100719 - DOI: 10.1097/MOG.0b013e328365d34d

Autophagy is redundant for the host defense against systemic Candida albicans infections.

Smeekens SP, Malireddi RK, Plantinga TS, Buffen K, Oosting M, Joosten LA, Kullberg BJ, Perfect JR, Scott WK, van de Veerdonk FL, Xavier RJ, van de Vosse E, Kanneganti TD, Johnson MD, Netea MG
Eur J Clin Microbiol Infect Dis. 2013;33(5):711-22 - PMID: 24202731 - DOI: 10.1007/s10096-013-2002-x

Autosis is a Na+,K+-ATPase-regulated form of cell death triggered by autophagy-inducing peptides, starvation, and hypoxia-ischemia.

Liu Y, Shoji-Kawata S, Sumpter RM, Wei Y, Ginet V, Zhang L, Posner B, Tran KA, Green DR, Xavier RJ, Shaw SY, Clarke PG, Puyal J, Levine B
Proc Natl Acad Sci U S A. 2013;110(51):20364-71 - PMID: 24277826 - PMCID: PMC3870705 - DOI: 10.1073/pnas.1319661110

Autophagy is essential for cardiac morphogenesis during vertebrate development.

Lee E, Koo Y, Ng A, Wei Y, Luby-Phelps K, Juraszek A, Xavier RJ, Cleaver O, Levine B, Amatruda JF
Autophagy. 2014;10(4):572-87 - PMID: 24441423 - PMCID: PMC4091146 - DOI: 10.4161/auto.27649

Differential Effect of Genetic Burden on Disease Phenotypes in Crohn's Disease and Ulcerative Colitis: Analysis of a North American Cohort.

Ananthakrishnan AN, Huang H, Nguyen DD, Sauk J, Yajnik V, Xavier RJ
Am J Gastroenterol. 2014;109(3):395-400 - PMID: 24419484 - PMCID: PMC4225079 - DOI: 10.1038/ajg.2013.464

SMAD3 gene variant is a risk factor for recurrent surgery in patients with Crohn's disease.

Fowler SA, Ananthakrishnan AN, Gardet A, Stevens CR, Korzenik JR, Sands BE, Daly MJ, Xavier RJ, Yajnik V
J Crohns Colitis. 2014;8(8):845-51 - PMID: 24461721 - PMCID: PMC4237062 - DOI: 10.1016/j.crohns.2014.01.003

The Microbiome in Inflammatory Bowel Diseases: Current Status and the Future Ahead.

Kostic AD, Xavier RJ, Gevers D
Gastroenterology. 2014;146(6):1489-99 - PMID: 24560869 - PMCID: PMC4034132 - DOI: 10.1053/j.gastro.2014.02.009

IL-1 receptor blockade restores autophagy and reduces inflammation in chronic granulomatous disease in mice and in humans.

de Luca A, Smeekens SP, Casagrande A, Iannitti R, Conway KL, Gresnigt MS, Begun J, Plantinga TS, Joosten LA, van der Meer JW, Chamilos G, Netea MG, Xavier RJ, Dinarello CA, Romani L, van de Veerdonk FL
Proc Natl Acad Sci U S A. 2014;111(9):3526-31 - PMID: 24550444 - PMCID: PMC3948220 - DOI: 10.1073/pnas.1322831111

Human Genome-Wide RNAi Screen Identifies an Essential Role for Inositol Pyrophosphates in Type-I Interferon Response.

Pulloor NK, Nair S, Kostic AD, Bist P, Weaver JD, Riley AM, Tyagi R, Uchil PD, York JD, Snyder SH, García-Sastre A, Potter BV, Lin R, Shears SB, Xavier RJ, Krishnan MN
PLoS Pathog. 2014;10(2):e1003981 - PMID: 24586175 - PMCID: PMC3937324 - DOI: 10.1371/journal.ppat.1003981

The treatment-naive microbiome in new-onset Crohn's disease.

Gevers D, Kugathasan S, Denson LA, Vázquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, González A, McDonald D, Haberman Y, Walters T, Baker S, Rosh J, Stephens M, Heyman M, Markowitz J, Baldassano R, Griffiths A, Sylvester F, Mack D, Kim S, Crandall W, Hyams J, Huttenhower C, Knight R, Xavier RJ
Cell Host Microbe. 2014;15(3):382-92 - PMID: 24629344 - PMCID: PMC4059512 - DOI: 10.1016/j.chom.2014.02.005

Genetic Polymorphisms in Metabolizing Enzymes Modifying the Association Between Smoking and Inflammatory Bowel Diseases.

Ananthakrishnan AN, Nguyen DD, Sauk J, Yajnik V, Xavier RJ
Inflamm Bowel Dis. 2014;20(5):783-9 - PMID: 24651583 - PMCID: PMC4113010 - DOI: 10.1097/MIB.0000000000000014

Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense.

Lassen KG, Kuballa P, Conway KL, Patel KK, Becker CE, Peloquin JM, Villablanca EJ, Norman JM, Liu TC, Heath RJ, Becker ML, Fagbami L, Horn H, Mercer J, Yilmaz OH, Jaffe JD, Shamji AF, Bhan AK, Carr SA, Daly MJ, Virgin HW, Schreiber SL, Stappenbeck TS, Xavier RJ
Proc Natl Acad Sci U S A. 2014;111(21):7741-7746 - PMID: 24821797 - PMCID: PMC4040621 - DOI: 10.1073/pnas.1407001111

Dectin-1 dependent LC3 recruitment to phagosomes enhances fungicidal activity in macrophages.

Tam JM, Mansour MK, Khan NS, Seward M, Puranam S, Tanne A, Sokolovska A, Becker CE, Acharya M, Baird MA, Choi AM, Davidson MW, Segal BH, Lacy-Hulbert A, Stuart LM, Xavier RJ, Vyas JM
J Infect Dis. 2014;210(11):1844-54 - PMID: 24842831 - PMCID: PMC4271056 - DOI: 10.1093/infdis/jiu290

Inflammatory Bowel Disease as a Model for Translating the Microbiome.

Huttenhower C, Kostic AD, Xavier RJ
Immunity. 2014;40(6):843-854 - PMID: 24950204 - PMCID: PMC4135443 - DOI: 10.1016/j.immuni.2014.05.013

SLCO3A1, a Novel Crohn's Disease-Associated Gene, Regulates NF-?B Activity and Associates with Intestinal Perforation.

Wei SC, Tan YY, Weng MT, Lai LC, Hsiao JH, Chuang EY, Shun CT, Wu DC, Kao AW, Chuang CS, Ni YH, Shieh MJ, Tung CC, Chen Y, Wang CY, Xavier RJ, Podolsky DK, Wong JM
PLoS One. 2014;9(6):e100515 - PMID: 24945726 - PMCID: PMC4063938 - DOI: 10.1371/journal.pone.0100515

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.

Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LA
J Clin Invest. 2014;124(8):3617-33 - PMID: 25003194 - PMCID: PMC4109533 - DOI: 10.1172/JCI75436

Small-molecule screening identifies inhibition of salt-inducible kinases as a therapeutic strategy to enhance immunoregulatory functions of dendritic cells.

Sundberg TB, Choi HG, Song JH, Russell CN, Hussain MM, Graham DB, Khor B, Gagnon J, O'Connell DJ, Narayan K, Dan?ík V, Perez JR, Reinecker HC, Gray NS, Schreiber SL, Xavier RJ, Shamji AF
Proc Natl Acad Sci U S A. 2014;111(34):12468-12473 - PMID: 25114223 - PMCID: PMC4151730 - DOI: 10.1073/pnas.1412308111

An alteration in ATG16L1 stability in Crohn disease.

Lassen KG, Xavier RJ
Autophagy. 2014;10(10):1858-1860 - PMID: 25136803 - PMCID: PMC4198368 - DOI: 10.4161/auto.29963

Multivariate inference of pathway activity in host immunity and response to therapeutics.

Goel G, Conway KL, Jaeger M, Netea MG, Xavier RJ
Nucleic Acids Res. 2014;42(16):10288-306 - PMID: 25147207 - PMCID: PMC4176341 - DOI: 10.1093/nar/gku722

mTOR- and HIF-1?-mediated aerobic glycolysis as metabolic basis for trained immunity.

Cheng SC, Quintin J, Cramer RA, Shepardson KM, Saeed S, Kumar V, Giamarellos-Bourboulis EJ, Martens JH, Rao NA, Aghajanirefah A, Manjeri GR, Li Y, Ifrim DC, Arts RJ, van der Meer BM, Deen PM, Logie C, O'Neill LA, Willems P, van de Veerdonk FL, van der Meer JW, Ng A, Joosten LA, Wijmenga C, Stunnenberg HG, Xavier RJ, Netea MG
Science. 2014;345(6204):1250684 - PMID: 25258083 - PMCID: PMC4226238 - DOI: 10.1126/science.1250684

Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity.

Saeed S, Quintin J, Kerstens HH, Rao NA, Aghajanirefah A, Matarese F, Cheng SC, Ratter J, Berentsen K, van der Ent MA, Sharifi N, Janssen-Megens EM, Ter Huurne M, Mandoli A, van Schaik T, Ng A, Burden F, Downes K, Frontini M, Kumar V, Giamarellos-Bourboulis EJ, Ouwehand WH, van der Meer JW, Joosten LA, Wijmenga C, Martens JH, Xavier RJ, Logie C, Netea MG, Stunnenberg HG
Science. 2014;345(6204):1251086 - PMID: 25258085 - PMCID: PMC4242194 - DOI: 10.1126/science.1251086

Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation.

Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE
Nat Biotechnol. 2014;32(12):1262-1267 - PMID: 25184501 - PMCID: PMC4262738 - DOI: 10.1038/nbt.3026

Immunochip SNP array identifies novel genetic variants conferring susceptibility to candidaemia.

Kumar V, Cheng SC, Johnson MD, Smeekens SP, Wojtowicz A, Giamarellos-Bourboulis E, Karjalainen J, Franke L, Withoff S, Plantinga TS, van de Veerdonk FL, van der Meer JW, Joosten LA, Sokol H, Bauer H, Herrmann BG, Bochud PY, Marchetti O, Perfect JR, Xavier RJ, Kullberg BJ, Wijmenga C, Netea MG
Nat Commun. 2014;5:4675 - PMID: 25197941 - PMCID: PMC5142444 - DOI: 10.1038/ncomms5675

Small-molecule control of cytokine function: new opportunities for treating immune disorders.

Sundberg TB, Xavier RJ, Schreiber SL, Shamji AF
Curr Opin Chem Biol. 2014;23C:23-30 - PMID: 25222143 - PMCID: PMC5087273 - DOI: 10.1016/j.cbpa.2014.08.013

Transmembrane adaptor protein PAG/CBP is involved in both positive and negative regulation of mast cell signaling.

Draberova L, Bugajev V, Potuckova L, Halova I, Bambouskova M, Polakovicova I, Xavier RJ, Seed B, Draber P
Mol Cell Biol. 2014;34(23):4285-300 - PMID: 25246632 - PMCID: PMC4248753 - DOI: 10.1128/MCB.00983-14

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling.

Platt RJ, Chen S, Zhou Y, Yim MJ, Swiech L, Kempton HR, Dahlman JE, Parnas O, Eisenhaure TM, Jovanovic M, Graham DB, Jhunjhunwala S, Heidenreich M, Xavier RJ, Langer R, Anderson DG, Hacohen N, Regev A, Feng G, Sharp PA, Zhang F
Cell. 2014;159(2):440-55 - PMID: 25263330 - PMCID: PMC4265475 - DOI: 10.1016/j.cell.2014.09.014

An Image-Based Genetic Assay Identifies Genes in T1D Susceptibility Loci Controlling Cellular Antiviral Immunity in Mouse.

Liao J, Jijon HB, Kim IR, Goel G, Doan A, Sokol H, Bauer H, Herrmann BG, Lassen KG, Xavier RJ
PLoS One. 2014;9(9):e108777 - PMID: 25268627 - PMCID: PMC4182575 - DOI: 10.1371/journal.pone.0108777

Genetics of immune-mediated disorders: from genome-wide association to molecular mechanism.

Kumar V, Wijmenga C, Xavier RJ
Curr Opin Immunol. 2014;31C:51-57 - PMID: 25458995 - PMCID: PMC5080657 - DOI: 10.1016/j.coi.2014.09.007

BCG-induced trained immunity in NK cells: Role for non-specific protection to infection.

Kleinnijenhuis J, Quintin J, Preijers F, Joosten LA, Jacobs C, Xavier RJ, van der Meer JW, van Crevel R, Netea MG
Clin Immunol. 2014;155(2):213-219 - PMID: 25451159 - PMCID: PMC5084088 - DOI: 10.1016/j.clim.2014.10.005

Autophagy Controls BCG-Induced Trained Immunity and the Response to Intravesical BCG Therapy for Bladder Cancer.

Buffen K, Oosting M, Quintin J, Ng A, Kleinnijenhuis J, Kumar V, van de Vosse E, Wijmenga C, van Crevel R, Oosterwijk E, Grotenhuis AJ, Vermeulen SH, Kiemeney LA, van de Veerdonk FL, Chamilos G, Xavier RJ, van der Meer JW, Netea MG, Joosten LA
PLoS Pathog. 2014;10(10):e1004485 - PMID: 25356988 - PMCID: PMC4214925 - DOI: 10.1371/journal.ppat.1004485

Autophagy and checkpoints for intracellular pathogen defense.

Paulus GL, Xavier RJ
Curr Opin Gastroenterol. 2014;31(1):14-23 - PMID: 25394238 - PMCID: PMC4330559 - DOI: 10.1097/MOG.0000000000000134

Complex host genetics influence the microbiome in inflammatory bowel disease.

Knights D, Silverberg MS, Weersma RK, Gevers D, Dijkstra G, Huang H, Tyler AD, van Sommeren S, Imhann F, Stempak JM, Huang H, Vangay P, Al-Ghalith GA, Russell C, Sauk J, Knight J, Daly MJ, Huttenhower C, Xavier RJ
Genome Med. 2014;6(12):107 - PMID: 25587358 - PMCID: PMC4292994 - DOI: 10.1186/s13073-014-0107-1

Early life environment and natural history of inflammatory bowel diseases.

Guo AY, Stevens BW, Wilson RG, Russell CN, Cohen MA, Sturgeon HC, Thornton A, Giallourakis C, Khalili H, Nguyen DD, Sauk J, Yajnik V, Xavier RJ, Ananthakrishnan AN
BMC Gastroenterol. 2014;14(1):216 - PMID: 25510175 - PMCID: PMC4300207 - DOI: 10.1186/s12876-014-0216-8

Pyruvate Kinase M2 Regulates Hif-1? Activity and IL-1? Induction and Is a Critical Determinant of the Warburg Effect in LPS-Activated Macrophages.

Palsson-McDermott EM, Curtis AM, Goel G, Lauterbach MA, Sheedy FJ, Gleeson LE, van den Bosch MW, Quinn SR, Domingo-Fernandez R, Johnson DG, Jiang J, Israelsen WJ, Keane J, Thomas C, Clish C, Vanden Heiden M, Xavier RJ, O'Neill LA
Cell Metab. 2015;21(1):65-80 - PMID: 25565206 - PMCID: PMC5198835 - DOI: 10.1016/j.cmet.2014.12.005

Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease.

Norman JM, Handley SA, Baldridge MT, Droit L, Liu CY, Keller BC, Kambal A, Monaco CL, Zhao G, Fleshner P, Stappenbeck TS, McGovern DP, Keshavarzian A, Mutlu EA, Sauk J, Gevers D, Xavier RJ, Wang D, Parkes M, Virgin HW
Cell. 2015;160(3):447-60 - PMID: 25619688 - PMCID: PMC4312520 - DOI: 10.1016/j.cell.2015.01.002

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes.

Kostic AD, Gevers D, Siljander H, Vatanen T, Hyötyläinen T, Hämäläinen AM, Peet A, Tillmann V, Pöhö P, Mattila I, Lähdesmäki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Oreši? M, Huttenhower C, Knip M, , Xavier RJ
Cell Host Microbe. 2015;17(2):260-273 - PMID: 25662751 - PMCID: PMC4689191 - DOI: 10.1016/j.chom.2015.01.001

A novel role for KLF14 in T regulatory cell differentiation.

Sarmento OF, Svingen PA, Xiong Y, Xavier RJ, McGovern D, Smyrk TC, Papadakis KA, Urrutia RA, Faubion WA
Cell Mol Gastroenterol Hepatol. 2015;1(2):188-202.e4 - PMID: 25750932 - PMCID: PMC4349492 - DOI: 10.1016/j.jcmgh.2014.12.007

Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature.

Haberman Y, Tickle TL, Dexheimer PJ, Kim MO, Tang D, Karns R, Baldassano RN, Noe JD, Rosh J, Markowitz J, Heyman MB, Griffiths AM, Crandall WV, Mack DR, Baker SS, Huttenhower C, Keljo DJ, Hyams JS, Kugathasan S, Walters TD, Aronow B, Xavier RJ, Gevers D, Denson LA
J Clin Invest. 2015;125(3):1363 - PMID: 25729854 - PMCID: PMC4362234 - DOI: 10.1172/JCI79657

Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease.

Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C
Genome Biol. 2015;16(1):67 - PMID: 25887922 - PMCID: PMC4414286 - DOI: 10.1186/s13059-015-0637-x

Discovery of a Small-Molecule Probe for V-ATPase Function.

Aldrich LN, Kuo SY, Castoreno AB, Goel G, Kuballa P, Rees MG, Seashore-Ludlow BA, Cheah JH, Latorre IJ, Schreiber SL, Shamji AF, Xavier RJ
J Am Chem Soc. 2015;137(16):5563-8 - PMID: 25860544 - PMCID: PMC4416280 - DOI: 10.1021/jacs.5b02150

An Integrative View of Microbiome-Host Interactions in Inflammatory Bowel Diseases.

Wlodarska M, Kostic AD, Xavier RJ
Cell Host Microbe. 2015;17(5):577-591 - PMID: 25974300 - PMCID: PMC4498258 - DOI: 10.1016/j.chom.2015.04.008

The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells.

Khor B, Gagnon JD, Goel G, Roche MI, Conway KL, Tran K, Aldrich LN, Sundberg TB, Paterson AM, Mordecai S, Dombkowski D, Schirmer M, Tan PH, Bhan AK, Roychoudhuri R, Restifo NP, O'Shea JJ, Medoff BD, Shamji AF, Schreiber SL, Sharpe AH, Shaw SY, Xavier RJ
Elife. 2015;4:ePub - PMID: 25998054 - PMCID: PMC4441007 - DOI: 10.7554/eLife.05920

CARMA3 Is Critical for the Initiation of Allergic Airway Inflammation.

Causton B, Ramadas RA, Cho JL, Jones K, Pardo-Saganta A, Rajagopal J, Xavier RJ, Medoff BD
J Immunol. 2015;195(2):683-94 - PMID: 26041536 - PMCID: PMC4489191 - DOI: 10.4049/jimmunol.1402983

Identification of an anti-inflammatory protein from Faecalibacterium prausnitzii, a commensal bacterium deficient in Crohn's disease.

Quévrain E, Maubert MA, Michon C, Chain F, Marquant R, Tailhades J, Miquel S, Carlier L, Bermúdez-Humarán LG, Pigneur B, Lequin O, Kharrat P, Thomas G, Rainteau D, Aubry C, Breyner N, Afonso C, Lavielle S, Grill JP, Chassaing G, Chatel JM, Trugnan G, Xavier R, Langella P, Sokol H, Seksik P
Gut. 2015;65(3):415-25 - PMID: 26045134 - PMCID: PMC5136800 - DOI: 10.1136/gutjnl-2014-307649

Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy.

Begun J, Lassen KG, Jijon HB, Baxt LA, Goel G, Heath RJ, Ng A, Tam JM, Kuo SY, Villablanca EJ, Fagbami L, Oosting M, Kumar V, Schenone M, Carr SA, Joosten LA, Vyas JM, Daly MJ, Netea MG, Brown GD, Wijmenga C, Xavier RJ
Cell Rep. 2015;11(12):1905-1918 - PMID: 26095365 - PMCID: PMC4507440 - DOI: 10.1016/j.celrep.2015.05.045

Role of Autophagy in the Maintenance of Intestinal Homeostasis.

Baxt LA, Xavier RJ
Gastroenterology. 2015;149(3):553-62 - PMID: 26170139 - PMCID: PMC4550567 - DOI: 10.1053/j.gastro.2015.06.046

Body Mass Index, Genetic Susceptibility, and Risk of Complications Among Individuals with Crohn's Disease.

Pringle PL, Stewart KO, Peloquin JM, Sturgeon HC, Nguyen D, Sauk J, Garber JJ, Yajnik V, Ananthakrishnan AN, Chan AT, Xavier RJ, Khalili H
Inflamm Bowel Dis. 2015;21(10):2304-2310 - PMID: 26181430 - PMCID: PMC4567407 - DOI: 10.1097/MIB.0000000000000498

Small-molecule enhancers of autophagy modulate cellular disease phenotypes suggested by human genetics.

Kuo SY, Castoreno AB, Aldrich LN, Lassen KG, Goel G, Dan?ík V, Kuballa P, Latorre I, Conway KL, Sarkar S, Maetzel D, Jaenisch R, Clemons PA, Schreiber SL, Shamji AF, Xavier RJ
Proc Natl Acad Sci U S A. 2015;112(31):E4281-7 - PMID: 26195741 - PMCID: PMC4534235 - DOI: 10.1073/pnas.1512289112

Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst.

Graham DB, Becker CE, Doan A, Goel G, Villablanca EJ, Knights D, Mok A, Ng AC, Doench JG, Root DE, Clish CB, Xavier RJ
Nat Commun. 2015;6:7838 - PMID: 26194095 - PMCID: PMC4518307 - DOI: 10.1038/ncomms8838

Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples.

Korem T, Zeevi D, Suez J, Weinberger A, Avnit-Sagi T, Pompan-Lotan M, Matot E, Jona G, Harmelin A, Cohen N, Sirota-Madi A, Thaiss CA, Pevsner-Fischer M, Sorek R, Xavier R, Elinav E, Segal E
Science. 2015;349(6252):1101-6 - PMID: 26229116 - PMCID: PMC5087275 - DOI: 10.1126/science.aac4812

Common Genetic Variants Influence Circulating Vitamin D Levels in Inflammatory Bowel Diseases.

Ananthakrishnan AN, Cagan A, Cai T, Gainer VS, Shaw SY, Churchill S, Karlson EW, Murphy SN, Kohane I, Liao KP, Xavier RJ
Inflamm Bowel Dis. 2015;21(11):2507-2514 - PMID: 26241000 - PMCID: PMC4615315 - DOI: 10.1097/MIB.0000000000000524

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.

Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier RJ, Regev A, Hung DT
Cell. 2015;162(6):1309-21 - PMID: 26343579 - PMCID: PMC4578813 - DOI: 10.1016/j.cell.2015.08.027

Pathogen Cell-to-Cell Variability Drives Heterogeneity in Host Immune Responses.

Avraham R, Haseley N, Brown D, Penaranda C, Jijon HB, Trombetta JJ, Satija R, Shalek AK, Xavier RJ, Regev A, Hung DT
Cell. 2015;162(6):1309-21 - PMID: 26343579 - PMCID: PMC4578813 - DOI: 10.1016/j.cell.2015.08.027

ConStrains identifies microbial strains in metagenomic datasets.

Luo C, Knight R, Siljander H, Knip M, Xavier RJ, Gevers D
Nat Biotechnol. 2015;33(10):1045-1052 - PMID: 26344404 - PMCID: PMC4676274 - DOI: 10.1038/nbt.3319

A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-?-Activated Human Cells.

Selleck EM, Orchard RC, Lassen KG, Beatty WL, Xavier RJ, Levine B, Virgin HW, Sibley LD
MBio. 2015;6(5):e01157-15 - PMID: 26350966 - PMCID: PMC4600106 - DOI: 10.1128/mBio.01157-15

A Noncanonical Autophagy Pathway Restricts Toxoplasma gondii Growth in a Strain-Specific Manner in IFN-?-Activated Human Cells.

Selleck EM, Orchard RC, Lassen KG, Beatty WL, Xavier RJ, Levine B, Virgin HW, Sibley LD
MBio. 2015;6(5):e01157-15 - PMID: 26350966 - PMCID: PMC4600106 - DOI: 10.1128/mBio.01157-15

The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids.

Fu J, Bonder MJ, Cenit MC, Tigchelaar E, Maatman A, Dekens JA, Brandsma E, Marczynska J, Imhann F, Weersma RK, Franke L, Poon TW, Xavier RJ, Gevers D, Hofker MH, Wijmenga C, Zhernakova A
Circ Res. 2015;117(9):817-24 - PMID: 26358192 - PMCID: PMC4596485 - DOI: 10.1161/CIRCRESAHA.115.306807

Ubiquitin Ligase TRIM62 Regulates CARD9-Mediated Anti-fungal Immunity and Intestinal Inflammation.

Cao Z, Conway KL, Heath RJ, Rush JS, Leshchiner ES, Ramirez-Ortiz ZG, Nedelsky NB, Huang H, Ng A, Gardet A, Cheng SC, Shamji AF, Rioux JD, Wijmenga C, Netea MG, Means TK, Daly MJ, Xavier RJ
Immunity. 2015;43(4):715-26 - PMID: 26488816 - PMCID: PMC4672733 - DOI: 10.1016/j.immuni.2015.10.005

Ubiquitin Ligase TRIM62 Regulates CARD9-Mediated Anti-fungal Immunity and Intestinal Inflammation.

Cao Z, Conway KL, Heath RJ, Rush JS, Leshchiner ES, Ramirez-Ortiz ZG, Nedelsky NB, Huang H, Ng A, Gardet A, Cheng SC, Shamji AF, Rioux JD, Wijmenga C, Netea MG, Means TK, Daly MJ, Xavier RJ
Immunity. 2015;43(4):715-726 - PMID: 26488816 - PMCID: PMC4672733 - DOI: 10.1016/j.immuni.2015.10.005

Flow Cytometric Analysis of Mononuclear Phagocytes in Non-diseased Human Lung and Lung-draining Lymph Nodes.

Desch AN, Gibbings SL, Goyal R, Kolde R, Bednarek J, Bruno T, Slansky JE, Jacobelli J, Mason R, Ito Y, Messier E, Randolph GJ, Prabagar M, Atif SM, Segura E, Xavier RJ, Bratton DL, Janssen WJ, Henson PM, Jakubzick CV
Am J Respir Crit Care Med. 2015;193(6):614-626 - PMID: 26551758 - PMCID: PMC4824940 - DOI: 10.1164/rccm.201507-1376OC

Proton pump inhibitors affect the gut microbiome.

Imhann F, Bonder MJ, Vich Vila A, Fu J, Mujagic Z, Vork L, Tigchelaar EF, Jankipersadsing SA, Cenit MC, Harmsen HJ, Dijkstra G, Franke L, Xavier RJ, Jonkers D, Wijmenga C, Weersma RK, Zhernakova A
Gut. 2015;65(5):740-8 - PMID: 26657899 - PMCID: PMC4853569 - DOI: 10.1136/gutjnl-2015-310376

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition).

Klionsky DJ, Abdelmohsen K, Abe A, Abedin MJ, Abeliovich H, Acevedo Arozena A, Adachi H, Adams CM, Adams PD, Adeli K, Adhihetty PJ, Adler SG, Agam G, Agarwal R, Aghi MK, Agnello M, Agostinis P, Aguilar PV, Aguirre-Ghiso J, Airoldi EM, Ait-Si-Ali S, Akematsu T, Akporiaye ET, Al-Rubeai M, Albaiceta GM, Albanese C, Albani D, Albert ML, Aldudo J, Algül H, Alirezaei M, Alloza I, Almasan A, Almonte-Beceril M, Alnemri ES, Alonso C, Altan-Bonnet N, Altieri DC, Alvarez S, Alvarez-Erviti L, Alves S, A ...
Autophagy. 2016;12(1):1-222 - PMID: 26799652 - PMCID: PMC4835977 - DOI: 10.1080/15548627.2015.1100356

Sub-clinical detection of gut microbial biomarkers of obesity and type 2 diabetes.

Yassour M, Lim MY, Yun HS, Tickle TL, Sung J, Song YM, Lee K, Franzosa EA, Morgan XC, Gevers D, Lander ES, Xavier RJ, Birren BW, Ko G, Huttenhower C
Genome Med. 2016;8(1):17 - PMID: 26884067 - PMCID: PMC4756455 - DOI: 10.1186/s13073-016-0271-6

New Regulatory Roles of Galectin-3 in the High-affinity IgE Receptor Signaling.

Bambouskova M, Polakovicova I, Halova I, Goel G, Draberova L, Bugajev V, Doan A, Utekal P, Gardet A, Xavier RJ, Draber P
Mol Cell Biol. 2016;36(9):1366-82 - PMID: 26929198 - PMCID: PMC4836217 - DOI: 10.1128/MCB.00064-16

Impaired antibacterial autophagy links granulomatous intestinal inflammation in Niemann-Pick disease type C1 and XIAP deficiency with NOD2 variants in Crohn's disease.

Schwerd T, Pandey S, Yang HT, Bagola K, Jameson E, Jung J, Lachmann RH, Shah N, Patel SY, Booth C, Runz H, Düker G, Bettels R, Rohrbach M, Kugathasan S, Chapel H, Keshav S, Elkadri A, Platt N, Muise AM, Koletzko S, Xavier RJ, Marquardt T, Powrie F, Wraith JE, Gyrd-Hansen M, Platt FM, Uhlig HH
Gut. 2016;66(6):1060-1073 - PMID: 26953272 - PMCID: PMC5532464 - DOI: 10.1136/gutjnl-2015-310382

?v Integrins combine with LC3 and atg5 to regulate Toll-like receptor signalling in B cells.

Acharya M, Sokolovska A, Tam JM, Conway KL, Stefani C, Raso F, Mukhopadhyay S, Feliu M, Paul E, Savill J, Hynes RO, Xavier RJ, Vyas JM, Stuart LM, Lacy-Hulbert A
Nat Commun. 2016;7:10917 - PMID: 26965188 - PMCID: PMC4792966 - DOI: 10.1038/ncomms10917

Timothy C. Wang, MD: Our next AGA President.

Abrams JA, Xavier RJ, Rustgi AK
Gastroenterology. 2016;150(5):1231-6 - PMID: 27018487 - DOI: 10.1053/j.gastro.2016.03.021

Trained immunity: A program of innate immune memory in health and disease.

Netea MG, Joosten LA, Latz E, Mills KH, Natoli G, Stunnenberg HG, O'Neill LA, Xavier RJ
Science. 2016;352(6284):aaf1098 - PMID: 27102489 - PMCID: PMC5087274 - DOI: 10.1126/science.aaf1098

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, , Xavier RJ
Cell. 2016;165(4):842-53 - PMID: 27133167 - PMCID: PMC4950857 - DOI: 10.1016/j.cell.2016.04.007

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, DIABIMMUNE Study Group, Xavier RJ
Cell. 2016;165(4):842-53 - PMID: 27133167 - PMCID: PMC4950857 - DOI: 10.1016/j.cell.2016.04.007

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity.

Zhernakova A, Kurilshikov A, Bonder MJ, Tigchelaar EF, Schirmer M, Vatanen T, Mujagic Z, Vila AV, Falony G, Vieira-Silva S, Wang J, Imhann F, Brandsma E, Jankipersadsing SA, Joossens M, Cenit MC, Deelen P, Swertz MA, , Weersma RK, Feskens EJ, Netea MG, Gevers D, Jonkers D, Franke L, Aulchenko YS, Huttenhower C, Raes J, Hofker MH, Xavier RJ, Wijmenga C, Fu J
Science. 2016;352(6285):565-9 - PMID: 27126040 - PMCID: PMC5240844 - DOI: 10.1126/science.aad3369

Mechanisms of Pediatric Inflammatory Bowel Disease.

Peloquin JM, Goel G, Villablanca EJ, Xavier RJ
Annu Rev Immunol. 2016;34:31-64 - PMID: 27168239 - DOI: 10.1146/annurev-immunol-032414-112151

Clinical Activity and Quality of Life Indices Are Valid Across Ulcerative Colitis But Not Crohn's Disease Phenotypes.

Taleban S, Stewart KO, Li DK, Singh P, Pardi DS, Sturgeon HC, Yajnik V, Xavier RJ, Ananthakrishnan AN, Khalili H
Dig Dis Sci. 2016;61(9):2627-35 - PMID: 27142671 - PMCID: PMC4982770 - DOI: 10.1007/s10620-016-4180-8

Gene-microbiota interactions contribute to the pathogenesis of inflammatory bowel disease.

Chu H, Khosravi A, Kusumawardhani IP, Kwon AH, Vasconcelos AC, Cunha LD, Mayer AE, Shen Y, Wu WL, Kambal A, Targan SR, Xavier RJ, Ernst PB, Green DR, McGovern DP, Virgin HW, Mazmanian SK
Science. 2016;352(6289):1116-20 - PMID: 27230380 - PMCID: PMC4996125 - DOI: 10.1126/science.aad9948

CARD9 impacts colitis by altering gut microbiota metabolism of tryptophan into aryl hydrocarbon receptor ligands.

Lamas B, Richard ML, Leducq V, Pham HP, Michel ML, Da Costa G, Bridonneau C, Jegou S, Hoffmann TW, Natividad JM, Brot L, Taleb S, Couturier-Maillard A, Nion-Larmurier I, Merabtene F, Seksik P, Bourrier A, Cosnes J, Ryffel B, Beaugerie L, Launay JM, Langella P, Xavier RJ, Sokol H
Nat Med. 2016;22(6):598-605 - PMID: 27158904 - PMCID: PMC5087285 - DOI: 10.1038/nm.4102

Simultaneous Pathway Activity Inference and Gene Expression Analysis Using RNA Sequencing.

O'Connell DJ, Kolde R, Sooknah M, Graham DB, Sundberg TB, Latorre IJ, Mikkelsen TS, Xavier RJ
Cell Syst. 2016;2(5):323-334 - PMID: 27211859 - PMCID: PMC5032147 - DOI: 10.1016/j.cels.2016.04.011

Development of Chemical Probes for Investigation of Salt-Inducible Kinase Function In Vivo.

Sundberg TB, Liang Y, Wu H, Choi HG, Kim ND, Sim T, Johannessen L, Petrone A, Khor B, Graham DB, Latorre IJ, Phillips AJ, Schreiber SL, Perez J, Shamji AF, Gray NS, Xavier RJ
ACS Chem Biol. 2016;11(8):2105-11 - PMID: 27224444 - PMCID: PMC4992440 - DOI: 10.1021/acschembio.6b00217

Metagenomic Characterization of Microbial Communities In Situ Within the Deeper Layers of the Ileum in Crohn's Disease.

Pedamallu CS, Bhatt AS, Bullman S, Fowler S, Freeman SS, Durand J, Jung J, Duke F, Manzo V, Cai D, Ananthakrishnan A, Ojesina AI, Ramachandran A, Gevers D, Xavier RJ, Bhan AK, Meyerson M, Yajnik V
Cell Mol Gastroenterol Hepatol. 2016;2(5):563-566.e5 - PMID: 28174737 - PMCID: PMC5042890 - DOI: 10.1016/j.jcmgh.2016.05.011

Natural history of the infant gut microbiome and impact of antibiotic treatment on bacterial strain diversity and stability.

Yassour M, Vatanen T, Siljander H, Hämäläinen AM, Härkönen T, Ryhänen SJ, Franzosa EA, Vlamakis H, Huttenhower C, Gevers D, Lander ES, Knip M, , Xavier RJ
Sci Transl Med. 2016;8(343):343ra81 - PMID: 27306663 - PMCID: PMC5032909 - DOI: 10.1126/scitranslmed.aad0917

Variation in Microbiome LPS Immunogenicity Contributes to Autoimmunity in Humans.

Vatanen T, Kostic AD, d'Hennezel E, Siljander H, Franzosa EA, Yassour M, Kolde R, Vlamakis H, Arthur TD, Hämäläinen AM, Peet A, Tillmann V, Uibo R, Mokurov S, Dorshakova N, Ilonen J, Virtanen SM, Szabo SJ, Porter JA, Lähdesmäki H, Huttenhower C, Gevers D, Cullen TW, Knip M, , Xavier RJ
Cell. 2016;165(6):1551 - PMID: 27259157 - DOI: 10.1016/j.cell.2016.05.056

Genetic Coding Variant in GPR65 Alters Lysosomal pH and Links Lysosomal Dysfunction with Colitis Risk.

Lassen KG, McKenzie CI, Mari M, Murano T, Begun J, Baxt LA, Goel G, Villablanca EJ, Kuo SY, Huang H, Macia L, Bhan AK, Batten M, Daly MJ, Reggiori F, Mackay CR, Xavier RJ
Immunity. 2016;44(6):1392-1405 - PMID: 27287411 - PMCID: PMC4936415 - DOI: 10.1016/j.immuni.2016.05.007

The T300A Crohn's disease risk polymorphism impairs function of the WD40 domain of ATG16L1.

Boada-Romero E, Serramito-Gómez I, Sacristán MP, Boone DL, Xavier RJ, Pimentel-Muiños FX
Nat Commun. 2016;7:11821 - PMID: 27273576 - PMCID: PMC4899871 - DOI: 10.1038/ncomms11821

Profiling DNA damage-induced phosphorylation in budding yeast reveals diverse signaling networks.

Zhou C, Elia AE, Naylor ML, Dephoure N, Ballif BA, Goel G, Xu Q, Ng A, Chou DM, Xavier RJ, Gygi SP, Elledge SJ
Proc Natl Acad Sci U S A. 2016;113(26):E3667-75 - PMID: 27298372 - PMCID: PMC4932963 - DOI: 10.1073/pnas.1602827113

Microbiota as Therapeutic Targets.

Xavier RJ
Dig Dis. 2016;34(5):558-565 - PMID: 27331403 - DOI: 10.1159/000445263

Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62.

DeJesus R, Moretti F, McAllister G, Wang Z, Bergman P, Liu S, Frias E, Alford J, Reece-Hoyes JS, Lindeman A, Kelliher J, Russ C, Knehr J, Carbone W, Beibel M, Roma G, Ng A, Tallarico JA, Porter JA, Xavier RJ, Mickanin C, Murphy LO, Hoffman GR, Nyfeler B
Elife. 2016;5:ePub - PMID: 27351204 - PMCID: PMC4924995 - DOI: 10.7554/eLife.17290

Inter-individual variability and genetic influences on cytokine responses to bacteria and fungi.

Li Y, Oosting M, Deelen P, Ricaño-Ponce I, Smeekens S, Jaeger M, Matzaraki V, Swertz MA, Xavier RJ, Franke L, Wijmenga C, Joosten LA, Kumar V, Netea MG
Nat Med. 2016;22(8):952-960 - PMID: 27376574 - PMCID: PMC5084084 - DOI: 10.1038/nm.4139

Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease.

Shaw KA, Bertha M, Hofmekler T, Chopra P, Vatanen T, Srivatsa A, Prince J, Kumar A, Sauer C, Zwick ME, Satten GA, Kostic AD, Mulle JG, Xavier RJ, Kugathasan S
Genome Med. 2016;8(1):75 - PMID: 27412252 - PMCID: PMC4944441 - DOI: 10.1186/s13073-016-0331-y

A pleiotropic missense variant in SLC39A8 is associated with Crohn's disease and human gut microbiome composition.

Li D, Achkar JP, Haritunians T, Jacobs JP, Hui KY, D'Amato M, Brand S, Radford-Smith G, Halfvarson J, Niess JH, Kugathasan S, Büning C, Schumm LP, Klei L, Ananthakrishnan A, Aumais G, Baidoo L, Dubinsky M, Fiocchi C, Glas J, Milgrom R, Proctor DD, Regueiro M, Simms LA, Stempak JM, Targan SR, Törkvist L, Sharma Y, Devlin B, Borneman J, Hakonarson H, Xavier RJ, Daly M, Brant SR, Rioux JD, Silverberg MS, Cho JH, Braun J, McGovern DP, Duerr RH
Gastroenterology. 2016;151(4):724-32 - PMID: 27492617 - PMCID: PMC5037008 - DOI: 10.1053/j.gastro.2016.06.051

Understanding human immune function using the resources from the Human Functional Genomics Project.

Netea MG, Joosten LA, Li Y, Kumar V, Oosting M, Smeekens S, Jaeger M, Ter Horst R, Schirmer M, Vlamakis H, Notebaart R, Pavelka N, Aguirre-Gamboa RR, Swertz MA, Tunjungputri RN, van de Heijden W, Franzosa EA, Ng A, Graham D, Lassen K, Schraa K, Netea-Maier R, Smit J, de Mast Q, van de Veerdonk F, Kullberg BJ, Tack C, van de Munckhof I, Rutten J, van der Graaf J, Franke L, Hofker M, Jonkers I, Platteel M, Maatman A, Fu J, Zhernakova A, van der Meer JW, Dinarello CA, van der Ven A, Huttenhouwe ...
Nat Med. 2016;22(8):831-833 - PMID: 27490433 - DOI: 10.1038/nm.4140

A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis.

Rivas MA, Graham D, Sulem P, Stevens C, Desch AN, Goyette P, Gudbjartsson D, Jonsdottir I, Thorsteinsdottir U, Degenhardt F, Mucha S, Kurki MI, Li D, D'Amato M, Annese V, Vermeire S, Weersma RK, Halfvarson J, Paavola-Sakki P, Lappalainen M, Lek M, Cummings B, Tukiainen T, Haritunians T, Halme L, Koskinen LL, Ananthakrishnan AN, Luo Y, Heap GA, Visschedijk MC, , , MacArthur DG, Neale BM, Ahmad T, Anderson CA, Brant SR, Duerr RH, Silverberg MS, Cho JH, Palotie A, Saavalainen P, Kontula K, Fä ...
Nat Commun. 2016;7:12342 - PMID: 27503255 - PMCID: PMC4980482 - DOI: 10.1038/ncomms12342

Characterization of candidate genes in inflammatory bowel disease-associated risk loci.

Peloquin JM, Goel G, Kong L, Huang H, Haritunians T, Sartor RB, Daly MJ, Newberry RD, McGovern DP, Yajnik V, Lira SA, Xavier RJ
JCI Insight. 2016;1(13):e87899 - PMID: 27668286 - PMCID: PMC5033062 - DOI: 10.1172/jci.insight.87899

Increased Intestinal Microbial Diversity Following Fecal Microbiota Transplant for Active Crohn's Disease.

Vaughn BP, Vatanen T, Allegretti JR, Bai A, Xavier RJ, Korzenik J, Gevers D, Ting A, Robson SC, Moss AC
Inflamm Bowel Dis. 2016;22(9):2182-90 - PMID: 27542133 - PMCID: PMC4995064 - DOI: 10.1097/MIB.0000000000000893

Succinate Dehydrogenase Supports Metabolic Repurposing of Mitochondria to Drive Inflammatory Macrophages.

Mills EL, Kelly B, Logan A, Costa AS, Varma M, Bryant CE, Tourlomousis P, Däbritz JH, Gottlieb E, Latorre I, Corr SC, McManus G, Ryan D, Jacobs HT, Szibor M, Xavier RJ, Braun T, Frezza C, Murphy MP, O'Neill LA
Cell. 2016;167(2):457-470.e13 - PMID: 27667687 - PMCID: PMC5863951 - DOI: 10.1016/j.cell.2016.08.064

Interplay of host genetics and gut microbiota underlying the onset and clinical presentation of inflammatory bowel disease.

Imhann F, Vich Vila A, Bonder MJ, Fu J, Gevers D, Visschedijk MC, Spekhorst LM, Alberts R, Franke L, van Dullemen HM, Ter Steege RW, Huttenhower C, Dijkstra G, Xavier RJ, Festen EA, Wijmenga C, Zhernakova A, Weersma RK
Gut. 2016;67(1):108-119 - PMID: 27802154 - PMCID: PMC5699972 - DOI: 10.1136/gutjnl-2016-312135

SIKs control osteocyte responses to parathyroid hormone.

Wein MN, Liang Y, Goransson O, Sundberg TB, Wang J, Williams EA, O'Meara MJ, Govea N, Beqo B, Nishimori S, Nagano K, Brooks DJ, Martins JS, Corbin B, Anselmo A, Sadreyev R, Wu JY, Sakamoto K, Foretz M, Xavier RJ, Baron R, Bouxsein ML, Gardella TJ, Divieti-Pajevic P, Gray NS, Kronenberg HM
Nat Commun. 2016;7:13176 - PMID: 27759007 - PMCID: PMC5075806 - DOI: 10.1038/ncomms13176

Vedolizumab Therapy Is Associated with an Improvement in Sleep Quality and Mood in Inflammatory Bowel Diseases.

Stevens BW, Borren NZ, Velonias G, Conway G, Cleland T, Andrews E, Khalili H, Garber JG, Xavier RJ, Yajnik V, Ananthakrishnan AN
Dig Dis Sci. 2016;62(1):197-206 - PMID: 27796768 - PMCID: PMC5218976 - DOI: 10.1007/s10620-016-4356-2

RNF166 Determines Recruitment of Adaptor Proteins during Antibacterial Autophagy.

Heath RJ, Goel G, Baxt LA, Rush JS, Mohanan V, Paulus GL, Jani V, Lassen KG, Xavier RJ
Cell Rep. 2016;17(9):2183-2194 - PMID: 27880896 - PMCID: PMC5192565 - DOI: 10.1016/j.celrep.2016.11.005

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LA, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ
Cell. 2016;167(4):1125-1136.e8 - PMID: 27814509 - PMCID: PMC5131922 - DOI: 10.1016/j.cell.2016.10.020

Host and Environmental Factors Influencing Individual Human Cytokine Responses.

Ter Horst R, Jaeger M, Smeekens SP, Oosting M, Swertz MA, Li Y, Kumar V, Diavatopoulos DA, Jansen AF, Lemmers H, Toenhake-Dijkstra H, van Herwaarden AE, Janssen M, van der Molen RG, Joosten I, Sweep FC, Smit JW, Netea-Maier RT, Koenders MM, Xavier RJ, van der Meer JW, Dinarello CA, Pavelka N, Wijmenga C, Notebaart RA, Joosten LA, Netea MG
Cell. 2016;167(4):1111-1124.e13 - PMID: 27814508 - PMCID: PMC5787854 - DOI: 10.1016/j.cell.2016.10.018

A Functional Genomics Approach to Understand Variation in Cytokine Production in Humans.

Li Y, Oosting M, Smeekens SP, Jaeger M, Aguirre-Gamboa R, Le KT, Deelen P, Ricaño-Ponce I, Schoffelen T, Jansen AF, Swertz MA, Withoff S, van de Vosse E, van Deuren M, van de Veerdonk F, Zhernakova A, van der Meer JW, Xavier RJ, Franke L, Joosten LA, Wijmenga C, Kumar V, Netea MG
Cell. 2016;167(4):1099-1110.e14 - PMID: 27814507 - DOI: 10.1016/j.cell.2016.10.017

Differential Effects of Environmental and Genetic Factors on T and B Cell Immune Traits.

Aguirre-Gamboa R, Joosten I, Urbano PC, van der Molen RG, van Rijssen E, van Cranenbroek B, Oosting M, Smeekens S, Jaeger M, Zorro M, Withoff S, van Herwaarden AE, Sweep FC, Netea RT, Swertz MA, Franke L, Xavier RJ, Joosten LA, Netea MG, Wijmenga C, Kumar V, Li Y, Koenen HJ
Cell Rep. 2016;17(9):2474-2487 - PMID: 27818087 - PMCID: PMC5130901 - DOI: 10.1016/j.celrep.2016.10.053

Glutaminolysis and Fumarate Accumulation Integrate Immunometabolic and Epigenetic Programs in Trained Immunity.

Arts RJ, Novakovic B, Ter Horst R, Carvalho A, Bekkering S, Lachmandas E, Rodrigues F, Silvestre R, Cheng SC, Wang SY, Habibi E, Gonçalves LG, Mesquita I, Cunha C, van Laarhoven A, van de Veerdonk FL, Williams DL, van der Meer JW, Logie C, O'Neill LA, Dinarello CA, Riksen NP, van Crevel R, Clish C, Notebaart RA, Joosten LA, Stunnenberg HG, Xavier RJ, Netea MG
Cell Metab. 2016;24(6):807-819 - PMID: 27866838 - PMCID: PMC5742541 - DOI: 10.1016/j.cmet.2016.10.008

Visceral Adiposity, Genetic Susceptibility, and Risk of Complications Among Individuals with Crohn's Disease.

Van Der Sloot KW, Joshi AD, Bellavance DR, Gilpin KK, Stewart KO, Lochhead P, Garber JJ, Giallourakis C, Yajnik V, Ananthakrishnan AN, Alizadeh BZ, Xavier RJ, Khalili H
Inflamm Bowel Dis. 2016;23(1):82-88 - PMID: 27893544 - PMCID: PMC5177457 - DOI: 10.1097/MIB.0000000000000978

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

Graham DB, Lefkovith A, Deelen P, de Klein N, Varma M, Boroughs A, Desch AN, Ng AC, Guzman G, Schenone M, Petersen CP, Bhan AK, Rivas MA, Daly MJ, Carr SA, Wijmenga C, Xavier RJ
Cell Rep. 2016;17(11):2955-2965 - PMID: 27974209 - PMCID: PMC5661940 - DOI: 10.1016/j.celrep.2016.11.042

Linking the Human Gut Microbiome to Inflammatory Cytokine Production Capacity.

Schirmer M, Smeekens SP, Vlamakis H, Jaeger M, Oosting M, Franzosa EA, Horst RT, Jansen T, Jacobs L, Bonder MJ, Kurilshikov A, Fu J, Joosten LA, Zhernakova A, Huttenhower C, Wijmenga C, Netea MG, Xavier RJ
Cell. 2016;167(7):1897 - PMID: 27984736 - DOI: 10.1016/j.cell.2016.11.046

The Csk-Associated Adaptor PAG Inhibits Effector T Cell Activation in Cooperation with Phosphatase PTPN22 and Dok Adaptors.

Davidson D, Zhong MC, Pandolfi PP, Bolland S, Xavier RJ, Seed B, Li X, Gu H, Veillette A
Cell Rep. 2016;17(10):2776-2788 - PMID: 27926878 - PMCID: PMC5656005 - DOI: 10.1016/j.celrep.2016.11.035

The Role of the Histone Methyltransferase Enhancer of Zeste Homolog 2 (EZH2) in the Pathobiological Mechanisms Underlying Inflammatory Bowel Disease (IBD).

Sarmento OF, Svingen PA, Xiong Y, Sun Z, Bamidele AO, Mathison AJ, Smyrk TC, Nair AA, Gonzalez MM, Sagstetter MR, Baheti S, McGovern DP, Friton JJ, Papadakis KA, Gautam G, Xavier RJ, Urrutia RA, Faubion WA
J Biol Chem. 2016;292(2):706-722 - PMID: 27909059 - PMCID: PMC5241744 - DOI: 10.1074/jbc.M116.749663

The Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis and Anti-tuberculous Host Defense.

Franco LH, Nair VR, Scharn CR, Xavier RJ, Torrealba JR, Shiloh MU, Levine B
Cell Host Microbe. 2016;21(1):59-72 - PMID: 28017659 - PMCID: PMC5699477 - DOI: 10.1016/j.chom.2016.11.002

Prediction of complicated disease course for children newly diagnosed with Crohn's disease: a multicentre inception cohort study.

Kugathasan S, Denson LA, Walters TD, Kim MO, Marigorta UM, Schirmer M, Mondal K, Liu C, Griffiths A, Noe JD, Crandall WV, Snapper S, Rabizadeh S, Rosh JR, Shapiro JM, Guthery S, Mack DR, Kellermayer R, Kappelman MD, Steiner S, Moulton DE, Keljo D, Cohen S, Oliva-Hemker M, Heyman MB, Otley AR, Baker SS, Evans JS, Kirschner BS, Patel AS, Ziring D, Trapnell BC, Sylvester FA, Stephens MC, Baldassano RN, Markowitz JF, Cho J, Xavier RJ, Huttenhower C, Aronow BJ, Gibson G, Hyams JS, Dubinsky MC
Lancet. 2017;389(10080):1710-1718 - PMID: 28259484 - PMCID: PMC5719489 - DOI: 10.1016/S0140-6736(17)30317-3

A Microbiome Foundation for the Study of Crohn's Disease.

Gevers D, Kugathasan S, Knights D, Kostic AD, Knight R, Xavier RJ
Cell Host Microbe. 2017;21(3):301-304 - PMID: 28279336 - PMCID: PMC5684696 - DOI: 10.1016/j.chom.2017.02.012

Maintenance of macrophage transcriptional programs and intestinal homeostasis by epigenetic reader SP140.

Mehta S, Cronkite DA, Basavappa M, Saunders TL, Adiliaghdam F, Amatullah H, Morrison SA, Pagan JD, Anthony RM, Tonnerre P, Lauer GM, Lee JC, Digumarthi S, Pantano L, Ho Sui SJ, Ji F, Sadreyev R, Zhou C, Mullen AC, Kumar V, Li Y, Wijmenga C, Xavier RJ, Means TK, Jeffrey KL
Sci Immunol. 2017;2(9):ePub - PMID: 28783698 - PMCID: PMC5549562 - DOI: 10.1126/sciimmunol.aag3160

Reovirus infection triggers inflammatory responses to dietary antigens and development of celiac disease.

Bouziat R, Hinterleitner R, Brown JJ, Stencel-Baerenwald JE, Ikizler M, Mayassi T, Meisel M, Kim SM, Discepolo V, Pruijssers AJ, Ernest JD, Iskarpatyoti JA, Costes LM, Lawrence I, Palanski BA, Varma M, Zurenski MA, Khomandiak S, McAllister N, Aravamudhan P, Boehme KW, Hu F, Samsom JN, Reinecker HC, Kupfer SS, Guandalini S, Semrad CE, Abadie V, Khosla C, Barreiro LB, Xavier RJ, Ng A, Dermody TS, Jabri B
Science. 2017;356(6333):44-50 - PMID: 28386004 - PMCID: PMC5506690 - DOI: 10.1126/science.aah5298

Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases.

Ananthakrishnan AN, Luo C, Yajnik V, Khalili H, Garber JJ, Stevens BW, Cleland T, Xavier RJ
Cell Host Microbe. 2017;21(5):603-610.e3 - PMID: 28494241 - PMCID: PMC5705050 - DOI: 10.1016/j.chom.2017.04.010

Epitope-specific immunotherapy targeting CD4-positive T cells in coeliac disease: two randomised, double-blind, placebo-controlled phase 1 studies.

Goel G, King T, Daveson AJ, Andrews JM, Krishnarajah J, Krause R, Brown GJE, Fogel R, Barish CF, Epstein R, Kinney TP, Miner PB, Tye-Din JA, Girardin A, Taavela J, Popp A, Sidney J, Mäki M, Goldstein KE, Griffin PH, Wang S, Dzuris JL, Williams LJ, Sette A, Xavier RJ, Sollid LM, Jabri B, Anderson RP
Lancet Gastroenterol Hepatol. 2017;2(7):479-493 - PMID: 28506538 - PMCID: PMC5676538 - DOI: 10.1016/S2468-1253(17)30110-3

Selective Induction of Homeostatic Th17 Cells in the Murine Intestine by Cholera Toxin Interacting with the Microbiota.

Zhao Q, Harbour SN, Kolde R, Latorre IJ, Tun HM, Schoeb TR, Turner H, Moon JJ, Khafipour E, Xavier RJ, Weaver CT, Elson CO
J Immunol. 2017;199(1):312-322 - PMID: 28539431 - PMCID: PMC5539960 - DOI: 10.4049/jimmunol.1700171

Dissecting the human microbiome with single-cell genomics.

Tolonen AC, Xavier RJ
Genome Med. 2017;9(1):56 - PMID: 28615076 - PMCID: PMC5471897 - DOI: 10.1186/s13073-017-0448-7

E3 Ubiquitin ligase ZNRF4 negatively regulates NOD2 signalling and induces tolerance to MDP.

Bist P, Cheong WS, Ng A, Dikshit N, Kim BH, Pulloor NK, Khameneh HJ, Hedl M, Shenoy AR, Balamuralidhar V, Malik NBA, Hong M, Neutzner A, Chin KC, Kobayashi KS, Bertoletti A, Mortellaro A, Abraham C, MacMicking JD, Xavier RJ, Sukumaran B
Nat Commun. 2017;8:15865 - PMID: 28656966 - PMCID: PMC5493756 - DOI: 10.1038/ncomms15865

Fine-mapping inflammatory bowel disease loci to single-variant resolution.

Huang H, Fang M, Jostins L, Umićević Mirkov M, Boucher G, Anderson CA, Andersen V, Cleynen I, Cortes A, Crins F, D'Amato M, Deffontaine V, Dmitrieva J, Docampo E, Elansary M, Farh KK, Franke A, Gori AS, Goyette P, Halfvarson J, Haritunians T, Knight J, Lawrance IC, Lees CW, Louis E, Mariman R, Meuwissen T, Mni M, Momozawa Y, Parkes M, Spain SL, Théâtre E, Trynka G, Satsangi J, van Sommeren S, Vermeire S, Xavier RJ, International Inflammatory Bowel Disease Genetics Consortium, Weersma RK, Due ...
Nature. 2017;547(7662):173-178 - PMID: 28658209 - PMCID: PMC5511510 - DOI: 10.1038/nature22969

Indoleacrylic Acid Produced by Commensal Peptostreptococcus Species Suppresses Inflammation.

Wlodarska M, Luo C, Kolde R, d'Hennezel E, Annand JW, Heim CE, Krastel P, Schmitt EK, Omar AS, Creasey EA, Garner AL, Mohammadi S, O'Connell DJ, Abubucker S, Arthur TD, Franzosa EA, Huttenhower C, Murphy LO, Haiser HJ, Vlamakis H, Porter JA, Xavier RJ
Cell Host Microbe. 2017;22(1):25-37.e6 - PMID: 28704649 - PMCID: PMC5672633 - DOI: 10.1016/j.chom.2017.06.007

Intestinal virome changes precede autoimmunity in type I diabetes-susceptible children.

Zhao G, Vatanen T, Droit L, Park A, Kostic AD, Poon TW, Vlamakis H, Siljander H, Härkönen T, Hämäläinen AM, Peet A, Tillmann V, Ilonen J, Wang D, Knip M, Xavier RJ, Virgin HW
Proc Natl Acad Sci U S A. 2017;114(30):E6166-E6175 - PMID: 28696303 - PMCID: PMC5544325 - DOI: 10.1073/pnas.1706359114

Paneth cells secrete lysozyme via secretory autophagy during bacterial infection of the intestine.

Bel S, Pendse M, Wang Y, Li Y, Ruhn KA, Hassell B, Leal T, Winter SE, Xavier RJ, Hooper LV
Science. 2017;357(6355):1047-1052 - PMID: 28751470 - PMCID: PMC5702267 - DOI: 10.1126/science.aal4677

Small-molecule studies identify CDK8 as a regulator of IL-10 in myeloid cells.

Johannessen L, Sundberg TB, O'Connell DJ, Kolde R, Berstler J, Billings KJ, Khor B, Seashore-Ludlow B, Fassl A, Russell CN, Latorre IJ, Jiang B, Graham DB, Perez JR, Sicinski P, Phillips AJ, Schreiber SL, Gray NS, Shamji AF, Xavier RJ
Nat Chem Biol. 2017;13(10):1102-1108 - PMID: 28805801 - PMCID: PMC5693369 - DOI: 10.1038/nchembio.2458

Human genetic variation and the gut microbiome in disease.

Hall AB, Tolonen AC, Xavier RJ
Nat Rev Genet. 2017;18(11):690-699 - PMID: 28824167 - DOI: 10.1038/nrg.2017.63

SHANK3 Regulates Intestinal Barrier Function Through Modulating ZO-1 Expression Through the PKCε-dependent Pathway.

Wei SC, Yang-Yen HF, Tsao PN, Weng MT, Tung CC, Yu LCH, Lai LC, Hsiao JH, Chuang EY, Shun CT, Ni YH, Xavier RJ, Podolsky DK, Yen JJY, Wong JM
Inflamm Bowel Dis. 2017;:ePub - PMID: 28922251

The Ubiquitin Ligase Smurf1 Functions in Selective Autophagy of Mycobacterium tuberculosis and Anti-tuberculous Host Defense.

Franco LH, Nair VR, Scharn CR, Xavier RJ, Torrealba JR, Shiloh MU, Levine B
Cell Host Microbe. 2017;22(3):421-423 - PMID: 28910640 - PMCID: PMC5818210 - DOI: 10.1016/j.chom.2017.08.005

Autophagy-Independent Lysosomal Targeting Regulated by ULK1/2-FIP200 and ATG9.

Goodwin JM, Dowdle WE, DeJesus R, Wang Z, Bergman P, Kobylarz M, Lindeman A, Xavier RJ, McAllister G, Nyfeler B, Hoffman G, Murphy LO
Cell Rep. 2017;20(10):2341-2356 - PMID: 28877469 - PMCID: PMC5699710 - DOI: 10.1016/j.celrep.2017.08.034

Ectopic colonization of oral bacteria in the intestine drives TH1 cell induction and inflammation.

Atarashi K, Suda W, Luo C, Kawaguchi T, Motoo I, Narushima S, Kiguchi Y, Yasuma K, Watanabe E, Tanoue T, Thaiss CA, Sato M, Toyooka K, Said HS, Yamagami H, Rice SA, Gevers D, Johnson RC, Segre JA, Chen K, Kolls JK, Elinav E, Morita H, Xavier RJ, Hattori M, Honda K
Science. 2017;358(6361):359-365 - PMID: 29051379 - PMCID: PMC5682622 - DOI: 10.1126/science.aan4526

SHANK3 Regulates Intestinal Barrier Function Through Modulating ZO-1 Expression Through the PKCε-dependent Pathway.

Wei SC, Yang-Yen HF, Tsao PN, Weng MT, Tung CC, Yu LCH, Lai LC, Hsiao JH, Chuang EY, Shun CT, Ni YH, Xavier RJ, Podolsky DK, Yen JJY, Wong JM
Inflamm Bowel Dis. 2017;23(10):1730-1740 - PMID: 28906292 - DOI: 10.1097/MIB.0000000000001250

Small-molecule inhibitors directly target CARD9 and mimic its protective variant in inflammatory bowel disease.

Leshchiner ES, Rush JS, Durney MA, Cao Z, Dančík V, Chittick B, Wu H, Petrone A, Bittker JA, Phillips A, Perez JR, Shamji AF, Kaushik VK, Daly MJ, Graham DB, Schreiber SL, Xavier RJ
Proc Natl Acad Sci U S A. 2017;114(43):11392-11397 - PMID: 29073062 - PMCID: PMC5664502 - DOI: 10.1073/pnas.1705748114

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

Li Y, Lv M, Su C, Long S, Zhang W, Conway KL, Li W, Xavier RJ, Shi HN
Front Immunol. 2017;8:1270 - PMID: 29062317 - PMCID: PMC5640886 - DOI: 10.3389/fimmu.2017.01270

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

Murano T, Najibi M, Paulus GLC, Adiliaghdam F, Valencia-Guerrero A, Selig M, Wang X, Jeffrey K, Xavier RJ, Lassen KG, Irazoqui JE
Sci Rep. 2017;7(1):13938 - PMID: 29066772 - PMCID: PMC5655326 - DOI: 10.1038/s41598-017-14370-4

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

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
Sci Transl Med. 2017;9(416):ePub - PMID: 29141885 - PMCID: PMC5808452 - DOI: 10.1126/scitranslmed.aah6888

A single-cell survey of the small intestinal epithelium.

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
Nature. 2017;551(7680):333-339 - PMID: 29144463 - PMCID: PMC6022292 - DOI: 10.1038/nature24489

Mechanisms and Function of Autophagy in Intestinal Disease.

Lassen KG, Xavier RJ
Autophagy. 2017;14(2):0 - PMID: 29130415 - PMCID: PMC5902220 - DOI: 10.1080/15548627.2017.1389358

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

Borren NZ, Conway G, Garber JJ, Khalili H, Budree S, Mallick H, Yajnik V, Xavier RJ, Ananthakrishnan AN
J Crohns Colitis. 2017;12(5):525-531 - PMID: 29145572 - PMCID: PMC6018966 - DOI: 10.1093/ecco-jcc/jjx154

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

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
Genome Med. 2017;9(1):103 - PMID: 29183332 - PMCID: PMC5704459 - DOI: 10.1186/s13073-017-0490-5

Dynamics of metatranscription in the inflammatory bowel disease gut microbiome.

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
Nat Microbiol. 2018;3(3):337-346 - PMID: 29311644 - PMCID: PMC6131705 - DOI: 10.1038/s41564-017-0089-z

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

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
J Crohns Colitis. 2018;12(5):582-588 - PMID: 29361163 - DOI: 10.1093/ecco-jcc/jjy001

Loss of Response to Anti-Tumor Necrosis Factor Alpha Therapy in Crohn's Disease Is Not Associated with Emergence of Novel Inflammatory Pathways.

Luther J, Gala M, Patel SJ, Dave M, Borren N, Xavier RJ, Ananthakrishnan AN
Dig Dis Sci. 2018;63(3):738-745 - PMID: 29372477 - PMCID: PMC6152907 - DOI: 10.1007/s10620-018-4932-8

Host genetic variation and its microbiome interactions within the Human Microbiome Project.

Kolde R, Franzosa EA, Rahnavard G, Hall AB, Vlamakis H, Stevens C, Daly MJ, Xavier RJ, Huttenhower C
Genome Med. 2018;10(1):6 - PMID: 29378630 - PMCID: PMC5789541 - DOI: 10.1186/s13073-018-0515-8

Strain Tracking Reveals the Determinants of Bacterial Engraftment in the Human Gut Following Fecal Microbiota Transplantation.

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
Cell Host Microbe. 2018;23(2):229-240.e5 - PMID: 29447696 - DOI: 10.1016/j.chom.2018.01.003

C1orf106 is a colitis risk gene that regulates stability of epithelial adherens junctions.

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
Science. 2018;359(6380):1161-1166 - PMID: 29420262 - PMCID: PMC6008784 - DOI: 10.1126/science.aan0814

A common mechanism links activities of butyrate in the colon.

Verma MS, Fink MJ, Salmon GL, Fornelos N, Ohara TE, Ryu SH, Vlamakis H, Xavier RJ, Stappenbeck TS, Whitesides GM
ACS Chem Biol. 2018;13(5):1291-1298 - PMID: 29584955 - DOI: 10.1021/acschembio.8b00073

Without Adaptive Immunity, There's a Cost to Responding STAT.

Brown EM, Xavier RJ
Cell Metab. 2018;27(4):705-707 - PMID: 29617636 - DOI: 10.1016/j.cmet.2018.03.011

Genetic Markers Predict Primary Nonresponse and Durable Response to Anti-Tumor Necrosis Factor Therapy in Ulcerative Colitis.

Burke KE, Khalili H, Garber JJ, Haritunians T, McGovern DPB, Xavier RJ, Ananthakrishnan AN
Inflamm Bowel Dis. 2018;24(8):1840-1848 - PMID: 29718226 - PMCID: PMC6128143 - DOI: 10.1093/ibd/izy083

Integration of multi-omics data and deep phenotyping enables prediction of cytokine responses.

Bakker OB, Aguirre-Gamboa R, Sanna S, Oosting M, Smeekens SP, Jaeger M, Zorro M, Võsa U, Withoff S, Netea-Maier RT, Koenen HJPM, Joosten I, Xavier RJ, Franke L, Joosten LAB, Kumar V, Wijmenga C, Netea MG, Li Y
Nat Immunol. 2018;19(7):776-786 - PMID: 29784908 - PMCID: PMC6022810 - DOI: 10.1038/s41590-018-0121-3

Insights into the genetic epidemiology of Crohn's and rare diseases in the Ashkenazi Jewish population.

Rivas MA, Avila BE, Koskela J, Huang H, Stevens C, Pirinen M, Haritunians T, Neale BM, Kurki M, Ganna A, Graham D, Glaser B, Peter I, Atzmon G, Barzilai N, Levine AP, Schiff E, Pontikos N, Weisburd B, Lek M, Karczewski KJ, Bloom J, Minikel EV, Petersen BS, Beaugerie L, Seksik P, Cosnes J, Schreiber S, Bokemeyer B, Bethge J, International IBD Genetics Consortium, NIDDK IBD Genetics Consortium, T2D-GENES Consortium, Heap G, Ahmad T, Plagnol V, Segal AW, Targan S, Turner D, Saavalainen P, Farkk ...
PLoS Genet. 2018;14(5):e1007329 - PMID: 29795570 - PMCID: PMC5967709 - DOI: 10.1371/journal.pgen.1007329

The causes and consequences of variation in human cytokine production in health.

Schirmer M, Kumar V, Netea MG, Xavier RJ
Curr Opin Immunol. 2018;54:50-58 - PMID: 29913309 - DOI: 10.1016/j.coi.2018.05.012

Nitric Oxide Engages an Anti-inflammatory Feedback Loop Mediated by Peroxiredoxin 5 in Phagocytes.

Graham DB, Jasso GJ, Mok A, Goel G, Ng ACY, Kolde R, Varma M, Doench JG, Root DE, Clish CB, Carr SA, Xavier RJ
Cell Rep. 2018;24(4):838-850 - PMID: 30044981 - PMCID: PMC6156773 - DOI: 10.1016/j.celrep.2018.06.081

Strain-Level Analysis of Mother-to-Child Bacterial Transmission during the First Few Months of Life.

Yassour M, Jason E, Hogstrom LJ, Arthur TD, Tripathi S, Siljander H, Selvenius J, Oikarinen S, Hyöty H, Virtanen SM, Ilonen J, Ferretti P, Pasolli E, Tett A, Asnicar F, Segata N, Vlamakis H, Lander ES, Huttenhower C, Knip M, Xavier RJ
Cell Host Microbe. 2018;24(1):146-154.e4 - PMID: 30001517 - PMCID: PMC6091882 - DOI: 10.1016/j.chom.2018.06.007

Impaired Aryl Hydrocarbon Receptor Ligand Production by the Gut Microbiota Is a Key Factor in Metabolic Syndrome.

Natividad JM, Agus A, Planchais J, Lamas B, Jarry AC, Martin R, Michel ML, Chong-Nguyen C, Roussel R, Straube M, Jegou S, McQuitty C, Le Gall M, da Costa G, Lecornet E, Michaudel C, Modoux M, Glodt J, Bridonneau C, Sovran B, Dupraz L, Bado A, Richard ML, Langella P, Hansel B, Launay JM, Xavier RJ, Duboc H, Sokol H
Cell Metab. 2018;28(5):737-749.e4 - PMID: 30057068 - DOI: 10.1016/j.cmet.2018.07.001

TMEM41B is a novel regulator of autophagy and lipid mobilization.

Moretti F, Bergman P, Dodgson S, Marcellin D, Claerr I, Goodwin JM, DeJesus R, Kang Z, Antczak C, Begue D, Bonenfant D, Graff A, Genoud C, Reece-Hoyes JS, Russ C, Yang Z, Hoffman GR, Mueller M, Murphy LO, Xavier RJ, Nyfeler B
EMBO Rep. 2018;19(9):ePub - PMID: 30126924 - PMCID: PMC6123663 - DOI: 10.15252/embr.201845889

Salt-Inducible Kinases: Physiology, Regulation by cAMP, and Therapeutic Potential.

Wein MN, Foretz M, Fisher DE, Xavier RJ, Kronenberg HM
Trends Endocrinol Metab. 2018;29(10):723-735 - PMID: 30150136 - PMCID: PMC6151151 - DOI: 10.1016/j.tem.2018.08.004

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course.

Schirmer M, Denson L, Vlamakis H, Franzosa EA, Thomas S, Gotman NM, Rufo P, Baker SS, Sauer C, Markowitz J, Pfefferkorn M, Oliva-Hemker M, Rosh J, Otley A, Boyle B, Mack D, Baldassano R, Keljo D, LeLeiko N, Heyman M, Griffiths A, Patel AS, Noe J, Kugathasan S, Walters T, Huttenhower C, Hyams J, Xavier RJ
Cell Host Microbe. 2018;24(4):600-610.e4 - PMID: 30308161 - DOI: 10.1016/j.chom.2018.09.009

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

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

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

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
Nature. 2018;562(7728):589-594 - PMID: 30356183 - DOI: 10.1038/s41586-018-0620-2

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

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
Cell. 2018;175(5):1307-1320.e22 - PMID: 30392957 - PMCID: PMC6239889 - DOI: 10.1016/j.cell.2018.10.008