Xavier Laboratory

The primary research goal of the Xavier Laboratory at Massachusetts General Hospital and the Broad Institute is to discover and understand the function of important mediators and effectors involved in both the innate and adaptive immune systems.

The primary research goal of the Xavier Laboratory at Massachusetts General Hospital and the Broad Institute is to discover and understand the function of important mediators and effectors involved in both the innate and adaptive immune systems. Of particular interest are the cellular components and regulatory networks that interact dynamically within temporal, spatial, and patho-physiological contexts of innate immunity. A second area of focus is to examine the pathway defects associated with genetic variants in inflammatory bowel disease and identify novel small molecules that interrupt signal transduction pathways associated with disease risk. We are pursuing integrative systems approaches that closely couple genome-wide experimentation with high-throughput assays and computational methods. Furthermore, we are pursuing studies of the microbiome in autoimmunity and inflammatory bowel disease.

Ramnik Xavier, MD, PhD
Kurt Isselbacher Professor of Medicine
Harvard Medical School
Massachusetts General Hospital
Simches Research Building
Boston, MA 02114
Phone: 617-643-3331

Fax: 617-643-3328

Leigh Baxt, PhD
Christine Becker, PhD
Angela Boroughs, BSc
Zhifang Cao, MSc, DSc
Kara Conway, PhD
Elizabeth Creasey, PhD
A. Nicole Desch, PhD
Kathy Devaney
Kevin Gao, BS
Gautam Goel, PhD
Jessica Gracias, MS
Daniel Graham, PhD
Robert Heath, PhD
Humberto Jijon, MD, PhD
Bernard Khor, MD, PhD
Raivo Kolde, PhD
Aleksandar Kostic, PhD
Szu-Yu (Meredith) Kuo, BS
Kara Lassen, PhD
Isabel Latorre, PhD
Aiping Liu
Chengwei Luo, PhD
Bibhu Mishra, PhD
Dileep Monie
Tatsuro Murano, MD, PhD
Daniel O'Connell, PhD
Geraldine Paulus, PhD
Thomas Sundberg, PhD
Moran Yassour, PhD

Innate and Adaptive Immunity 

In research driven by insights from IBD genetics, we use functional genomics to discover and understand the function of important mediators and effectors involved in innate and adaptive immunity.

To this end, we are pursuing integrative systems approaches that closely couple genome-wide experimentation with high-throughput assays, chemical biology, and computational methods. Using these techniques, we are interested in understanding the role of regulatory circuits in mucosal immunity, in particular using (1) insights from human genetics and whole-genome sequencing to understand regulatory mechanisms in innate and adaptive immunity, (2) chemical approaches to controlling cellular disease phenotypes suggested by human genetics, and (3) harnessing computational approaches to uncover both broad and precise patterns of pathway activation in the context of disease and treatment.



The goal of the microbiome program in the Xavier lab is to use informatics to understand the function of the human microbiome in health and disease. We are particularly interested in identifying microbial small molecules with immunomodulatory activities and to characterize their mechanisms of immune modulation.

Commensal gut microbiota are both ecologically and functionally perturbed during immune-mediated diseases such as inflammatory bowel diseases (IBD) and type 1 diabetes (T1D). Using these diseases as models for understanding the human microbiome’s role in complex inflammatory disease, our recent studies have characterized the microbiome of treatment-naïve Crohn’s disease, and identified trends in the development of the human infant gut microbiome along with specific alterations that precede T1D onset and distinguish T1D progressors from nonprogressors.



The immune system is implicated in a vast array of diseases along a spectrum of hyperinflammatory, hyperimmune, and autoimmune states. Among these diseases, inflammatory bowel diseases (IBDs), comprising Crohn’s disease and ulcerative colitis, are of particular interest in our lab. More than a million individuals in the United States have a form of IBD. These diseases have no known cause, but significant progress is underway in understanding the underlying mechanisms of these disorders. Our current model of IBD is based on a combination of increased genetic risk and an immune system that overreacts to environmental and microbial stresses.

To uncover basic mechanisms of IBD that can be used to develop treatment, our research takes three general and complementary approaches: using insights from human genetics to understand the biological mechanisms underlying disease, using genetic and chemical screens to identify the function of genes implicated in IBD risk, and gathering primary data from patients themselves. These approaches are guided by the lab’s central philosophy, which is to understand compelling biological and clinical questions, and drive innovation through development, optimization, and adaptation of new technologies.


Human Biology

Massachusetts General Hospital and its collaborating institutions are important destinations for world-class care for patients with IBD. As part of the initiative to link bench and bedside, we invite patients to participate in research efforts by providing clinical samples to both basic and translational IBD researchers. The Xavier lab participates in many such cohort-building efforts, such as PRISM, SHARE, 500FG, and others. Insights from patient samples have led to advances in our understanding of both genetic and environmental risk factors for IBD, responses to treatment, and the role of the microbiome in IBD.


  1. Wlodarska M, Kostic AD, Xavier RJ. An integrative view of microbiome-host interactions in inflammatory bowel diseases. Cell Host Microbe. 2015;17(5):577-91. PMID: 25974300.
  2. Jaeger M, van der Lee R, Cheng SC, Johnson MD, Kumar V, Ng A, Plantinga TS, Smeekens SP, Oosting M, Wang X, Barchet W, Fitzgerald K, Joosten LA, Perfect JR, Wijmenga C, van de Veerdonk FL, Huynen MA, Xavier RJ, Kullberg BJ, Netea MG. The RIG-I-like helicase receptor MDA5 (IFIH1) is involved in the host defense against Candida infections. Eur J Clin Microbiol Infect Dis. 2015;34(5):963-74. PMID: 25579795.
  3. Sarmento OF, Svingen PA, Xiong Y, Xavier RJ, McGovern D, Smyrk TC, Papadakis KA, Urrutia RA, Faubion WA. A novel role for KLF14 in T regulatory cell differentiation. Cell Mol Gastroenterol Hepatol. 2015;1(2):188-202 e4. PMID: 25750932.
  4. 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. Integrated Genomics of Crohn's Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy. Cell Rep. 2015;11(12):1905-18. PMID: 26095365.
  5. Causton B, Ramadas RA, Cho JL, Jones K, Pardo-Saganta A, Rajagopal J, Xavier RJ, Medoff BD. CARMA3 Is Critical for the Initiation of Allergic Airway Inflammation. J Immunol. 2015;195(2):683-94. PMID: 26041536.
  6. 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. Disease-specific alterations in the enteric virome in inflammatory bowel disease. Cell. 2015;160(3):447-60. PMID: 25619688.
  7. Palsson-McDermott EM, Curtis AM, Goel G, Lauterbach MA, Sheedy FJ, Gleeson LE, van den Bosch MW, Quinn SR, Domingo-Fernandez R, Johnston DG, Jiang JK, Israelsen WJ, Keane J, Thomas C, Clish C, Vanden Heiden M, Xavier RJ, O'Neill LA. Pyruvate kinase M2 regulates Hif-1alpha activity and IL-1beta induction and is a critical determinant of the warburg effect in LPS-activated macrophages. Cell Metab. 2015;21(1):65-80. PMID: 25565206.
  8. Paulus GL, Xavier RJ. Autophagy and checkpoints for intracellular pathogen defense. Curr Opin Gastroenterol. 2015;31(1):14-23. PMID: 25394238.
  9. Qian F, Goel G, Meng H, Wang X, You F, Devine L, Raddassi K, Garcia MN, Murray KO, Bolen CR, Gaujoux R, Shen-Orr SS, Hafler D, Fikrig E, Xavier R, Kleinstein SH, Montgomery RR. Systems immunology reveals markers of susceptibility to West Nile virus infection. Clin Vaccine Immunol. 2015;22(1):6-16. PMID: 25355795.
  10. Kostic AD, Gevers D, Siljander H, Vatanen T, Hyotylainen T, Hamalainen AM, Peet A, Tillmann V, Poho P, Mattila I, Lahdesmaki H, Franzosa EA, Vaarala O, de Goffau M, Harmsen H, Ilonen J, Virtanen SM, Clish CB, Oresic M, Huttenhower C, Knip M, Group DS, Xavier RJ. The dynamics of the human infant gut microbiome in development and in progression toward type 1 diabetes. Cell Host Microbe. 2015;17(2):260-73. PMID: 25662751.
  11. Goyette P, Boucher G, Mallon D, Ellinghaus E, Jostins L, Huang H, Ripke S, Gusareva ES, Annese V, Hauser SL, Oksenberg JR, Thomsen I, Leslie S, International Inflammatory Bowel Disease Genetics C, Australia, New Zealand I, Belgium IBDGC, Italian Group for IBDGC, Consortium NIBDG, United Kingdom I, Wellcome Trust Case Control C, Quebec IBDGC, Daly MJ, Van Steen K, Duerr RH, Barrett JC, McGovern DP, Schumm LP, Traherne JA, Carrington MN, Kosmoliaptsis V, Karlsen TH, Franke A, Rioux JD. High-density mapping of the MHC identifies a shared role for HLA-DRB1*01:03 in inflammatory bowel diseases and heterozygous advantage in ulcerative colitis. Nat Genet. 2015;47(2):172-9. PMID: 25559196.
  12. 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. Discovery of a Small-Molecule Probe for V-ATPase Function. J Am Chem Soc. 2015;137(16):5563-8. PMID: 25860544.
  13. 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. The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells. Elife. 2015;4. PMID: 25998054.
  14. Morgan XC, Kabakchiev B, Waldron L, Tyler AD, Tickle TL, Milgrom R, Stempak JM, Gevers D, Xavier RJ, Silverberg MS, Huttenhower C. Associations between host gene expression, the mucosal microbiome, and clinical outcome in the pelvic pouch of patients with inflammatory bowel disease. Genome Biol. 2015;16(1):67. PMID: 25887922.
  15. 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. Epigenetic programming of monocyte-to-macrophage differentiation and trained innate immunity. Science. 2014;345(6204):1251086. PMID: 25258085.
  16. 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 Veer 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. mTOR- and HIF-1alpha-mediated aerobic glycolysis as metabolic basis for trained immunity. Science. 2014;345(6204):1250684. PMID: 25258083.
  17. 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. CRISPR-Cas9 knockin mice for genome editing and cancer modeling. Cell. 2014;159(2):440-55. PMID: 25263330.
  18. 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. Autophagy controls BCG-induced trained immunity and the response to intravesical BCG therapy for bladder cancer. PLoS Pathog. 2014;10(10):e1004485. PMID: 25356988.
  19. 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. Atg16L1 T300A variant decreases selective autophagy resulting in altered cytokine signaling and decreased antibacterial defense. Proc Natl Acad Sci U S A. 2014;111(21):7741-6. PMID: 24821797.
  20. Huttenhower C, Kostic AD, Xavier RJ. Inflammatory bowel disease as a model for translating the microbiome. Immunity. 2014;40(6):843-54. PMID: 24950204.
  21. Dunne JL, Triplett EW, Gevers D, Xavier R, Insel R, Danska J, Atkinson MA. The intestinal microbiome in type 1 diabetes. Clin Exp Immunol. 2014;177(1):30-7. PMID: 24628412.
  22. Canny SP, Goel G, Reese TA, Zhang X, Xavier R, Virgin HW. Latent gammaherpesvirus 68 infection induces distinct transcriptional changes in different organs. J Virol. 2014;88(1):730-8. PMID: 24155394.
  23. 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. Early life environment and natural history of inflammatory bowel diseases. BMC Gastroenterol. 2014;14(1):216. PMID: 25510175.
  24. Draberova L, Bugajev V, Potuckova L, Halova I, Bambouskova M, Polakovicova I, Xavier RJ, Seed B, Draber P. Transmembrane adaptor protein PAG/CBP is involved in both positive and negative regulation of mast cell signaling. Mol Cell Biol. 2014;34(23):4285-300. PMID: 25246632.
  25. 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. Dectin-1-dependent LC3 recruitment to phagosomes enhances fungicidal activity in macrophages. J Infect Dis. 2014;210(11):1844-54. PMID: 24842831.
  26. Doench JG, Hartenian E, Graham DB, Tothova Z, Hegde M, Smith I, Sullender M, Ebert BL, Xavier RJ, Root DE. Rational design of highly active sgRNAs for CRISPR-Cas9-mediated gene inactivation. Nat Biotechnol. 2014;32(12):1262-7. PMID: 25184501.
  27. Kumar V, Wijmenga C, Xavier RJ. Genetics of immune-mediated disorders: from genome-wide association to molecular mechanism. Curr Opin Immunol. 2014;31:51-7. PMID: 25458995.
  28. Sundberg TB, Xavier RJ, Schreiber SL, Shamji AF. Small-molecule control of cytokine function: new opportunities for treating immune disorders. Curr Opin Chem Biol. 2014;23:23-30. PMID: 25222143.
  29. Kleinnijenhuis J, Quintin J, Preijers F, Joosten LA, Jacobs C, Xavier RJ, van der Meer JW, van Crevel R, Netea MG. BCG-induced trained immunity in NK cells: Role for non-specific protection to infection. Clin Immunol. 2014;155(2):213-9. PMID: 25451159.
  30. Sundberg TB, Choi HG, Song JH, Russell CN, Hussain MM, Graham DB, Khor B, Gagnon J, O'Connell DJ, Narayan K, Dancik V, Perez JR, Reinecker HC, Gray NS, Schreiber SL, Xavier RJ, Shamji AF. Small-molecule screening identifies inhibition of salt-inducible kinases as a therapeutic strategy to enhance immunoregulatory functions of dendritic cells. Proc Natl Acad Sci U S A. 2014;111(34):12468-73. PMID: 25114223.
  31. 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. Pediatric Crohn disease patients exhibit specific ileal transcriptome and microbiome signature. J Clin Invest. 2014;124(8):3617-33. PMID: 25003194.
  32. 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. Complex host genetics influence the microbiome in inflammatory bowel disease. Genome Med. 2014;6(12):107. PMID: 25587358.
  33. 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. SLCO3A1, A novel crohn's disease-associated gene, regulates nf-kappaB activity and associates with intestinal perforation. PLoS One. 2014;9(6):e100515. PMID: 24945726.
  34. Goel G, Conway KL, Jaeger M, Netea MG, Xavier RJ. Multivariate inference of pathway activity in host immunity and response to therapeutics. Nucleic Acids Res. 2014;42(16):10288-306. PMID: 25147207.
  35. Liao J, Jijon HB, Kim IR, Goel G, Doan A, Sokol H, Bauer H, Herrmann BG, Lassen KG, Xavier RJ. An image-based genetic assay identifies genes in T1D susceptibility loci controlling cellular antiviral immunity in mouse. PLoS One. 2014;9(9):e108777. PMID: 25268627.
  36. 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. Immunochip SNP array identifies novel genetic variants conferring susceptibility to candidaemia. Nat Commun. 2014;5:4675. PMID: 25197941.
  37. Ananthakrishnan AN, Nguyen DD, Sauk J, Yajnik V, Xavier RJ. Genetic polymorphisms in metabolizing enzymes modifying the association between smoking and inflammatory bowel diseases. Inflamm Bowel Dis. 2014;20(5):783-9. PMID: 24651583.
  38. Gevers D, Kugathasan S, Denson LA, Vazquez-Baeza Y, Van Treuren W, Ren B, Schwager E, Knights D, Song SJ, Yassour M, Morgan XC, Kostic AD, Luo C, Gonzalez 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. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host Microbe. 2014;15(3):382-92. PMID: 24629344.
  39. Pulloor NK, Nair S, Kostic AD, Bist P, Weaver JD, Riley AM, Tyagi R, Uchil PD, York JD, Snyder SH, Garcia-Sastre A, Potter BV, Lin R, Shears SB, Xavier RJ, Krishnan MN. Human genome-wide RNAi screen identifies an essential role for inositol pyrophosphates in Type-I interferon response. PLoS Pathog. 2014;10(2):e1003981. PMID: 24586175.
  40. Kostic AD, Xavier RJ, Gevers D. The microbiome in inflammatory bowel disease: current status and the future ahead. Gastroenterology. 2014;146(6):1489-99. PMID: 24560869.
  41. 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. IL-1 receptor blockade restores autophagy and reduces inflammation in chronic granulomatous disease in mice and in humans. Proc Natl Acad Sci U S A. 2014;111(9):3526-31. PMID: 24550444.
  42. Fowler SA, Ananthakrishnan AN, Gardet A, Stevens CR, Korzenik JR, Sands BE, Daly MJ, Xavier RJ, Yajnik V. SMAD3 gene variant is a risk factor for recurrent surgery in patients with Crohn's disease. J Crohns Colitis. 2014. PMID: 24461721.
  43. Lee E, Koo Y, Ng A, Wei Y, Luby-Phelps K, Juraszek A, Xavier RJ, Cleaver O, Levine B, Amatruda JF. Autophagy is essential for cardiac morphogenesis during vertebrate development. Autophagy. 2014;10(4):572-87. PMID: 24441423.
  44. Ananthakrishnan AN, Huang H, Nguyen DD, Sauk J, Yajnik V, Xavier RJ. Differential effect of genetic burden on disease phenotypes in Crohn's disease and ulcerative colitis: analysis of a North American cohort. Am J Gastroenterol. 2014;109(3):395-400. PMID: 24419484.
  45. 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. Novel Mechanism of Tumor Suppression by Polarity Gene Discs Large 1 (DLG1) Revealed in a Murine Model of Pediatric B-ALL. Cancer Immunol Res. 2013;1(6):426-37. PMID: 24778134.
  46. Liu Y, Shoji-Kawata S, Sumpter RM, Jr., Wei Y, Ginet V, Zhang L, Posner B, Tran KA, Green DR, Xavier RJ, Shaw SY, Clarke PG, Puyal J, Levine B. Autosis is a Na+,K+-ATPase-regulated form of cell death triggered by autophagy-inducing peptides, starvation, and hypoxia-ischemia. Proc Natl Acad Sci U S A. 2013;110(51):20364-71. PMID: 24277826.
  47. 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. Autophagy is redundant for the host defense against systemic Candida albicans infections. Eur J Clin Microbiol Infect Dis. 2013. PMID: 24202731.
  48. 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. Long-Lasting Effects of BCG Vaccination on Both Heterologous Th1/Th17 Responses and Innate Trained Immunity. J Innate Immun. 2013. PMID: 24192057.
  49. 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. Genetic Variants Synthesize to Produce Paneth Cell Phenotypes that Define Subtypes of Crohn's Disease. Gastroenterology. 2013. PMID: 24076061.
  50. Ananthakrishnan AN, Oxford EC, Nguyen DD, Sauk J, Yajnik V, Xavier RJ. Genetic risk factors for Clostridium difficile infection in ulcerative colitis. Aliment Pharmacol Ther. 2013;38(5):522-30. PMID: 23848254.
  51. Sokol H, Conway KL, Zhang M, Choi M, Morin B, Cao Z, Villablanca EJ, Li C, Wijmenga C, Yun SH, Shi HN, Xavier RJ. Card9 mediates intestinal epithelial cell restitution, T-helper 17 responses, and control of bacterial infection in mice. Gastroenterology. 2013;145(3):591-601 e3. PMID: 23732773.
  52. Beaudoin M, Goyette P, Boucher G, Lo KS, Rivas MA, Stevens C, Alikashani A, Ladouceur M, Ellinghaus D, Torkvist L, Goel G, Lagace 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, Quebec IBDGC, Consortium NIG, International IBDGC, D'Amato M, Vermeire S, Franke A, Lettre G, Xavier RJ, Daly MJ, Rioux JD. Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis. PLoS Genet. 2013;9(9):e1003723. PMID: 24068945.
  53. 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. Selective Modulation of Autophagy, Innate Immunity, and Adaptive Immunity by Small Molecules. ACS Chem Biol. 2013. PMID: 24168452.
  54. Knights D, Lassen KG, Xavier RJ. Advances in inflammatory bowel disease pathogenesis: linking host genetics and the microbiome. Gut. 2013;62(10):1505-10. PMID: 24037875.
  55. Begun J, Xavier RJ. Autophagy at the crossroads of metabolism and cellular defense. Curr Opin Gastroenterol. 2013;29(6):588-96. PMID: 24100719.
  56. 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. Concomitant BRAF and PI3K/mTOR blockade is required for effective treatment of BRAF(V600E) colorectal cancer. Clin Cancer Res. 2013;19(10):2688-98. PMID: 23549875.
  57. 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. Receptor interacting protein kinase 2-mediated mitophagy regulates inflammasome activation during virus infection. Nat Immunol. 2013;14(5):480-8. PMID: 23525089.
  58. Gmyrek GB, Graham DB, Sandoval GJ, Blaufuss GS, Akilesh HM, Fujikawa K, Xavier RJ, Swat W. Polarity gene discs large homolog 1 regulates the generation of memory T cells. Eur J Immunol. 2013;43(5):1185-94. PMID: 23436244.
  59. Buffen K, Oosting M, Mennens S, Anand PK, Plantinga TS, Sturm P, van de Veerdonk FL, van der Meer JW, Xavier RJ, Kanneganti TD, Netea MG, Joosten LA. Autophagy modulates Borrelia burgdorferi-induced production of interleukin-1beta (IL-1beta). J Biol Chem. 2013;288(12):8658-66. PMID: 23386602.
  60. Sandoval GJ, Graham DB, Bhattacharya D, Sleckman BP, Xavier RJ, Swat W. Cutting edge: cell-autonomous control of IL-7 response revealed in a novel stage of precursor B cells. J Immunol. 2013;190(6):2485-9. PMID: 23420891.
  61. Kirby A, Gnirke A, Jaffe DB, Baresova V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, DeFelice M, Hulkova H, Sovova 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. Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing. Nat Genet. 2013;45(3):299-303. PMID: 23396133.
  62. Smeekens SP, Huttenhower C, Riza A, van de Veerdonk FL, Zeeuwen PL, Schalkwijk J, van der Meer JW, Xavier RJ, Netea MG, Gevers D. Skin Microbiome Imbalance in Patients with STAT1/STAT3 Defects Impairs Innate Host Defense Responses. J Innate Immun. 2013. PMID: 23796786.
  63. Martin ES, Belmont PJ, Sinnamon MJ, Richard LG, Yuan J, Coffee EM, Roper J, Lee L, Heidari P, Lunt SY, Goel G, Ji X, Xie Z, Xie T, Lamb J, Weinrich SL, VanArsdale T, Bronson RT, Xavier RJ, Vander Heiden MG, Kan JL, Mahmood U, Hung KE. Development of a colon cancer GEMM-derived orthotopic transplant model for drug discovery and validation. Clin Cancer Res. 2013;19(11):2929-40. PMID: 23403635.
  64. Giallourakis CC, Benita Y, Molinie B, Cao Z, Despo O, Pratt HE, Zukerberg LR, Daly MJ, Rioux JD, Xavier RJ. Genome-wide analysis of immune system genes by expressed sequence Tag profiling. J Immunol. 2013;190(11):5578-87. PMID: 23616578.
  65. Bornigen D, Morgan XC, Franzosa EA, Ren B, Xavier RJ, Garrett WS, Huttenhower C. Functional profiling of the gut microbiome in disease-associated inflammation. Genome Med. 2013;5(7):65. PMID: 23906180.
  66. 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. Angiotensin II drives the production of tumor-promoting macrophages. Immunity. 2013;38(2):296-308. PMID: 23333075.
  67. O'Rourke EJ, Kuballa P, Xavier R, Ruvkun G. omega-6 Polyunsaturated fatty acids extend life span through the activation of autophagy. Genes Dev. 2013;27(4):429-40. PMID: 23392608.
  68. 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. Identification of a candidate therapeutic autophagy-inducing peptide. Nature. 2013;494(7436):201-6. PMID: 23364696.
  69. 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. Beclin 2 functions in autophagy, degradation of g protein-coupled receptors, and metabolism. Cell. 2013;154(5):1085-99. PMID: 23954414.
  70. 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. Atg16l1 is Required for Autophagy in Intestinal Epithelial Cells and Protection of Mice From Salmonella Infection. Gastroenterology. 2013. PMID: 23973919.
  71. Graham DB, Xavier RJ. From genetics of inflammatory bowel disease towards mechanistic insights. Trends Immunol. 2013;34(8):371-8. PMID: 23639549.
  72. Ananthakrishnan AN, Xavier RJ. How does genotype influence disease phenotype in inflammatory bowel disease? Inflamm Bowel Dis. 2013;19(9):2021-30. PMID: 23644824.
  73. 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. Succinate is an inflammatory signal that induces IL-1beta through HIF-1alpha. Nature. 2013;496(7444):238-42. PMID: 23535595.
  74. Conway KL, Kuballa P, Khor B, Zhang M, Shi HN, Virgin HW, Xavier RJ. ATG5 regulates plasma cell differentiation. Autophagy. 2013;9(4):528-37. PMID: 23327930.
  75. 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. Functional genomics identifies type I interferon pathway as central for host defense against Candida albicans. Nat Commun. 2013;4:1342. PMID: 23299892.
  76. Cho JL, Roche MI, Sandall B, Brass AL, Seed B, Xavier RJ, Medoff BD. Enhanced Tim3 activity improves survival after influenza infection. J Immunol. 2012;189(6):2879-89. PMID: 22875804.
  77. 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. Bacille Calmette-Guerin induces NOD2-dependent nonspecific protection from reinfection via epigenetic reprogramming of monocytes. Proc Natl Acad Sci U S A. 2012;109(43):17537-42. PMID: 22988082.
  78. Conway KL, Goel G, Sokol H, Manocha M, Mizoguchi E, Terhorst C, Bhan AK, Gardet A, Xavier RJ. p40phox expression regulates neutrophil recruitment and function during the resolution phase of intestinal inflammation. J Immunol. 2012;189(7):3631-40. PMID: 22914050.
  79. Gardet A, Xavier RJ. Common alleles that influence autophagy and the risk for inflammatory bowel disease. Curr Opin Immunol. 2012;24(5):522-9. PMID: 23041451.
  80. 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. Establishment and characterization of a novel chordoma cell line: CH22. J Orthop Res. 2012;30(10):1666-73. PMID: 22504929.
  81. 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, Buning 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, Gearry R, Georges M, Gieger C, Glas J, Haritunians T, Hart A, Hawkey C, Hedl M, Hu X, Karlsen TH, Kupcinskas L, Kugathasan S, Latiano A, Laukens D, Lawrance IC, Lees CW, Louis E, Mahy G, Mansfield J, Morgan AR, Mowat C, Newman W, Palmieri O, Ponsioen CY, Potocnik U, Prescott NJ, Regueiro M, Rotter JI, Russell RK, Sanderson JD, Sans M, Satsangi J, Schreiber S, Simms LA, Sventoraityte J, Targan SR, Taylor KD, Tremelling M, Verspaget HW, De Vos M, Wijmenga C, Wilson DC, Winkelmann J, Xavier RJ, Zeissig S, Zhang B, Zhang CK, Zhao H, International IBDGC, Silverberg MS, Annese V, Hakonarson H, Brant SR, Radford-Smith G, Mathew CG, Rioux JD, Schadt EE, Daly MJ, Franke A, Parkes M, Vermeire S, Barrett JC, Cho JH. Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease. Nature. 2012;491(7422):119-24. PMID: 23128233.
  82. Duerr EM, Mizukami Y, Moriichi K, Gala M, Jo WS, Kikuchi H, Xavier RJ, Chung DC. Oncogenic KRAS regulates BMP4 expression in colon cancer cell lines. Am J Physiol Gastrointest Liver Physiol. 2012;302(10):G1223-30. PMID: 22383492.
  83. Wei SC, Rosenberg IM, Cao Z, Huett AS, Xavier RJ, Podolsky DK. Tribbles 2 (Trib2) is a novel regulator of toll-like receptor 5 signaling. Inflamm Bowel Dis. 2012;18(5):877-88. PMID: 22271508.
  84. Labbe C, Boucher G, Foisy S, Alikashani A, Nkwimi H, David G, Beaudoin M, Goyette P, Charron G, Xavier RJ, Rioux JD. Genome-wide expression profiling implicates a MAST3-regulated gene set in colonic mucosal inflammation of ulcerative colitis patients. Inflamm Bowel Dis. 2012;18(6):1072-80. PMID: 21994190.
  85. Xavier RJ, Gala MK, Bronzo BK, Kelly PJ. Case records of the Massachusetts General Hospital. Case 23-2012. A 59-year-old man with abdominal pain and weight loss. N Engl J Med. 2012;367(4):363-73. PMID: 22830467.
  86. Gewurz BE, Towfic F, Mar JC, Shinners NP, Takasaki K, Zhao B, Cahir-McFarland ED, Quackenbush J, Xavier RJ, Kieff E. Genome-wide siRNA screen for mediators of NF-kappaB activation. Proc Natl Acad Sci U S A. 2012;109(7):2467-72. PMID: 22308454.
  87. Lee J, Kim HR, Quinley C, Kim J, Gonzalez-Navajas J, Xavier R, Raz E. Autophagy suppresses interleukin-1beta (IL-1beta) signaling by activation of p62 degradation via lysosomal and proteasomal pathways. J Biol Chem. 2012;287(6):4033-40. PMID: 22167182.
  88. Huett A, Heath RJ, Begun J, Sassi SO, Baxt LA, Vyas JM, Goldberg MB, Xavier RJ. The LRR and RING domain protein LRSAM1 is an E3 ligase crucial for ubiquitin-dependent autophagy of intracellular Salmonella Typhimurium. Cell Host Microbe. 2012;12(6):778-90. PMID: 23245322.
  89. Maloney NS, Thackray LB, Goel G, Hwang S, Duan E, Vachharajani P, Xavier R, Virgin HW. Essential cell-autonomous role for interferon (IFN) regulatory factor 1 in IFN-gamma-mediated inhibition of norovirus replication in macrophages. J Virol. 2012;86(23):12655-64. PMID: 22973039.
  90. 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. Candida albicans infection affords protection against reinfection via functional reprogramming of monocytes. Cell Host Microbe. 2012;12(2):223-32. PMID: 22901542.
  91. Su CW, Cao Y, Zhang M, Kaplan J, Su L, Fu Y, Walker WA, Xavier R, Cherayil BJ, Shi HN. Helminth infection impairs autophagy-mediated killing of bacterial enteropathogens by macrophages. J Immunol. 2012;189(3):1459-66. PMID: 22732589.
  92. 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. Nondegradative role of Atg5-Atg12/ Atg16L1 autophagy protein complex in antiviral activity of interferon gamma. Cell Host Microbe. 2012;11(4):397-409. PMID: 22520467.
  93. 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. Regulation of monocyte functional heterogeneity by miR-146a and Relb. Cell Rep. 2012;1(4):317-24. PMID: 22545247.
  94. Zhao Y, Alonso C, Ballester I, Song JH, Chang SY, Guleng B, Arihiro S, Murray PJ, Xavier R, Kobayashi KS, Reinecker HC. Control of NOD2 and Rip2-dependent innate immune activation by GEF-H1. Inflamm Bowel Dis. 2012;18(4):603-12. PMID: 21887730.
  95. Klionsky DJ, et al. Autophagy. 2012;8(4):445-544. PMID: 22966490.
  96. 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. Non-invasive mapping of the gastrointestinal microbiota identifies children with inflammatory bowel disease. PLoS One. 2012;7(6):e39242. PMID: 22768065.
  97. Kuballa P, Nolte WM, Castoreno AB, Xavier RJ. Autophagy and the immune system. Annu Rev Immunol. 2012;30:611-46. PMID: 22449030.
  98. 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. Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment. Genome Biol. 2012;13(9):R79. PMID: 23013615.
  99. Russo BC, Horzempa J, O'Dee DM, Schmitt DM, Brown MJ, Carlson PE, Jr., Xavier RJ, Nau GJ. A Francisella tularensis locus required for spermine responsiveness is necessary for virulence. Infect Immun. 2011;79(9):3665-76. PMID: 21670171.
  100. Ng A, Xavier RJ. Leucine-rich repeat (LRR) proteins: integrators of pattern recognition and signaling in immunity. Autophagy. 2011;7(9):1082-4. PMID: 21606681.
  101. 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, Lagace C, Neale B, Lo KS, Schumm P, Torkvist L, National Institute of D, Digestive Kidney Diseases Inflammatory Bowel Disease Genetics C, United Kingdom Inflammatory Bowel Disease Genetics C, International Inflammatory Bowel Disease Genetics C, 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. Deep resequencing of GWAS loci identifies independent rare variants associated with inflammatory bowel disease. Nat Genet. 2011;43(11):1066-73. PMID: 21983784.
  102. Ng AC, Eisenberg JM, Heath RJ, Huett A, Robinson CM, Nau GJ, Xavier RJ. Human leucine-rich repeat proteins: a genome-wide bioinformatic categorization and functional analysis in innate immunity. Proc Natl Acad Sci U S A. 2011;108 Suppl 1:4631-8. PMID: 20616063.
  103. Anderson CA, Boucher G, Lees CW, Franke A, D'Amato M, Taylor KD, Lee JC, Goyette P, Imielinski M, Latiano A, Lagace C, Scott R, Amininejad L, Bumpstead S, Baidoo L, Baldassano RN, Barclay M, Bayless TM, Brand S, Buning 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, Lemann M, Levine A, Libioulle C, Louis E, McGovern DP, Milla M, Montgomery GW, Morley KI, Mowat C, Ng A, Newman W, Ophoff RA, Papi L, Palmieri O, Peyrin-Biroulet L, Panes J, Phillips A, Prescott NJ, Proctor DD, Roberts R, Russell R, Rutgeerts P, Sanderson J, Sans M, Schumm P, Seibold F, Sharma Y, Simms LA, Seielstad M, Steinhart AH, Targan SR, van den Berg LH, Vatn M, Verspaget H, Walters T, Wijmenga C, Wilson DC, Westra HJ, Xavier RJ, Zhao ZZ, Ponsioen CY, Andersen V, Torkvist L, Gazouli M, Anagnou NP, Karlsen TH, Kupcinskas L, Sventoraityte J, Mansfield JC, Kugathasan S, Silverberg MS, Halfvarson J, Rotter JI, Mathew CG, Griffiths AM, Gearry R, Ahmad T, Brant SR, Chamaillard M, Satsangi J, Cho JH, Schreiber S, Daly MJ, Barrett JC, Parkes M, Annese V, Hakonarson H, Radford-Smith G, Duerr RH, Vermeire S, Weersma RK, Rioux JD. Meta-analysis identifies 29 additional ulcerative colitis risk loci, increasing the number of confirmed associations to 47. Nat Genet. 2011;43(3):246-52. PMID: 21297633.
  104. Khor B, Gardet A, Xavier RJ. Genetics and pathogenesis of inflammatory bowel disease. Nature. 2011;474(7351):307-17. PMID: 21677747.
  105. 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. NLRP3 inflammasome plays a key role in the regulation of intestinal homeostasis. Inflamm Bowel Dis. 2011;17(6):1359-72. PMID: 20872834.
  106. 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. MyD88-dependent TLR1/2 signals educate dendritic cells with gut-specific imprinting properties. J Immunol. 2011;187(1):141-50. PMID: 21646294.
  107. Ramadas RA, Roche MI, Moon JJ, Ludwig T, Xavier RJ, Medoff BD. CARMA1 is necessary for optimal T cell responses in a murine model of allergic asthma. J Immunol. 2011;187(12):6197-207. PMID: 22075698.
  108. Orvedahl A, Sumpter R, Jr., 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. Image-based genome-wide siRNA screen identifies selective autophagy factors. Nature. 2011;480(7375):113-7. PMID: 22020285.
  109. O'Donnell MA, Perez-Jimenez E, Oberst A, Ng A, Massoumi R, Xavier R, Green DR, Ting AT. Caspase 8 inhibits programmed necrosis by processing CYLD. Nat Cell Biol. 2011;13(12):1437-42. PMID: 22037414.
  110. 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. Crohn disease: a current perspective on genetics, autophagy and immunity. Autophagy. 2011;7(4):355-74. PMID: 20729636.
  111. Heath RJ, Leong JM, Visegrady B, Machesky LM, Xavier RJ. Bacterial and host determinants of MAL activation upon EPEC infection: the roles of Tir, ABRA, and FLRT3. PLoS Pathog. 2011;7(4):e1001332. PMID: 21490959.
  112. Rossin EJ, Lage K, Raychaudhuri S, Xavier RJ, Tatar D, Benita Y, International Inflammatory Bowel Disease Genetics C, Cotsapas C, Daly MJ. Proteins encoded in genomic regions associated with immune-mediated disease physically interact and suggest underlying biology. PLoS Genet. 2011;7(1):e1001273. PMID: 21249183.
  113. Tam JM, Castro CE, Heath RJ, Mansour MK, Cardenas ML, Xavier RJ, Lang MJ, Vyas JM. Use of an optical trap for study of host-pathogen interactions for dynamic live cell imaging. J Vis Exp. 2011(53). PMID: 21841755.
  114. Merquiol E, Uzi D, Mueller T, Goldenberg D, Nahmias Y, Xavier RJ, Tirosh B, Shibolet O. HCV causes chronic endoplasmic reticulum stress leading to adaptation and interference with the unfolded protein response. PLoS One. 2011;6(9):e24660. PMID: 21949742.
  115. Lindquist S, Karitkina D, Langnaese K, Posevitz-Fejfar A, Schraven B, Xavier R, Seed B, Lindquist JA. Phosphoprotein associated with glycosphingolipid-enriched microdomains differentially modulates SRC kinase activity in brain maturation. PLoS One. 2011;6(9):e23978. PMID: 21915273.
  116. Le LP, Nielsen GP, Rosenberg AE, Thomas D, Batten JM, Deshpande V, Schwab J, Duan Z, Xavier RJ, Hornicek FJ, Iafrate AJ. Recurrent chromosomal copy number alterations in sporadic chordomas. PLoS One. 2011;6(5):e18846. PMID: 21602918.
  117. 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. 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. J Cell Biol. 2010;191(3):537-52. PMID: 21041446.
  118. Gardet A, Benita Y, Li C, Sands BE, Ballester I, Stevens C, Korzenik JR, Rioux JD, Daly MJ, Xavier RJ, Podolsky DK. LRRK2 is involved in the IFN-gamma response and host response to pathogens. J Immunol. 2010;185(9):5577-85. PMID: 20921534.
  119. Cadwell K, Patel KK, Maloney NS, Liu TC, Ng AC, Storer CE, Head RD, Xavier R, Stappenbeck TS, Virgin HW. Virus-plus-susceptibility gene interaction determines Crohn's disease gene Atg16L1 phenotypes in intestine. Cell. 2010;141(7):1135-45. PMID: 20602997.
  120. Lipinski MM, Hoffman G, Ng A, Zhou W, Py BF, Hsu E, Liu X, Eisenberg J, Liu J, Blenis J, Xavier RJ, Yuan J. A genome-wide siRNA screen reveals multiple mTORC1 independent signaling pathways regulating autophagy under normal nutritional conditions. Dev Cell. 2010;18(6):1041-52. PMID: 20627085.
  121. Yang C, Hornicek FJ, Wood KB, Schwab JH, Choy E, Iafrate J, Rosenberg A, Nielsen GP, Xavier RJ, Mankin H, Duan Z. Characterization and analysis of human chordoma cell lines. Spine (Phila Pa 1976). 2010;35(13):1257-64. PMID: 20461036.
  122. Duan Z, Choy E, Nielsen GP, Rosenberg A, Iafrate J, Yang C, Schwab J, Mankin H, Xavier R, Hornicek FJ. Differential expression of microRNA (miRNA) in chordoma reveals a role for miRNA-1 in Met expression. J Orthop Res. 2010;28(6):746-52. PMID: 20041488.
  123. Yoon JC, Ng A, Kim BH, Bianco A, Xavier RJ, Elledge SJ. Wnt signaling regulates mitochondrial physiology and insulin sensitivity. Genes Dev. 2010;24(14):1507-18. PMID: 20634317.
  124. Benita Y, Cao Z, Giallourakis C, Li C, Gardet A, Xavier RJ. Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor. Blood. 2010;115(26):5376-84. PMID: 20410506.
  125. Huett A, Goel G, Xavier RJ. A systems biology viewpoint on autophagy in health and disease. Curr Opin Gastroenterol. 2010;26(4):302-9. PMID: 20571384.
  126. Beck PL, Ihara E, Hirota SA, MacDonald JA, Meng D, Nanthakumar NN, Podolsky DK, Xavier RJ. Exploring the interplay of barrier function and leukocyte recruitment in intestinal inflammation by targeting fucosyltransferase VII and trefoil factor 3. Am J Physiol Gastrointest Liver Physiol. 2010;299(1):G43-53. PMID: 20299601.
  127. Lapaquette P, Glasser AL, Huett A, Xavier RJ, Darfeuille-Michaud A. Crohn's disease-associated adherent-invasive E. coli are selectively favoured by impaired autophagy to replicate intracellularly. Cell Microbiol. 2010;12(1):99-113. PMID: 19747213.
  128. Huett A, Xavier RJ. Autophagy at the gut interface: mucosal responses to stress and the consequences for inflammatory bowel diseases. Inflamm Bowel Dis. 2010;16(1):152-74. PMID: 19575363.
  129. Kuballa P, Xavier RJ. Failure and exploitation of autophagy in human pathologies-cellular integrity between inflammation, infection, and cell survival. Semin Immunopathol. 2010;32(4):319-22. PMID: 21107575.
  130. Bekpen C, Xavier RJ, Eichler EE. Human IRGM gene "to be or not to be". Semin Immunopathol. 2010;32(4):437-44. PMID: 20737271.
  131. Lipinski MM, Zheng B, Lu T, Yan Z, Py BF, Ng A, Xavier RJ, Li C, Yankner BA, Scherzer CR, Yuan J. Genome-wide analysis reveals mechanisms modulating autophagy in normal brain aging and in Alzheimer's disease. Proc Natl Acad Sci U S A. 2010;107(32):14164-9. PMID: 20660724.
  132. McGovern DP, Gardet A, Torkvist L, Goyette P, Essers J, Taylor KD, Neale BM, Ong RT, Lagace C, Li C, Green T, Stevens CR, Beauchamp C, Fleshner PR, Carlson M, D'Amato M, Halfvarson J, Hibberd ML, Lordal M, Padyukov L, Andriulli A, Colombo E, Latiano A, Palmieri O, Bernard EJ, Deslandres C, Hommes DW, de Jong DJ, Stokkers PC, Weersma RK, Consortium NIG, 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, Vasiliauskas EA, Targan SR, Annese V, Wijmenga C, Pettersson S, Rotter JI, Xavier RJ, Daly MJ, Rioux JD, Seielstad M. Genome-wide association identifies multiple ulcerative colitis susceptibility loci. Nat Genet. 2010;42(4):332-7. PMID: 20228799.
  133. Tam JM, Castro CE, Heath RJ, Cardenas ML, Xavier RJ, Lang MJ, Vyas JM. Control and manipulation of pathogens with an optical trap for live cell imaging of intercellular interactions. PLoS One. 2010;5(12):e15215. PMID: 21217821.
  134. Li Q, Brass AL, Ng A, Hu Z, Xavier RJ, Liang TJ, Elledge SJ. A genome-wide genetic screen for host factors required for hepatitis C virus propagation. Proc Natl Acad Sci U S A. 2009;106(38):16410-5. PMID: 19717417.
  135. 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. Regulation of inflammatory responses by gut microbiota and chemoattractant receptor GPR43. Nature. 2009;461(7268):1282-6. PMID: 19865172.
  136. Heath RJ, Xavier RJ. Autophagy, immunity and human disease. Curr Opin Gastroenterol. 2009;25(6):512-20. PMID: 19826372.
  137. Adams JC, Seed B, Lu N, Landry A, Xavier RJ. Selective activation of nuclear factor kappa B in the cochlea by sensory and inflammatory stress. Neuroscience. 2009;160(2):530-9. PMID: 19285117.
  138. Tai AW, Benita Y, Peng LF, Kim SS, Sakamoto N, Xavier RJ, Chung RT. A functional genomic screen identifies cellular cofactors of hepatitis C virus replication. Cell Host Microbe. 2009;5(3):298-307. PMID: 19286138.
  139. Medoff BD, Landry AL, Wittbold KA, Sandall BP, Derby MC, Cao Z, Adams JC, Xavier RJ. CARMA3 mediates lysophosphatidic acid-stimulated cytokine secretion by bronchial epithelial cells. Am J Respir Cell Mol Biol. 2009;40(3):286-94. PMID: 18757306.
  140. Raychaudhuri S, Plenge RM, Rossin EJ, Ng AC, International Schizophrenia C, Purcell SM, Sklar P, Scolnick EM, Xavier RJ, Altshuler D, Daly MJ. Identifying relationships among genomic disease regions: predicting genes at pathogenic SNP associations and rare deletions. PLoS Genet. 2009;5(6):e1000534. PMID: 19557189.
  141. Festen EA, Goyette P, Scott R, Annese V, Zhernakova A, Lian J, Lefebvre 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. Genetic variants in the region harbouring IL2/IL21 associated with ulcerative colitis. Gut. 2009;58(6):799-804. PMID: 19201773.
  142. Huett A, Leong JM, Podolsky DK, Xavier RJ. The cytoskeletal scaffold Shank3 is recruited to pathogen-induced actin rearrangements. Exp Cell Res. 2009;315(12):2001-11. PMID: 19371741.
  143. Stephenson LM, Miller BC, Ng A, Eisenberg J, Zhao Z, Cadwell K, Graham DB, Mizushima NN, Xavier R, Virgin HW, Swat W. Identification of Atg5-dependent transcriptional changes and increases in mitochondrial mass in Atg5-deficient T lymphocytes. Autophagy. 2009;5(5):625-35. PMID: 19276668.
  144. Medoff BD, Sandall BP, Landry A, Nagahama K, Mizoguchi A, Luster AD, Xavier RJ. Differential requirement for CARMA1 in agonist-selected T-cell development. Eur J Immunol. 2009;39(1):78-84. PMID: 19130560.
  145. Huett A, McCarroll SA, Daly MJ, Xavier RJ. On the level: IRGM gene function is all about expression. Autophagy. 2009;5(1):96-9. PMID: 19029815.
  146. Imamura T, Kikuchi H, Herraiz MT, Park DY, Mizukami Y, Mino-Kenduson M, Lynch MP, Rueda BR, Benita Y, Xavier RJ, Chung DC. HIF-1alpha and HIF-2alpha have divergent roles in colon cancer. Int J Cancer. 2009;124(4):763-71. PMID: 19030186.
  147. 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. The IFITM proteins mediate cellular resistance to influenza A H1N1 virus, West Nile virus, and dengue virus. Cell. 2009;139(7):1243-54. PMID: 20064371.
  148. 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, Western Regional Alliance for Pediatric IBD, Silber G, Wrobel I, Quiros A, International IBDGC, Barrett JC, Hansoul S, Nicolae DL, Cho JH, Duerr RH, Rioux JD, Brant SR, Silverberg MS, Taylor KD, Barmuda 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, Consortium NIG, 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, Belgian-French IBDC, Wellcome Trust Case Control C, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwillam R, Tremelling M, Delukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ, Heyman MB, Ferry GD, Kirschner B, Lee J, Essers J, Grand R, Stephens M, Levine A, Piccoli D, Van Limbergen J, Cucchiara S, Monos DS, Guthery SL, Denson L, Wilson DC, Grant SF, Daly M, Silverberg MS, Satsangi J, Hakonarson H. Common variants at five new loci associated with early-onset inflammatory bowel disease. Nat Genet. 2009;41(12):1335-40. PMID: 19915574.
  149. Benita Y, Kikuchi H, Smith AD, Zhang MQ, Chung DC, Xavier RJ. An integrative genomics approach identifies Hypoxia Inducible Factor-1 (HIF-1)-target genes that form the core response to hypoxia. Nucleic Acids Res. 2009;37(14):4587-602. PMID: 19491311.
  150. Huett A, Xavier R. Building complex biological networks based upon model organisms: mapping the human autophagy interactome via a hybrid yeast-human protein interaction network. Autophagy. 2009;5(6):884-6. PMID: 19535904.
  151. Avruch J, Xavier R, Bardeesy N, Zhang XF, Praskova M, Zhou D, Xia F. Rassf family of tumor suppressor polypeptides. J Biol Chem. 2009;284(17):11001-5. PMID: 19091744.
  152. Huett A, Ng A, Cao Z, Kuballa P, Komatsu M, Daly MJ, Podolsky DK, Xavier RJ. A novel hybrid yeast-human network analysis reveals an essential role for FNBP1L in antibacterial autophagy. J Immunol. 2009;182(8):4917-30. PMID: 19342671.
  153. 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. RNA interference screen for human genes associated with West Nile virus infection. Nature. 2008;455(7210):242-5. PMID: 18690214.
  154. 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. Deletion polymorphism upstream of IRGM associated with altered IRGM expression and Crohn's disease. Nat Genet. 2008;40(9):1107-12. PMID: 19165925.
  155. Fujiki K, Duerr EM, Kikuchi H, Ng A, Xavier RJ, Mizukami Y, Imamura T, Kulke MH, Chung DC. Hoxc6 is overexpressed in gastrointestinal carcinoids and interacts with JunD to regulate tumor growth. Gastroenterology. 2008;135(3):907-16, 916 e1-2. PMID: 18655788.
  156. Friedman CS, O'Donnell MA, Legarda-Addison D, Ng A, Cardenas WB, Yount JS, Moran TM, Basler CF, Komuro A, Horvath CM, Xavier R, Ting AT. The tumour suppressor CYLD is a negative regulator of RIG-I-mediated antiviral response. EMBO Rep. 2008;9(9):930-6. PMID: 18636086.
  157. Upadhyay G, Goessling W, North TE, Xavier R, Zon LI, Yajnik V. Molecular association between beta-catenin degradation complex and Rac guanine exchange factor DOCK4 is essential for Wnt/beta-catenin signaling. Oncogene. 2008;27(44):5845-55. PMID: 18641688.
  158. Labbe 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. MAST3: a novel IBD risk factor that modulates TLR4 signaling. Genes Immun. 2008;9(7):602-12. PMID: 18650832.
  159. 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 HWt. A key role for autophagy and the autophagy gene Atg16l1 in mouse and human intestinal Paneth cells. Nature. 2008;456(7219):259-63. PMID: 18849966.
  160. Irazoqui JE, Ng A, Xavier RJ, Ausubel FM. Role for beta-catenin and HOX transcription factors in Caenorhabditis elegans and mammalian host epithelial-pathogen interactions. Proc Natl Acad Sci U S A. 2008;105(45):17469-74. PMID: 18981407.
  161. Sims KB, Pastores GM, Weinreb NJ, Barranger J, Rosenbloom BE, Packman S, Kaplan P, Mankin H, Xavier R, Angell J, Fitzpatrick MA, Rosenthal D. 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. Clin Genet. 2008;73(5):430-40. PMID: 18312448.
  162. Duerr EM, Mizukami Y, Ng A, Xavier RJ, Kikuchi H, Deshpande V, Warshaw AL, Glickman J, Kulke MH, Chung DC. Defining molecular classifications and targets in gastroenteropancreatic neuroendocrine tumors through DNA microarray analysis. Endocr Relat Cancer. 2008;15(1):243-56. PMID: 18310291.
  163. 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. Gene-centric association mapping of chromosome 3p implicates MST1 in IBD pathogenesis. Mucosal Immunol. 2008;1(2):131-8. PMID: 19079170.
  164. 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. SPTLC1 binds ABCA1 to negatively regulate trafficking and cholesterol efflux activity of the transporter. Biochemistry. 2008;47(23):6138-47. PMID: 18484747.
  165. Huett A, Xavier RJ. Neither hide nor hair: the difficulty of identifying useful disease biomarkers. Gastroenterology. 2008;134(7):2164-8. PMID: 18486617.
  166. Xavier RJ, Huett A, Rioux JD. Autophagy as an important process in gut homeostasis and Crohn's disease pathogenesis. Gut. 2008;57(6):717-20. PMID: 18272545.
  167. Yagi T, Giallourakis C, Mohanty S, Scheidig C, Shen J, Zheng H, Xavier RJ, Shaw AC. Defective signal transduction in B lymphocytes lacking presenilin proteins. Proc Natl Acad Sci U S A. 2008;105(3):979-84. PMID: 18195359.
  168. Huett A, Xavier R. SNPping away at the pathogenesis of Crohn's disease. Inflamm Bowel Dis. 2008;14(1):136-7. PMID: 17941076.
  169. Cao Z, Huett A, Kuballa P, Giallourakis C, Xavier RJ. DLG1 is an anchor for the E3 ligase MARCH2 at sites of cell-cell contact. Cell Signal. 2008;20(1):73-82. PMID: 17980554.
  170. Brass AL, Dykxhoorn DM, Benita Y, Yan N, Engelman A, Xavier RJ, Lieberman J, Elledge SJ. Identification of host proteins required for HIV infection through a functional genomic screen. Science. 2008;319(5865):921-6. PMID: 18187620.
  171. Sugimoto K, Ogawa A, Mizoguchi E, Shimomura Y, Andoh A, Bhan AK, Blumberg RS, Xavier RJ, Mizoguchi A. IL-22 ameliorates intestinal inflammation in a mouse model of ulcerative colitis. J Clin Invest. 2008;118(2):534-44. PMID: 18172556.
  172. Hitomi J, Christofferson DE, Ng A, Yao J, Degterev A, Xavier RJ, Yuan J. Identification of a molecular signaling network that regulates a cellular necrotic cell death pathway. Cell. 2008;135(7):1311-23. PMID: 19109899.
  173. Zhou D, Medoff BD, Chen L, Li L, Zhang XF, Praskova M, Liu M, Landry A, Blumberg RS, Boussiotis VA, Xavier R, Avruch J. The Nore1B/Mst1 complex restrains antigen receptor-induced proliferation of naive T cells. Proc Natl Acad Sci U S A. 2008;105(51):20321-6. PMID: 19073936.
  174. Xavier RJ, Rioux JD. Genome-wide association studies: a new window into immune-mediated diseases. Nat Rev Immunol. 2008;8(8):631-43. PMID: 18654571.
  175. 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, Consortium NIG, 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, Belgian-French IBDC, Wellcome Trust Case Control C, Cardon LR, Anderson CA, Drummond H, Nimmo E, Ahmad T, Prescott NJ, Onnie CM, Fisher SA, Marchini J, Ghori J, Bumpstead S, Gwilliam R, Tremelling M, Deloukas P, Mansfield J, Jewell D, Satsangi J, Mathew CG, Parkes M, Georges M, Daly MJ. Genome-wide association defines more than 30 distinct susceptibility loci for Crohn's disease. Nat Genet. 2008;40(8):955-62. PMID: 18587394.
  176. Seed B, Xavier R. Spinophilin and the immune synapse. J Cell Biol. 2008;181(2):181-3. PMID: 18411314.
  177. Kuballa P, Huett A, Rioux JD, Daly MJ, Xavier RJ. Impaired autophagy of an intracellular pathogen induced by a Crohn's disease associated ATG16L1 variant. PLoS One. 2008;3(10):e3391. PMID: 18852889.
  178. Cotta-de-Almeida V, Westerberg L, Maillard MH, Onaldi D, Wachtel H, Meelu P, Chung UI, Xavier R, Alt FW, Snapper SB. Wiskott Aldrich syndrome protein (WASP) and N-WASP are critical for T cell development. Proc Natl Acad Sci U S A. 2007;104(39):15424-9. PMID: 17878299.
  179. Shibolet O, Giallourakis C, Rosenberg I, Mueller T, Xavier RJ, Podolsky DK. AKAP13, a RhoA GTPase-specific guanine exchange factor, is a novel regulator of TLR2 signaling. J Biol Chem. 2007;282(48):35308-17. PMID: 17878165.
  180. Stephenson LM, Sammut B, Graham DB, Chan-Wang J, Brim KL, Huett AS, Miletic AV, Kloeppel T, Landry A, Xavier R, Swat W. DLGH1 is a negative regulator of T-lymphocyte proliferation. Mol Cell Biol. 2007;27(21):7574-81. PMID: 17724087.
  181. 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. Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis. Nat Genet. 2007;39(5):596-604. PMID: 17435756.
  182. Ishiguro K, Ando T, Goto H, Xavier R. Bcl10 is phosphorylated on Ser138 by Ca2+/calmodulin-dependent protein kinase II. Mol Immunol. 2007;44(8):2095-100. PMID: 17052756.
  183. Fitzgerald ML, Xavier R, Haley KJ, Welti R, Goss JL, Brown CE, Zhuang DZ, Bell SA, Lu N, McKee M, Seed B, Freeman MW. ABCA3 inactivation in mice causes respiratory failure, loss of pulmonary surfactant, and depletion of lung phosphatidylglycerol. J Lipid Res. 2007;48(3):621-32. PMID: 17142808.
  184. Xavier RJ, Podolsky DK. Unravelling the pathogenesis of inflammatory bowel disease. Nature. 2007;448(7152):427-34. PMID: 17653185.
  185. Miletic AV, Graham DB, Montgrain V, Fujikawa K, Kloeppel T, Brim K, Weaver B, Schreiber R, Xavier R, Swat W. Vav proteins control MyD88-dependent oxidative burst. Blood. 2007;109(8):3360-8. PMID: 17158234.
  186. Huett A, Benita Y, Xavier RJ. The role of the calmodulin- dependent protein kinase II ( CaMKII ) in the regulation of T lymphocyte development and activation. Lymphocyte Activation and Signal Transduction. 2007;661(2).
  187. Goyette P, Labbe C, Trinh TT, Xavier RJ, Rioux JD. Molecular pathogenesis of inflammatory bowel disease: genotypes, phenotypes and personalized medicine. Ann Med. 2007;39(3):177-99. PMID: 17457716.
  188. Ishiguro K, Avruch J, Landry A, Qin S, Ando T, Goto H, Xavier R. Nore1B regulates TCR signaling via Ras and Carma1. Cell Signal. 2006;18(10):1647-54. PMID: 16520020.
  189. Yamamoto-Furusho JK, Barnich N, Xavier R, Hisamatsu T, Podolsky DK. Centaurin beta1 down-regulates nucleotide-binding oligomerization domains 1- and 2-dependent NF-kappaB activation. J Biol Chem. 2006;281(47):36060-70. PMID: 17005562.
  190. Ishiguro K, Ando T, Maeda O, Hasegawa M, Kadomatsu K, Ohmiya N, Niwa Y, Xavier R, Goto H. Paeonol attenuates TNBS-induced colitis by inhibiting NF-kappaB and STAT1 transactivation. Toxicol Appl Pharmacol. 2006;217(1):35-42. PMID: 16928387.
  191. Medoff BD, Seed B, Jackobek R, Zora J, Yang Y, Luster AD, Xavier R. CARMA1 is critical for the development of allergic airway inflammation in a murine model of asthma. J Immunol. 2006;176(12):7272-7. PMID: 16751370.
  192. Ishiguro K, Green T, Rapley J, Wachtel H, Giallourakis C, Landry A, Cao Z, Lu N, Takafumi A, Goto H, Daly MJ, Xavier RJ. Ca2+/calmodulin-dependent protein kinase II is a modulator of CARMA1-mediated NF-kappaB activation. Mol Cell Biol. 2006;26(14):5497-508. PMID: 16809782.
  193. Mahoney ZX, Sammut B, Xavier RJ, Cunningham J, Go G, Brim KL, Stappenbeck TS, Miner JH, Swat W. Discs-large homolog 1 regulates smooth muscle orientation in the mouse ureter. Proc Natl Acad Sci U S A. 2006;103(52):19872-7. PMID: 17172448.
  194. 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. Immune cell transcriptome datasets reveal novel leukocyte subset-specific genes and genes associated with allergic processes. J Allergy Clin Immunol. 2006;118(2):496-503. PMID: 16890777.
  195. Giallourakis C, Cao Z, Green T, Wachtel H, Xie X, Lopez-Illasaca M, Daly M, Rioux J, Xavier R. A molecular-properties-based approach to understanding PDZ domain proteins and PDZ ligands. Genome Res. 2006;16(8):1056-72. PMID: 16825666.
  196. Landry A, Xavier R. Isolation and analysis of lipid rafts in cell-cell interactions. Methods Mol Biol. 2006;341:251-82. PMID: 16799204.
  197. Barnich N, Hisamatsu T, Aguirre JE, Xavier R, Reinecker HC, Podolsky DK. GRIM-19 interacts with nucleotide oligomerization domain 2 and serves as downstream effector of anti-bacterial function in intestinal epithelial cells. J Biol Chem. 2005;280(19):19021-6. PMID: 15753091.
  198. Xavier R, Seed B. PDZ domains and the politics of polarity in lymphocytes. Immunity. 2005;22(6):655-6. PMID: 15963778.
  199. Barnich N, Aguirre JE, Reinecker HC, Xavier R, Podolsky DK. Membrane recruitment of NOD2 in intestinal epithelial cells is essential for nuclear factor-{kappa}B activation in muramyl dipeptide recognition. J Cell Biol. 2005;170(1):21-6. PMID: 15998797.
  200. Lopez-Ilasaca MA, Bernabe-Ortiz JC, Na SY, Dzau VJ, Xavier RJ. Bioluminescence resonance energy transfer identify scaffold protein CNK1 interactions in intact cells. FEBS Lett. 2005;579(3):648-54. PMID: 15670823.
  201. Xavier R, Podolsky DK. Commensal flora: wolf in sheep's clothing. Gastroenterology. 2005;128(4):1122-6. PMID: 15825094.
  202. Ting A, Lichtenthaler S, Xavier R, Na SY, Rabizadeh S, Holmes T, Seed B. Large-scale screens for cDNAs with in vivo activity. Novartis Found Symp. 2005;267:219-29; discussion 229-30. PMID: 15999809.
  203. Ishiguro K, Xavier R. Homer-3 regulates activation of serum response element in T cells via its EVH1 domain. Blood. 2004;103(6):2248-56. PMID: 14645007.
  204. Beck PL, Wong JF, Li Y, Swaminathan S, Xavier RJ, Devaney KL, Podolsky DK. Chemotherapy- and radiotherapy-induced intestinal damage is regulated by intestinal trefoil factor. Gastroenterology. 2004;126(3):796-808. PMID: 14988834.
  205. Xavier R, Rabizadeh S, Ishiguro K, Andre N, Ortiz JB, Wachtel H, Morris DG, Lopez-Ilasaca M, Shaw AC, Swat W, Seed B. Discs large (Dlg1) complexes in lymphocyte activation. J Cell Biol. 2004;166(2):173-8. PMID: 15263016.
  206. Rabizadeh S, Xavier RJ, Ishiguro K, Bernabeortiz J, Lopez-Ilasaca M, Khokhlatchev A, Mollahan P, Pfeifer GP, Avruch J, Seed B. The scaffold protein CNK1 interacts with the tumor suppressor RASSF1A and augments RASSF1A-induced cell death. J Biol Chem. 2004;279(28):29247-54. PMID: 15075335.
  207. Beck PL, Xavier R, Wong J, Ezedi I, Mashimo H, Mizoguchi A, Mizoguchi E, Bhan AK, Podolsky DK. Paradoxical roles of different nitric oxide synthase isoforms in colonic injury. Am J Physiol Gastrointest Liver Physiol. 2004;286(1):G137-47. PMID: 14665440.
  208. Ishiguro K, Cao Z, Ilasca ML, Ando T, Xavier R. Wave2 activates serum response element via its VCA region and functions downstream of Rac. Exp Cell Res. 2004;301(2):331-7. PMID: 15530867.
  209. Mizoguchi E, Xavier RJ, Reinecker HC, Uchino H, Bhan AK, Podolsky DK, Mizoguchi A. Colonic epithelial functional phenotype varies with type and phase of experimental colitis. Gastroenterology. 2003;125(1):148-61. PMID: 12851880.
  210. Swat W, Xavier R, Mizoguchi A, Mizoguchi E, Fredericks J, Fujikawa K, Bhan AK, Alt FW. Essential role for Vav1 in activation, but not development, of gammadelta T cells. Int Immunol. 2003;15(2):215-21. PMID: 12578851.
  211. Beck PL, Rosenberg IM, Xavier RJ, Koh T, Wong JF, Podolsky DK. Transforming growth factor-beta mediates intestinal healing and susceptibility to injury in vitro and in vivo through epithelial cells. Am J Pathol. 2003;162(2):597-608. PMID: 12547717.
  212. Schiffmann R, Mankin H, Dambrosia JM, Xavier RJ, Kreps C, Hill SC, Barton NW, Rosenthal DI. Decreased bone density in splenectomized Gaucher patients receiving enzyme replacement therapy. Blood Cells Mol Dis. 2002;28(2):288-96. PMID: 12064924.
  213. Mizoguchi E, Mizoguchi A, Takedatsu H, Cario E, de Jong YP, Ooi CJ, Xavier RJ, Terhorst C, Podolsky DK, Bhan AK. Role of tumor necrosis factor receptor 2 (TNFR2) in colonic epithelial hyperplasia and chronic intestinal inflammation in mice. Gastroenterology. 2002;122(1):134-44. PMID: 11781288.
  214. Khokhlatchev A, Rabizadeh S, Xavier R, Nedwidek M, Chen T, Zhang XF, Seed B, Avruch J. Identification of a novel Ras-regulated proapoptotic pathway. Curr Biol. 2002;12(4):253-65. PMID: 11864565.
  215. Colucci R, Fleming JV, Xavier R, Wang TC. L-histidine decarboxylase decreases its own transcription through downregulation of ERK activity. Am J Physiol Gastrointest Liver Physiol. 2001;281(4):G1081-91. PMID: 11557529.
  216. Mankin HJ, Rosenthal DI, Xavier R. Gaucher disease. New approaches to an ancient disease. J Bone Joint Surg Am. 2001;83-A(5):748-62. PMID: 11379747.
  217. 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. TBX1 is responsible for cardiovascular defects in velo-cardio-facial/DiGeorge syndrome. Cell. 2001;104(4):619-29. PMID: 11239417.
  218. Chung RT, He W, Saquib A, Contreras AM, Xavier RJ, Chawla A, Wang TC, Schmidt EV. Hepatitis C virus replication is directly inhibited by IFN-alpha in a full-length binary expression system. Proc Natl Acad Sci U S A. 2001;98(17):9847-52. PMID: 11493707.
  219. Chawla N, Andre N, Choi M, Bernabe-Ortiz JC, Xavier R. An update on lymphocyte activation and signal transduction in inflammation. VI International Symposium on Inflammatory Bowel Diseases. 2001:11-30.
  220. Xavier RJ, Podolsky DK. Microbiology. How to get along--friendly microbes in a hostile world. Science. 2000;289(5484):1483-4. PMID: 10991734.
  221. Beck PL, Xavier R, Lu N, Nanda NN, Dinauer M, Podolsky DK, Seed B. Mechanisms of NSAID-induced gastrointestinal injury defined using mutant mice. Gastroenterology. 2000;119(3):699-705. PMID: 10982764.
  222. Muehlhoefer A, Saubermann LJ, Gu X, Luedtke-Heckenkamp K, Xavier R, Blumberg RS, Podolsky DK, MacDermott RP, Reinecker HC. Fractalkine is an epithelial and endothelial cell-derived chemoattractant for intraepithelial lymphocytes in the small intestinal mucosa. J Immunol. 2000;164(6):3368-76. PMID: 10706732.
  223. Xavier R, Seed B. Membrane compartmentation and the response to antigen. Curr Opin Immunol. 1999;11(3):265-9. PMID: 10375560.
  224. Itoh H, Beck PL, Inoue N, Xavier R, Podolsky DK. A paradoxical reduction in susceptibility to colonic injury upon targeted transgenic ablation of goblet cells. J Clin Invest. 1999;104(11):1539-47. PMID: 10587517.
  225. Fukumura D, Xavier R, Sugiura T, Chen Y, Park EC, Lu N, Selig M, Nielsen G, Taksir T, Jain RK, Seed B. Tumor induction of VEGF promoter activity in stromal cells. Cell. 1998;94(6):715-25. PMID: 9753319.
  226. Lown B, Bukachi F, Xavier R. Health information in the developing world. Lancet. 1998;352 Suppl 2:SII34-8. PMID: 9798645.
  227. 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. SEK1/MKK4 is required for maintenance of a normal peripheral lymphoid compartment but not for lymphocyte development. Immunity. 1998;8(5):625-34. PMID: 9620683.
  228. Xavier R, Brennan T, Li Q, McCormack C, Seed B. Membrane compartmentation is required for efficient T cell activation. Immunity. 1998;8(6):723-32. PMID: 9655486.
  229. Liang TJ, Reid AE, Xavier R, Cardiff RD, Wang TC. Transgenic expression of tpr-met oncogene leads to development of mammary hyperplasia and tumors. J Clin Invest. 1996;97(12):2872-7. PMID: 8675700.
  230. Amstalden EM, Xavier R, Kattapuram SV, Bertolo MB, Swartz MN, Rosenberg AE. Paracoccidioidomycosis of bones and joints. A clinical, radiologic, and pathologic study of 9 cases. Medicine (Baltimore). 1996;75(4):213-25. PMID: 8699961.
  231. Greenberg S, Chang P, Wang DC, Xavier R, Seed B. Clustered syk tyrosine kinase domains trigger phagocytosis. Proc Natl Acad Sci U S A. 1996;93(3):1103-7. PMID: 8577722.
  232. Xavier R, Podolsky DK. Addressing lymphocytes for mucosal delivery in ibd. Inflamm Bowel Dis. 1995;1(4):343-4. PMID: 23282439.
  233. Rosenthal DI, Doppelt SH, Mankin HJ, Dambrosia JM, Xavier RJ, McKusick KA, Rosen BR, Baker J, Niklason LT, Hill SC, et al. Enzyme replacement therapy for Gaucher disease: skeletal responses to macrophage-targeted glucocerebrosidase. Pediatrics. 1995;96(4 Pt 1):629-37. PMID: 7567322.
  234. Thadhani RI, Camargo CA, Jr., Xavier RJ, Fang LS, Bazari H. Atheroembolic renal failure after invasive procedures. Natural history based on 52 histologically proven cases. Medicine (Baltimore). 1995;74(6):350-8. PMID: 7500898.
  235. Pins MR, Mankin HJ, Xavier RJ, Rosenthal DI, Dickersin GR, Rosenberg AE. Malignant epithelioid hemangioendothelioma of the tibia associated with a bone infarct in a patient who had Gaucher disease. A case report. J Bone Joint Surg Am. 1995;77(5):777-81. PMID: 7744904.
  236. Mullaney J, Xavier R. SatelLife: Building an Electronic Health Network in the Developing World. Studies in Health Technology and Informatics. 1995;23:265-276.
  237. Seed B, Kolanus W, Romeo C, Xavier R. Nonreceptor tyrosine kinases in aggregation-mediated cell activation. Adv Exp Med Biol. 1994;365:111-9. PMID: 7887297.
  238. Rachmilewitz D, Stamler JS, Karmeli F, Loscalzo J, Xavier RJ, Podolsky DK. Role of nitric oxide in the pathogenesis of IBD. Inflammatory Bowel Diseases 1994. 1994:82-90.
  239. Rachmilewitz D, Stamler JS, Karmeli F, Mullins ME, Singel DJ, Loscalzo J, Xavier RJ, Podolsky DK. Peroxynitrite-induced rat colitis--a new model of colonic inflammation. Gastroenterology. 1993;105(6):1681-8. PMID: 8253344.
  240. Xavier RJ, Stein CM, Kiire CF, Arrow J, Kitai I. Value of the history and stool occult blood test in selection of patients for upper endoscopy in Zimbabwe. East Afr Med J. 1992;69(5):268-71. PMID: 1644046.
  241. Xavier RJ, Mann J, Tarantola DJ, Netter TW. AIDS and tuberculosis: A dangerous synergy. AIDS in the World. 1992:148-163.
  242. Bigger RJ, Xavier RJ. AIDS and Cancer. AIDS in the World. 1992:134-143.