Now showing items 1-20 of 31

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

      Buffen, Kathrin; Oosting, Marije; Quintin, Jessica; Ng, Aylwin; Kleinnijenhuis, Johanneke; Kumar, Vinod; van de Vosse, Esther; Wijmenga, Cisca; van Crevel, Reinout; Oosterwijk, Egbert; Grotenhuis, Anne J.; Vermeulen, Sita H.; Kiemeney, Lambertus A.; van de Veerdonk, Frank L.; Chamilos, Georgios; Xavier, Ramnik J.; van der Meer, Jos W. M.; Netea, Mihai G.; Joosten, Leo A. B. (Public Library of Science, 2014)
      The anti-tuberculosis-vaccine Bacillus Calmette-Guérin (BCG) is the most widely used vaccine in the world. In addition to its effects against tuberculosis, BCG vaccination also induces non-specific beneficial effects against ...
    • Bacterial and Host Determinants of MAL Activation upon EPEC Infection: The Roles of Tir, ABRA, and FLRT3 

      Heath, Robert John William; Leong, John M.; Visegrády, Balázs; Machesky, Laura M.; Xavier, Ramnik (Public Library of Science, 2011)
      Infection of host cells by pathogenic microbes triggers signal transduction pathways leading to a multitude of host cell responses including actin cytoskeletal re-arrangements and transcriptional programs. The diarrheagenic ...
    • Complex host genetics influence the microbiome in inflammatory bowel disease 

      Knights, Dan; Silverberg, Mark S; Weersma, Rinse K; Gevers, Dirk; Dijkstra, Gerard; Huang, Hailiang; Tyler, Andrea D; van Sommeren, Suzanne; Imhann, Floris; Stempak, Joanne M; Huang, Hu; Vangay, Pajau; Al-Ghalith, Gabriel A; Russell, Caitlin; Sauk, Jenny; Knight, Jo; Daly, Mark J; Huttenhower, Curtis; Xavier, Ramnik J (BioMed Central, 2014)
      Background: Human genetics and host-associated microbial communities have been associated independently with a wide range of chronic diseases. One of the strongest associations in each case is inflammatory bowel disease ...
    • ConStrains identifies microbial strains in metagenomic datasets 

      Luo, Chengwei; Knight, Rob; Siljander, Heli; Knip, Mikael; Xavier, Ramnik J; Gevers, Dirk (2015)
      An important fraction of microbial diversity is harbored in strain individuality, so identification of conspecific bacterial strains is imperative for improved understanding of microbial community functions. Limitations ...
    • Control and Manipulation of Pathogens with an Optical Trap for Live Cell Imaging of Intercellular Interactions 

      Tam, Jenny M.; Castro, Carlos E.; Heath, Robert John William; Cardenas, Michael L.; Xavier, Ramnik; Lang, Matthew J.; Vyas, Jatin Mahesh (Public Library of Science, 2010)
      The application of live cell imaging allows direct visualization of the dynamic interactions between cells of the immune system. Some preliminary observations challenge long-held beliefs about immune responses to microorganisms; ...
    • Deep Resequencing of GWAS Loci Identifies Rare Variants in CARD9, IL23R and RNF186 That Are Associated with Ulcerative Colitis 

      Beaudoin, Mélissa; Goyette, Philippe; Boucher, Gabrielle; Lo, Ken Sin; Rivas, Manuel A.; Stevens, Christine; Alikashani, Azadeh; Ladouceur, Martin; Ellinghaus, David; Törkvist, Leif; Goel, Gautam; Lagacé, Caroline; Annese, Vito; Bitton, Alain; Begun, Jakob; Brant, Steve R.; Bresso, Francesca; Cho, Judy H.; Duerr, Richard H.; Halfvarson, Jonas; McGovern, Dermot P. B.; Radford-Smith, Graham; Schreiber, Stefan; Schumm, Philip L.; Sharma, Yashoda; Silverberg, Mark S.; Weersma, Rinse K.; D'Amato, Mauro; Vermeire, Severine; Franke, Andre; Lettre, Guillaume; Xavier, Ramnik J.; Daly, Mark J.; Rioux, John D. (Public Library of Science, 2013)
      Genome-wide association studies and follow-up meta-analyses in Crohn's disease (CD) and ulcerative colitis (UC) have recently identified 163 disease-associated loci that meet genome-wide significance for these two inflammatory ...
    • Discovery of a Small-Molecule Probe for V-ATPase Function 

      Aldrich, Leslie N.; Kuo, Szu-Yu; Castoreno, Adam B.; Goel, Gautam; Kuballa, Petric; Rees, Matthew G.; Seashore-Ludlow, Brinton A.; Cheah, Jaime H.; Latorre, Isabel J.; Schreiber, Stuart L.; Shamji, Alykhan F.; Xavier, Ramnik J. (American Chemical Society, 2015)
      Lysosomes perform a critical cellular function as a site of degradation for diverse cargoes including proteins, organelles, and pathogens delivered through distinct pathways, and defects in lysosomal function have been ...
    • Dysbiosis, inflammation, and response to treatment: a longitudinal study of pediatric subjects with newly diagnosed inflammatory bowel disease 

      Shaw, Kelly A.; Bertha, Madeline; Hofmekler, Tatyana; Chopra, Pankaj; Vatanen, Tommi; Srivatsa, Abhiram; Prince, Jarod; Kumar, Archana; Sauer, Cary; Zwick, Michael E.; Satten, Glen A.; Kostic, Aleksandar D.; Mulle, Jennifer G.; Xavier, Ramnik J.; Kugathasan, Subra (BioMed Central, 2016)
      Background: Gut microbiome dysbiosis has been demonstrated in subjects with newly diagnosed and chronic inflammatory bowel disease (IBD). In this study we sought to explore longitudinal changes in dysbiosis and ascertain ...
    • Dysfunction of the Intestinal Microbiome in Inflammatory Bowel Disease and Treatment 

      Morgan, Xochitl C; Sokol, Harry; Gevers, Dirk; Ward, Doyle V; LeLeiko, Neal; Sands, Bruce E; Tickle, Timothy L.; Devaney, Kathryn L; Reyes, Joshua Anthony; Shah, Samir A; Snapper, Scott Brian; Bousvaros, Athos; Korzenik, Joshua; Xavier, Ramnik; Huttenhower, Curtis (BioMed Central, 2012)
      Background: The inflammatory bowel diseases (IBD) Crohn's disease and ulcerative colitis result from alterations in intestinal microbes and the immune system. However, the precise dysfunctions of microbial metabolism in ...
    • Early life environment and natural history of inflammatory bowel diseases 

      Guo, Abra Y; Stevens, Betsy W; Wilson, Robin G; Russell, Caitlin N; Cohen, Melissa A; Sturgeon, Holly C; Thornton, Anna; Giallourakis, Cosmas; Khalili, Hamed; Nguyen, Deanna D; Sauk, Jenny; Yajnik, Vijay; Xavier, Ramnik J; Ananthakrishnan, Ashwin N (BioMed Central, 2014)
      Background: Early life exposures may modify risk of inflammatory bowel diseases (IBD; Crohn’s disease (CD), ulcerative colitis (UC)). However, the relationship between early life exposures and natural history of IBD has ...
    • Functional CRISPR screening identifies the ufmylation pathway as a regulator of SQSTM1/p62 

      DeJesus, Rowena; Moretti, Francesca; McAllister, Gregory; Wang, Zuncai; Bergman, Phil; Liu, Shanming; Frias, Elizabeth; Alford, John; Reece-Hoyes, John S; Lindeman, Alicia; Kelliher, Jennifer; Russ, Carsten; Knehr, Judith; Carbone, Walter; Beibel, Martin; Roma, Guglielmo; Ng, Aylwin; Tallarico, John A; Porter, Jeffery A; Xavier, Ramnik J; Mickanin, Craig; Murphy, Leon O; Hoffman, Gregory R; Nyfeler, Beat (eLife Sciences Publications, Ltd, 2016)
      SQSTM1 is an adaptor protein that integrates multiple cellular signaling pathways and whose expression is tightly regulated at the transcriptional and post-translational level. Here, we describe a forward genetic screening ...
    • Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst 

      Graham, Daniel B.; Becker, Christine E.; Doan, Aivi; Goel, Gautam; Villablanca, Eduardo J.; Knights, Dan; Mok, Amanda; Ng, Aylwin C.Y.; Doench, John G.; Root, David E.; Clish, Clary B.; Xavier, Ramnik J. (Nature Pub. Group, 2015)
      The phagocyte oxidative burst, mediated by Nox2 NADPH oxidase-derived reactive oxygen species, confers host defense against a broad spectrum of bacterial and fungal pathogens. Loss-of-function mutations that impair function ...
    • Functional profiling of the gut microbiome in disease-associated inflammation 

      Börnigen, Daniela; Morgan, Xochitl C; Franzosa, Eric A; Ren, Boyu; Xavier, Ramnik J; Garrett, Wendy S; Huttenhower, Curtis (BioMed Central, 2013)
      The microbial residents of the human gut are a major factor in the development and lifelong maintenance of health. The gut microbiota differs to a large degree from person to person and has an important influence on health ...
    • The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids 

      Fu, Jingyuan; Bonder, Marc Jan; Cenit, María Carmen; Tigchelaar, Ettje F.; Maatman, Astrid; Dekens, Jackie A.M.; Brandsma, Eelke; Marczynska, Joanna; Imhann, Floris; Weersma, Rinse K.; Franke, Lude; Poon, Tiffany W.; Xavier, Ramnik J.; Gevers, Dirk; Hofker, Marten H.; Wijmenga, Cisca; Zhernakova, Alexandra (Lippincott Williams & Wilkins, 2015)
      Rationale: Evidence suggests that the gut microbiome is involved in the development of cardiovascular disease, with the host–microbe interaction regulating immune and metabolic pathways. However, there was no firm evidence ...
    • Host-microbe interactions have shaped the genetic architecture of inflammatory bowel disease 

      Jostins, Luke; Ripke, Stephan; Weersma, Rinse K; Duerr, Richard H; McGovern, Dermot P; Hui, Ken Y; Lee, James C; Schumm, L Philip; Sharma, Yashoda; Anderson, Carl A; Essers, Jonah Bryan; Mitrovic, Mitja; Ning, Kaida; Cleynen, Isabelle; Theatre, Emilie; Spain, Sarah L; Raychaudhuri, Soumya; Goyette, Philippe; Wei, Zhi; Abraham, Clara; Achkar, Jean-Paul; Ahmad, Tariq; Amininejad, Leila; Ananthakrishnan, Ashwin N; Andersen, Vibeke; Andrews, Jane M; Baidoo, Leonard; Balschun, Tobias; Bampton, Peter A; Bitton, Alain; Boucher, Gabrielle; Brand, Stephan; Büning, Carsten; Cohain, Ariella; Cichon, Sven; D’Amato, Mauro; De Jong, Dirk; Devaney, Kathy L; Dubinsky, Marla; Edwards, Cathryn; Ellinghaus, David; Ferguson, Lynnette R; Franchimont, Denis; Fransen, Karin; Gearry, Richard; Georges, Michel; Gieger, Christian; Glas, Jürgen; Haritunians, Talin; Hart, Ailsa; Hawkey, Chris; Hedl, Matija; Hu, Xinli; Karlsen, Tom H; Kupcinskas, Limas; Kugathasan, Subra; Latiano, Anna; Laukens, Debby; Lawrance, Ian C; Lees, Charlie W; Louis, Edouard; Mahy, Gillian; Mansfield, John; Morgan, Angharad R; Mowat, Craig; Newman, William; Palmieri, Orazio; Ponsioen, Cyriel Y; Potocnik, Uros; Prescott, Natalie J; Regueiro, Miguel; Rotter, Jerome I; Russell, Richard K; Sanderson, Jeremy D; Sans, Miquel; Satsangi, Jack; Schreiber, Stefan; Simms, Lisa A; Sventoraityte, Jurgita; Targan, Stephan R; Taylor, Kent D; Tremelling, Mark; Verspaget, Hein W; De Vos, Martine; Wijmenga, Cisca; Wilson, David C; Winkelmann, Juliane; Xavier, Ramnik; Zeissig, Sebastian; Zhang, Bin; Zhang, Clarence K; Zhao, Hongyu; Silverberg, Mark S; Annese, Vito; Hakonarson, Hakon; Brant, Steven R; Radford-Smith, Graham; Mathew, Christopher G; Rioux, John D; Schadt, Eric E; Daly, Mark Joseph; Franke, Andre; Parkes, Miles; Vermeire, Severine; Barrett, Jeffrey C; Cho, Judy H (2012)
      Crohn’s disease (CD) and ulcerative colitis (UC), the two common forms of inflammatory bowel disease (IBD), affect over 2.5 million people of European ancestry with rising prevalence in other populations1. Genome-wide ...
    • Human Genome-Wide RNAi Screen Identifies an Essential Role for Inositol Pyrophosphates in Type-I Interferon Response 

      Pulloor, Niyas Kudukkil; Nair, Sajith; Kostic, Aleksandar D.; Bist, Pradeep; Weaver, Jeremy D.; Riley, Andrew M.; Tyagi, Richa; Uchil, Pradeep D.; York, John D.; Snyder, Solomon H.; García-Sastre, Adolfo; Potter, Barry V. L.; Lin, Rongtuan; Shears, Stephen B.; Xavier, Ramnik J.; Krishnan, Manoj N. (Public Library of Science, 2014)
      The pattern recognition receptor RIG-I is critical for Type-I interferon production. However, the global regulation of RIG-I signaling is only partially understood. Using a human genome-wide RNAi-screen, we identified 226 ...
    • An Image-Based Genetic Assay Identifies Genes in T1D Susceptibility Loci Controlling Cellular Antiviral Immunity in Mouse 

      Liao, Juan; Jijon, Humberto B.; Kim, Ira R.; Goel, Gautam; Doan, Aivi; Sokol, Harry; Bauer, Hermann; Herrmann, Bernhard G.; Lassen, Kara G.; Xavier, Ramnik J. (Public Library of Science, 2014)
      The pathogenesis of complex diseases, such as type 1 diabetes (T1D), derives from interactions between host genetics and environmental factors. Previous studies have suggested that viral infection plays a significant role ...
    • Impaired Autophagy of an Intracellular Pathogen Induced by a Crohn's Disease Associated ATG16L1 Variant 

      Rioux, John D.; Gay, Nick; Kuballa, Petric; Huett, Alan Stephen; Daly, Mark Joseph; Xavier, Ramnik (Public Library of Science, 2008)
      The genetic risk factors predisposing individuals to the development of inflammatory bowel disease are beginning to be deciphered by genome-wide association studies. Surprisingly, these new data point towards a critical ...
    • The kinase DYRK1A reciprocally regulates the differentiation of Th17 and regulatory T cells 

      Khor, Bernard; Gagnon, John D; Goel, Gautam; Roche, Marly I; Conway, Kara L; Tran, Khoa; Aldrich, Leslie N; Sundberg, Thomas B; Paterson, Alison M; Mordecai, Scott; Dombkowski, David; Schirmer, Melanie; Tan, Pauline H; Bhan, Atul K; Roychoudhuri, Rahul; Restifo, Nicholas P; O'Shea, John J; Medoff, Benjamin D; Shamji, Alykhan F; Schreiber, Stuart L; Sharpe, Arlene H; Shaw, Stanley Y; Xavier, Ramnik J (eLife Sciences Publications, Ltd, 2015)
      The balance between Th17 and T regulatory (Treg) cells critically modulates immune homeostasis, with an inadequate Treg response contributing to inflammatory disease. Using an unbiased chemical biology approach, we identified ...
    • Multivariate inference of pathway activity in host immunity and response to therapeutics 

      Goel, Gautam; Conway, Kara L.; Jaeger, Martin; Netea, Mihai G.; Xavier, Ramnik J. (Oxford University Press, 2014)
      Developing a quantitative view of how biological pathways are regulated in response to environmental factors is central for understanding of disease phenotypes. We present a computational framework, named Multivariate ...