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

by Benita, Yair, Kikuchi, Hirotoshi, Smith, Andrew D., Zhang, Michael Q., Chung, Daniel C., Xavier, Ramnik J.
Published 2009

Bacterial and Host Determinants of MAL Activation upon EPEC Infection: The Roles of Tir, ABRA, and FLRT3

by Heath, Robert J. W., Leong, John M., Visegrády, Balázs, Machesky, Laura M., Xavier, Ramnik J.
Published 2011

ConStrains identifies microbial strains in metagenomic datasets

by Luo, Chengwei, Knight, Rob, Siljander, Heli, Knip, Mikael, Xavier, Ramnik J, Gevers, Dirk
Published 2015

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

by Goel, Gautam, Conway, Kara L., Jaeger, Martin, Netea, Mihai G., Xavier, Ramnik J.
Published 2014

HCV Causes Chronic Endoplasmic Reticulum Stress Leading to Adaptation and Interference with the Unfolded Protein Response

by Merquiol, Emmanuelle, Uzi, Dotan, Mueller, Tobias, Goldenberg, Daniel, Nahmias, Yaakov, Xavier, Ramnik J., Tirosh, Boaz, Shibolet, Oren
Published 2011

Functional profiling of the gut microbiome in disease-associated inflammation

by Börnigen, Daniela, Morgan, Xochitl C, Franzosa, Eric A, Ren, Boyu, Xavier, Ramnik J, Garrett, Wendy S, Huttenhower, Curtis
Published 2013

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

by Boada-Romero, Emilio, Serramito-Gómez, Inmaculada, Sacristán, María P., Boone, David L., Xavier, Ramnik J., Pimentel-Muiños, Felipe X.
Published 2016

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

by Morgan, Xochitl C, Kabakchiev, Boyko, Waldron, Levi, Tyler, Andrea D, Tickle, Timothy L, Milgrom, Raquel, Stempak, Joanne M, Gevers, Dirk, Xavier, Ramnik J, Silverberg, Mark S, Huttenhower, Curtis
Published 2015

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

by Selleck, Elizabeth M., Orchard, Robert C., Lassen, Kara G., Beatty, Wandy L., Xavier, Ramnik J., Levine, Beth, Virgin, Herbert W., Sibley, L. David
Published 2015

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

by 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.
Published 2014

A Novel Role for Kruppel-like Factor 14 (KLF14) in T-Regulatory Cell Differentiation

by Sarmento, Olga F., Svingen, Phyllis A., Xiong, Yuning, Xavier, Ramnik J., McGovern, Dermot, Smyrk, Thomas C., Papadakis, Konstantinos A., Urrutia, Raul A., Faubion, William A.
Published 2014

Recurrent Chromosomal Copy Number Alterations in Sporadic Chordomas

by Le, Long Phi, Nielsen, G. Petur, Rosenberg, Andrew Eric, Thomas, Dafydd, Batten, Julie M., Deshpande, Vikram, Schwab, Joseph, Duan, Zhenfeng, Xavier, Ramnik J., Hornicek, Francis J., Iafrate, A. John
Published 2011

Non-Invasive Mapping of the Gastrointestinal Microbiota Identifies Children with Inflammatory Bowel Disease

by Papa, Eliseo, Docktor, Michael, Smillie, Christopher, Weber, Sarah, Preheim, Sarah P., Gevers, Dirk, Giannoukos, Georgia, Ciulla, Dawn, Tabbaa, Diana, Ingram, Jay, Schauer, David B., Ward, Doyle V., Korzenik, Joshua R., Xavier, Ramnik J., Bousvaros, Athos, Alm, Eric J.
Published 2012

Dysfunction of the intestinal microbiome in inflammatory bowel disease and treatment

by Morgan, Xochitl C, Tickle, Timothy L, Sokol, Harry, Gevers, Dirk, Devaney, Kathryn L, Ward, Doyle V, Reyes, Joshua A, Shah, Samir A, LeLeiko, Neal, Snapper, Scott B, Bousvaros, Athos, Korzenik, Joshua, Sands, Bruce E, Xavier, Ramnik J, Huttenhower, Curtis
Published 2012

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

by Lupfer, Christopher, Thomas, Paul G., Anand, Paras K., Vogel, Peter, Milasta, Sandra, Martinez, Jennifer, Huang, Gonghua, Green, Maggie, Kundu, Mondira, Chi, Hongbo, Xavier, Ramnik J., Green, Douglas R., Lamkanfi, Mohamed, Dinarello, Charles A., Doherty, Peter C., Kanneganti, Thirumala-Devi
Published 2013

Functional genomics identifies negative regulatory nodes controlling phagocyte oxidative burst

by 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.
Published 2015

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

by Pedamallu, Chandra Sekhar, Bhatt, Ami S., Bullman, Susan, Fowler, Sharyle, Freeman, Samuel S., Durand, Jacqueline, Jung, Joonil, Duke, Fujiko, Manzo, Veronica, Cai, Diana, Ananthakrishnan, Ashwin, Ojesina, Akinyemi I., Ramachandran, Aruna, Gevers, Dirk, Xavier, Ramnik J., Bhan, Atul K., Meyerson, Matthew, Yajnik, Vijay
Published 2016

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

by Yassour, Moran, Lim, Mi Young, Yun, Hyun Sun, Tickle, Timothy L., Sung, Joohon, Song, Yun-Mi, Lee, Kayoung, Franzosa, Eric A., Morgan, Xochitl C., Gevers, Dirk, Lander, Eric S., Xavier, Ramnik J., Birren, Bruce W., Ko, GwangPyo, Huttenhower, Curtis
Published 2016

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

by 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.
Published 2015

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

by Acharya, Mridu, Sokolovska, Anna, Tam, Jenny M., Conway, Kara L., Stefani, Caroline, Raso, Fiona, Mukhopadhyay, Subhankar, Feliu, Marianela, Paul, Elahna, Savill, John, Hynes, Richard O., Xavier, Ramnik J., Vyas, Jatin M., Stuart, Lynda M., Lacy-Hulbert, Adam
Published 2016