ConStrains identifies microbial strains in metagenomic datasets by Luo, Chengwei, Knight, Rob, Siljander, Heli, Knip, Mikael, Xavier, Ramnik J, Gevers, Dirk

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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.

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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

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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.

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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

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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.

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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.

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

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Early life environment and natural history of inflammatory bowel diseases by 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

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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

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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

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

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Proton pump inhibitors affect the gut microbiome by Imhann, Floris, Bonder, Marc Jan, Vich Vila, Arnau, Fu, Jingyuan, Mujagic, Zlatan, Vork, Lisa, Tigchelaar, Ettje F, Jankipersadsing, Soesma A, Cenit, Maria Carmen, Harmsen, Hermie J M, Dijkstra, Gerard, Franke, Lude, Xavier, Ramnik J, Jonkers, Daisy, Wijmenga, Cisca, Weersma, Rinse K, Zhernakova, Alexandra

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Complex host genetics influence the microbiome in inflammatory bowel disease by 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

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Integrated Genomics of Crohn’s Disease Risk Variant Identifies a Role for CLEC12A in Antibacterial Autophagy by Begun, Jakob, Lassen, Kara G., Jijon, Humberto B., Baxt, Leigh A., Goel, Gautam, Heath, Robert J., Ng, Aylwin, Tam, Jenny M., Kuo, Szu-Yu, Villablanca, Eduardo J., Fagbami, Lola, Oosting, Marije, Kumar, Vinod, Schenone, Monica, Carr, Steven A., Joosten, Leo A.B., Vyas, Jatin M., Daly, Mark J., Netea, Mihai G., Brown, Gordon D., Wijmenga, Cisca, Xavier, Ramnik J.

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

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

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A protein-truncating R179X variant in RNF186 confers protection against ulcerative colitis by Rivas, Manuel A., Graham, Daniel, Sulem, Patrick, Stevens, Christine, Desch, A. Nicole, Goyette, Philippe, Gudbjartsson, Daniel, Jonsdottir, Ingileif, Thorsteinsdottir, Unnur, Degenhardt, Frauke, Mucha, Sören, Kurki, Mitja I., Li, Dalin, D'Amato, Mauro, Annese, Vito, Vermeire, Severine, Weersma, Rinse K., Halfvarson, Jonas, Paavola-Sakki, Paulina, Lappalainen, Maarit, Lek, Monkol, Cummings, Beryl, Tukiainen, Taru, Haritunians, Talin, Halme, Leena, Koskinen, Lotta L. E., Ananthakrishnan, Ashwin N., Luo, Yang, Heap, Graham A., Visschedijk, Marijn C., MacArthur, Daniel G., Neale, Benjamin M., Ahmad, Tariq, Anderson, Carl A., Brant, Steven R., Duerr, Richard H., Silverberg, Mark S., Cho, Judy H, Palotie, Aarno, Saavalainen, Päivi, Kontula, Kimmo, Färkkilä, Martti, McGovern, Dermot P. B., Franke, Andre, Stefansson, Kari, Rioux, John D., Xavier, Ramnik J., Daly, Mark J., Barrett, J., de Lane, K., Edwards, C., Hart, A., Hawkey, C., Jostins, L., Kennedy, N., Lamb, C., Lee, J., Lees, C., Mansfield, J., Mathew, C., Mowatt, C., Newman, B., Nimmo, E., Parkes, M., Pollard, M., Prescott, N., Randall, J., Rice, D., Satsangi, J., Simmons, A., Tremelling, M., Uhlig, H., Wilson, D., Abraham, C., Achkar, J. P., Bitton, A., Boucher, G., Croitoru, K., Fleshner, P., Glas, J., Kugathasan, S., Limbergen, J. V., Milgrom, R., Proctor, D., Regueiro, M., Schumm, P. L., Sharma, Y., Stempak, J. M., Targan, S. R., Wang, M. H.

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