Genomic dissection of conserved transcriptional regulation in intestinal epithelial cells von Lickwar, Colin R, Camp, J Gray, Weiser, Matthew, Cocchiaro, Jordan L, Kingsley, David M, Furey, Terrence S, Sheikh, Shehzad Z, Rawls, John F

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Redefining the IBDs using genome-scale molecular phenotyping von Furey, Terrence S., Sethupathy, Praveen, Sheikh, Shehzad Z.

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CoVar: A generalizable machine learning approach to identify the coordinated regulators driving variational gene expression von Roy, Satyaki, Sheikh, Shehzad Z, Furey, Terrence S

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Ancient Transposable Elements Transformed the Uterine Regulatory Landscape and Transcriptome during the Evolution of Mammalian Pregnancy von Lynch, Vincent J., Nnamani, Mauris C., Kapusta, Aurélie, Brayer, Kathryn, Plaza, Silvia L., Mazur, Erik C., Emera, Deena, Sheikh, Shehzad Z., Grützner, Frank, Bauersachs, Stefan, Graf, Alexander, Young, Steven L., Lieb, Jason D., DeMayo, Francesco J., Feschotte, Cédric, Wagner, Günter P.

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A machine learning approach identifies 5-ASA and ulcerative colitis as being linked with higher COVID-19 mortality in patients with IBD von Roy, Satyaki, Sheikh, Shehzad Z., Furey, Terrence S.

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Linking gene expression to clinical outcomes in pediatric Crohn’s disease using machine learning von Chen, Kevin A., Nishiyama, Nina C., Kennedy Ng, Meaghan M., Shumway, Alexandria, Joisa, Chinmaya U., Schaner, Matthew R., Lian, Grace, Beasley, Caroline, Zhu, Lee-Ching, Bantumilli, Surekha, Kapadia, Muneera R., Gomez, Shawn M., Furey, Terrence S., Sheikh, Shehzad Z.

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An anti-inflammatory role for carbon monoxide and heme oxygenase-1 in chronic Th2-mediated murine colitis von Sheikh, Shehzad Z, Hegazi, Refaat A, Kobayashi, Taku, Onyiah, Joseph C, Russo, Steven M, Matsuoka, Katsuyoshi, Sepulveda, Antonia R, Li, Fengling, Otterbein, Leo E, Plevy, Scott E

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MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility von Peck, Bailey C E, Weiser, Matthew, Lee, Saangyoung E, Gipson, Gregory R, Iyer, Vishal B, Sartor, Ryan B, Herfarth, Hans H, Long, Millie D, Hansen, Jonathan J, Isaacs, Kim L, Trembath, Dimitri G, Rahbar, Reza, Sadiq, Timothy S, Furey, Terrence S, Sethupathy, Praveen, Sheikh, Shehzad Z

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Crohn’s Disease Differentially Affects Region-Specific Composition and Aerotolerance Profiles of Mucosally Adherent Bacteria von Shahir, Nur M, Wang, Jeremy R, Wolber, E Ashley, Schaner, Matthew S, Frank, Daniel N, Ir, Diana, Robertson, Charles E, Chaumont, Nicole, Sadiq, Timothy S, Koruda, Mark J, Rahbar, Reza, Nix, B Darren, Newberry, Rodney D, Sartor, R Balfour, Sheikh, Shehzad Z, Furey, Terrence S

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NFIL3 is a regulator of IL-12 p40 in macrophages and mucosal immunity von Kobayashi, Taku, Matsuoka, Katsuyoshi, Sheikh, Shehzad Z, Elloumi, Houda Z, Kamada, Nobuhiko, Hisamatsu, Tadakazu, Hansen, Jonathan J, Doty, Kevin R, Pope, Scott D, Smale, Stephen T, Hibi, Toshifumi, Rothman, Paul B, Kashiwada, Masaki, Plevy, Scott E

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The role of the macrophage in sentinel responses in intestinal immunity von Sheikh, Shehzad Z, Plevy, Scott E

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IL-10 regulates Il12b expression via histone deacetylation: implications for intestinal macrophage homeostasis von Kobayashi, Taku, Matsuoka, Katsuyoshi, Sheikh, Shehzad Z, Russo, Steven M, Mishima, Yoshiyuki, Collins, Colm, deZoeten, Edwin F, Karp, Christopher L, Ting, Jenny P Y, Sartor, R Balfour, Plevy, Scott E

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NFIL3-deficient mice develop microbiota-dependent, IL-12/23-driven spontaneous colitis von Kobayashi, Taku, Steinbach, Erin C, Russo, Steven M, Matsuoka, Katsuyoshi, Nochi, Tomonori, Maharshak, Nitsan, Borst, Luke B, Hostager, Bruce, Garcia-Martinez, J Victor, Rothman, Paul B, Kashiwada, Masaki, Sheikh, Shehzad Z, Murray, Peter J, Plevy, Scott E

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BET Protein Inhibition Regulates Macrophage Chromatin Accessibility and Microbiota-Dependent Colitis von Hoffner O'Connor, Michelle, Berglind, Ana, Kennedy Ng, Meaghan M, Keith, Benjamin P, Lynch, Zachary J, Schaner, Matthew R, Steinbach, Erin C, Herzog, Jeremy, Trad, Omar K, Jeck, William R, Arthur, Janelle C, Simon, Jeremy M, Sartor, R Balfour, Furey, Terrence S, Sheikh, Shehzad Z

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Single-Cell Analysis Reveals Unexpected Cellular Changes and Transposon Expression Signatures in the Colonic Epithelium of Treatment-Naïve Adult Crohn’s Disease Patients von Kanke, Matt, Kennedy Ng, Meaghan M., Connelly, Sean, Singh, Manvendra, Schaner, Matthew, Shanahan, Michael T., Wolber, Elizabeth A., Beasley, Caroline, Lian, Grace, Jain, Animesh, Long, Millie D., Barnes, Edward L., Herfarth, Hans H., Isaacs, Kim L., Hansen, Jonathon J., Kapadia, Muneera, Guillem, Jose Gaston, Feschotte, Cedric, Furey, Terrence S., Sheikh, Shehzad Z., Sethupathy, Praveen

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TNF Promoter Hypomethylation Is Associated With Mucosal Inflammation in IBD and Anti-TNF Response von Levic, Daniel S., Niedzwiecki, Donna, Kandakatla, Apoorva, Karlovich, Norah S., Juneja, Arjun, Park, Jieun, Stolarchuk, Christina, Adams, Shanté, Willer, Jason R., Schaner, Matthew R., Lian, Grace, Beasley, Caroline, Marjoram, Lindsay, Flynn, Ann D., Valentine, John F., Onken, Jane E., Sheikh, Shehzad Z., Davis, Erica E., Evason, Kimberley J., Garman, Katherine S., Bagnat, Michel

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Perigastric abscess as a delayed adverse event in endoscopic sleeve gastroplasty von James, Theodore W., Sheikh, Shehzad Z., McGowan, Christopher E.

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Biochemical and rheological analysis of human colonic culture mucus reveals similarity to gut mucus von Howard, R. Logan, Markovetz, Matthew, Wang, Yuli, Ehre, Camille, Sheikh, Shehzad Z., Allbritton, Nancy L., Hill, David B.

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Cutting Edge: Hypoxia Sensing by the Histone Demethylase UTX (KDM6A) Limits Colitogenic CD4+ T Cells in Mucosal Inflammation von Cheng, Mandy I, Hong, Lee, Bustillos, Christian, Chen, Bryan, Chin, Scott, Luthers, Christopher R, Vo, Au, Sheikh, Shehzad Z, Su, Maureen A

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Molecular classification of Crohn's disease reveals two clinically relevant subtypes von Weiser, Matthew, Simon, Jeremy M, Kochar, Bharati, Tovar, Adelaide, Israel, Jennifer W, Robinson, Adam, Gipson, Gregory R, Schaner, Matthew S, Herfarth, Hans H, Sartor, R Balfour, McGovern, Dermot P B, Rahbar, Reza, Sadiq, Timothy S, Koruda, Mark J, Furey, Terrence S, Sheikh, Shehzad Z

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