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Gene coexpression networks reveal a broad role for lncRNAs in inflammatory bowel disease Johnson, John L.; Sargsyan, Davit; Neiman, Eric M.; Hart, Amy; Stojmirovic, Aleksandar; Kosoy, Roman; Irizar, Haritz; Suarez-Farinas, Mayte; Song, Won-Min; Argmann, Carmen; Avey, Stefan; Shmuel-Galia, Liraz; Vierbuchen, Tim; Bongers, Gerold; Sun, Yu; Edelstein, Leonard; Perrigoue, Jacqueline; Towne, Jennifer E.; Hall, Aisling O'Hara; Fitzgerald, Katherine A.; Hoebe, Kasper Share Save
Using Computer Vision to Improve Endoscopic Disease Quantification in Therapeutic Clinical Trials of Ulcerative Colitis Stidham, Ryan W.; Cai, Lingrui; Cheng, Shuyang; Rajaei, Flora; Hiatt, Tadd; Wittrup, Emily; Rice, Michael D.; Bishu, Shrinivas; Wehkamp, Jan; Schultz, Weiwei; Khan, Najat; Stojmirovic, Aleksandar; Ghanem, Louis R.; Najarian, Kayvan Share Save
Deep Learning Models Capture Histological Disease Activity in Crohn's Disease and Ulcerative Colitis with High Fidelity Rymarczyk, Dawid; Schultz, Weiwei; Borowa, Adriana; Friedman, Joshua R.; Danel, Tomasz; Branigan, Patrick; Chalupczak, Michal; Bracha, Anna; Krawiec, Tomasz; Warchol, Michal; Li, Katherine; De Hertogh, Gert; Zielinski, Bartosz; Ghanem, Louis R.; Stojmirovic, Aleksandar Share Save
A temporal classifier predicts histopathology state and parses acute-chronic phasing in inflammatory bowel disease patients Peters, Lauren A.; Friedman, Joshua R.; Stojmirovic, Aleksandar; Hagen, Jacob; Houten, Sander; Dodatko, Tetyana; Amaro, Mariana P.; Restrepo, Paula; Chai, Zhi; Rodrigo Mora, J.; Raymond, Holly A.; Curran, Mark; Dobrin, Radu; Das, Anuk; Xiong, Huabao; Schadt, Eric E.; Argmann, Carmen; Losic, Bojan Share Save
Integrative Analysis of the Inflammatory Bowel Disease Serum Metabolome Improves Our Understanding of Genetic Etiology and Points to Novel Putative Therapeutic Targets Di'Narzo, Antonio F.; Houten, Sander M.; Kosoy, Roman; Huang, Ruiqi; Vaz, Frederic M.; Hou, Ruixue; Wei, Gabrielle; Wang, Wenhui; Comella, Phillip H.; Dodatko, Tetyana; Rogatsky, Eduard; Stojmirovic, Aleksandar; Brodmerkel, Carrie; Perrigoue, Jacqueline; Hart, Amy; Curran, Mark; Friedman, Joshua R.; Zhu, Jun; Agrawal, Manasi; Cho, Judy; Ungaro, Ryan; Dubinsky, Marla C.; Sands, Bruce E.; Suarez-Farinas, Mayte; Schadt, Eric E.; Colombel, Jean-Frederic; Kasarskis, Andrew; Hao, Ke; Argmann, Carmen Share Save
Ulcerative colitis is characterized by a plasmablast-skewed humoral response associated with disease activity Uzzan, Mathieu; Martin, Jerome C.; Mesin, Luka; Livanos, Alexandra E.; Castro-Dopico, Tomas; Huang, Ruiqi; Petralia, Francesca; Magri, Giuliana; Kumar, Shashi; Zhao, Qing; Rosenstein, Adam K.; Tokuyama, Minami; Sharma, Keshav; Ungaro, Ryan; Kosoy, Roman; Jha, Divya; Fischer, Jeremy; Singh, Harpriya; Keir, Mary E.; Ramamoorthi, Nandhini; O' Gorman, William E.; Cohen, Benjamin L.; Rahman, Adeeb; Cossarini, Francesca; Seki, Akihiro; Leyre, Louise; Vaquero, Sonia Tejedor; Gurunathan, Sakteesh; Grasset, Emilie K.; Losic, Bojan; Dubinsky, Marla; Greenstein, Alexander J.; Gottlieb, Zoe; Legnani, Peter; George, James; Irizar, Haritz; Stojmirovic, Aleksandar; Brodmerkel, Carrie; Kasarkis, Andrew; Sands, Bruce E.; Furtado, Glaucia; Lira, Sergio A.; Tuong, Zewen K.; Ko, Huaibin M.; Cerutti, Andrea; Elson, Charles O.; Clatworthy, Menna R.; Merad, Miriam; Suarez-Farinas, Mayte; Argmann, Carmen; Hackney, Jason A.; Victora, Gabriel D.; Randolph, Gwendalyn J.; Kenigsberg, Ephraim; Colombel, Jean Frederic; Mehandru, Saurabh Share Save
Molecular Characterization of Limited Ulcerative Colitis Reveals Novel Biology and Predictors of Disease Extension Argmann, Carmen; Tokuyama, Minami; Ungaro, Ryan C.; Huang, Ruiqi; Hou, Ruixue; Gurunathan, Sakteesh; Kosoy, Roman; Di'Narzo, Antonio; Wang, Wenhui; Losic, Bojan; Irizar, Haritz; Peters, Lauren; Stojmirovic, Aleksandar; Wei, Gabrielle; Comella, Phillip H.; Curran, Mark; Brodmerkel, Carrie; Friedman, Joshua R.; Hao, Ke; Schadt, Eric E.; Zhu, Jun; Cho, Judy; Harpaz, Noam; Dubinsky, Marla C.; Sands, Bruce E.; Kasarskis, Andrew; Mehandru, Saurabh; Colombel, Jean-Frederic; Suarez-Farinas, Mayte Share Save
Polygenic risk score for alcohol drinking behavior improves prediction of inflammatory bowel disease risk Di Narzo, Antonio F.; Hart, Amy; Kosoy, Roman; Peters, Lauren; Stojmirovic, Aleksandar; Cheng, Haoxiang; Zhang, Zhongyang; Shan, Mingxu; Cho, Judy; Kasarskis, Andrew; Argmann, Carmen; Peter, Inga; Schadt, Eric E.; Hao, Ke Share Save
Deep Analysis of the Peripheral Immune System in IBD Reveals New Insight in Disease Subtyping and Response to Monotherapy or Combination Therapy Kosoy, Roman; Kim-Schulze, Seunghee; Rahman, Adeeb; Friedman, Joshua R.; Huang, Ruiqi; Peters, Lauren A.; Amir, El-ad; Perrigoue, Jacqueline; Stojmirovic, Aleksandar; Song, Won-min; Ke, Hao; Ungaro, Ryan; Mehandru, Saurabh; Cho, Judy; Dubinsky, Marla; Curran, Mark; Brodmerkel, Carrie; Schadt, Eric E.; Sands, Bruce E.; Colombel, Jean-Frederic; Kasarskis, Andrew; Argmann, Carmen A.; Suarez-Farinas, Mayte Share Save
Intestinal Inflammation Modulates the Expression of ACE2 and TMPRSS2 and Potentially Overlaps With the Pathogenesis of SARS-CoV-2-related Disease Suarez-Farinas, Mayte; Tokuyama, Minami; Wei, Gabrielle; Huang, Ruiqi; Livanos, Alexandra; Jha, Divya; Levescot, Anais; Irizar, Haritz; Kosoy, Roman; Cording, Sascha; Wang, Wenhui; Losic, Bojan; Ungaro, Ryan C.; Di'Narzo, Antonio; Martinez-Delgado, Gustavo; Suprun, Maria; Corley, Michael J.; Stojmirovic, Aleksandar; Houten, Sander M.; Peters, Lauren; Curran, Mark; Brodmerkel, Carrie; Perrigoue, Jacqueline; Friedman, Joshua R.; Hao, Ke; Schadt, Eric E.; Zhu, Jun; Ko, Huaibin M.; Cho, Judy; Dubinsky, Marla C.; Sands, Bruce E.; Ndhlovu, Lishomwa; Cerf-Bensusan, Nadine; Kasarskis, Andrew; Colombel, Jean-Frederic; Harpaz, Noam; Argmann, Carmen; Mehandru, Saurabh Share Save
PAI-1 augments mucosal damage in colitis Kaiko, Gerard E.; Chen, Feidi; Lai, Chin-Wen; Chiang, I-Ling; Perrigoue, Jacqueline; Stojmirovic, Aleksandar; Li, Katherine; Muegge, Brian D.; Jain, Umang; VanDussen, Kelli L.; Goggins, Bridie J.; Keely, Simon; Weaver, Jessica; Foster, Paul S.; Lawrence, Daniel A.; Liu, Ta-Chiang; Stappenbeck, Thaddeus S. Share Save
A molecular measure of inflammation in IBD patients based on transcriptional profiles from 2495 intestinal biopsies Huang, R.; Irizar, H.; Kosoy, R.; Song, W. -M.; Dinarzo, A.; Hao, K.; Rogers, J.; Atreja, A.; Mahajan, M.; Stojmirovic, A.; Perrigoue, J.; Brodmerkel, C.; Plevy, S.; Friedman, J.; Colombel, J. -F.; Dubinsky, M.; Sands, B.; Schadt, E.; Kasarskis, A.; Losic, B.; Argmann, C.; Suarez-Farinas, M. Share Save
Abnormal Small Intestinal Epithelial Microvilli in Patients With Crohn's Disease VanDussen, Kelli L.; Stojmirovic, Aleksandar; Li, Katherine; Liu, Ta-Chiang; Kimes, Patrick K.; Muegge, Brian D.; Simpson, Katherine F.; Ciorba, Matthew A.; Perrigoue, Jacqueline G.; Friedman, Joshua R.; Towne, Jennifer E.; Head, Richard D.; Stappenbeck, Thaddeus S. Share Save
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A functional genomics predictive network model identifies regulators of inflammatory bowel disease Peters, Lauren A.; Perrigoue, Jacqueline; Mortha, Arthur; Iuga, Alina; Song, Won-min; Neiman, Eric M.; Llewellyn, Sean R.; Di Narzo, Antonio; Kidd, Brian A.; Telesco, Shannon E.; Zhao, Yongzhong; Stojmirovic, Aleksandar; Sendecki, Jocelyn; Shameer, Khader; Miotto, Riccardo; Losic, Bojan; Shah, Hardik; Lee, Eunjee; Wang, Minghui; Faith, Jeremiah J.; Kasarskis, Andrew; Brodmerkel, Carrie; Curran, Mark; Das, Anuk; Friedman, Joshua R.; Fukui, Yoshinori; Humphrey, Mary Beth; Iritani, Brian M.; Sibinga, Nicholas; Tarrant, Teresa K.; Argmann, Carmen; Hao, Ke; Roussos, Panos; Zhu, Jun; Zhang, Bin; Dobrin, Radu; Mayer, Lloyd F.; Schadt, Eric E. Share Save
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Blood and Intestine eQTLs from an Anti-TNF-Resistant Crohn's Disease Cohort Inform IBD Genetic Association Loci Di Narzo, Antonio F.; Peters, Lauren A.; Argmann, Carmen; Stojmirovic, Aleksandar; Perrigoue, Jacqueline; Li, Katherine; Telesco, Shannon; Kidd, Brian; Walker, Jennifer; Dudley, Joel; Cho, Judy; Schadt, Eric E.; Kasarskis, Andrew; Curran, Mark; Dobrin, Radu; Hao, Ke Share Save
Integrative Networks Identify Novel Regulators of Susceptibility and Pathogenesis of Inflammatory Bowel Disease Peters, Lauren; Perrigoue, Jacqueline; Mortha, Arthur; Stojmirovic, Aleksandar; Neiman, Eric M.; Iuga, Alina; Song, Won-min; Kidd, Brian A.; Losic, Bojan; Llewellyn, Sean; Miotto, Riccardo; Shameer, Khader; Zhao, Yongzhong; Di Narzo, Antonio; Shah, Hardik; Cohain, Ariella; Dudley, Joel T.; Faith, Jeremiah; Merad, Miriam; Fukui, Fumiyuki; Iritani, Brian; Sibinga, Nicholas; Tarrant, Teresa; Argmann, Carmen; Kasarskis, Andrew; Curran, Mark; Das, Anuk; Dobrin, Radu; Hao, Ke; Roussos, Panos; Zhang, Bin; Zhu, Jun; Mayer, Lloyd F.; Friedman, Joshua; Schadt, Eric E. Share Save
NDEx, the Network Data Exchange Pratt, Dexter; Chen, Jing; Welker, David; Rivas, Ricardo; Pillich, Rudolf; Rynkov, Vladimir; Ono, Keiichiro; Miello, Carol; Hicks, Lyndon; Szalma, Sandor; Stojmirovic, Aleksandar; Dobrin, Radu; Braxenthaler, Michael; Kuentzer, Jan; Demchak, Barry; Ideker, Trey Share Save
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