Correcting nucleotide-specific biases in high-throughput sequencing data by Jeremy R. Wang, Bryan Quach, Terrence S. Furey

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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 by Satyaki Roy, Shehzad Z. Sheikh, Terrence S. Furey

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

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Evidence of influence of genomic DNA sequence on human X chromosome inactivation. by Zhong Wang, Huntington F Willard, Sayan Mukherjee, Terrence S Furey

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Correction: A Predictive Framework for Integrating Disparate Genomic Data Types Using Sample-Specific Gene Set Enrichment Analysis and Multi-Task Learning. by Brian D. Bennett, Qing Xiong, Sayan Mukherjee, Terrence S. Furey

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A predictive framework for integrating disparate genomic data types using sample-specific gene set enrichment analysis and multi-task learning. by Brian D Bennett, Qing Xiong, Sayan Mukherjee, Terrence S Furey

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

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Chromatin accessibility mapping identifies mediators of basal transcription and retinoid-induced repression of OTX2 in medulloblastoma. by Matthew Wortham, Changcun Guo, Monica Zhang, Lingyun Song, Bum-Kyu Lee, Vishwanath R Iyer, Terrence S Furey, Gregory E Crawford, Hai Yan, Yiping He

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Nuclear actin structure regulates chromatin accessibility by Buer Sen, Zhihui Xie, Michelle D. Thomas, Samantha G. Pattenden, Sean Howard, Cody McGrath, Maya Styner, Gunes Uzer, Terrence S. Furey, Janet Rubin

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

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Prdm6 drives ductus arteriosus closure by promoting ductus arteriosus smooth muscle cell identity and contractility by Meng Zou, Kevin D. Mangum, Justin C. Magin, Heidi H. Cao, Michael T. Yarboro, Elaine L. Shelton, Joan M. Taylor, Jeff Reese, Terrence S. Furey, Christopher P. Mack

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Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation. by Gregory R Keele, Bryan C Quach, Jennifer W Israel, Grace A Chappell, Lauren Lewis, Alexias Safi, Jeremy M Simon, Paul Cotney, Gregory E Crawford, William Valdar, Ivan Rusyn, Terrence S Furey

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Identification and characterization of cell type-specific and ubiquitous chromatin regulatory structures in the human genome. by Hualin Xi, Hennady P Shulha, Jane M Lin, Teresa R Vales, Yutao Fu, David M Bodine, Ronald D G McKay, Josh G Chenoweth, Paul J Tesar, Terrence S Furey, Bing Ren, Zhiping Weng, Gregory E Crawford

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

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Extensive evolutionary changes in regulatory element activity during human origins are associated with altered gene expression and positive selection. by Yoichiro Shibata, Nathan C Sheffield, Olivier Fedrigo, Courtney C Babbitt, Matthew Wortham, Alok K Tewari, Darin London, Lingyun Song, Bum-Kyu Lee, Vishwanath R Iyer, Stephen C J Parker, Elliott H Margulies, Gregory A Wray, Terrence S Furey, Gregory E Crawford

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Mutational signatures of de-differentiation in functional non-coding regions of melanoma genomes. by Stephen C J Parker, Jared Gartner, Isabel Cardenas-Navia, Xiaomu Wei, Hatice Ozel Abaan, Subramanian S Ajay, Nancy F Hansen, Lingyun Song, Umesh K Bhanot, J Keith Killian, Yevgeniy Gindin, Robert L Walker, Paul S Meltzer, James C Mullikin, Terrence S Furey, Gregory E Crawford, Steven A Rosenberg, Yardena Samuels, Elliott H Margulies

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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 PatientsSummary by Matt Kanke, Meaghan M. Kennedy Ng, Sean Connelly, Manvendra Singh, Matthew Schaner, Michael T. Shanahan, Elizabeth A. Wolber, Caroline Beasley, Grace Lian, Animesh Jain, Millie D. Long, Edward L. Barnes, Hans H. Herfarth, Kim L. Isaacs, Jonathon J. Hansen, Muneera Kapadia, Jose Gaston Guillem, Cedric Feschotte, Terrence S. Furey, Shehzad Z. Sheikh, Praveen Sethupathy

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Increased colonic expression of ACE2 associates with poor prognosis in Crohn’s disease by Takahiko Toyonaga, Kenza C. Araba, Meaghan M. Kennedy, Benjamin P. Keith, Elisabeth A. Wolber, Caroline Beasley, Erin C. Steinbach, Matthew R. Schaner, Animesh Jain, Millie D. Long, Edward L. Barnes, Hans H. Herfarth, Kim L. Isaacs, Jonathan J. Hansen, Muneera R. Kapadia, José Gaston Guillem, Ajay S. Gulati, Praveen Sethupathy, Terrence S. Furey, Camille Ehre, Shehzad Z. Sheikh

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New loci for body fat percentage reveal link between adiposity and cardiometabolic disease risk by Yingchang Lu, Felix R. Day, Stefan Gustafsson, Martin L. Buchkovich, Jianbo Na, Veronique Bataille, Diana L. Cousminer, Zari Dastani, Alexander W. Drong, Tõnu Esko, David M. Evans, Mario Falchi, Mary F. Feitosa, Teresa Ferreira, Åsa K. Hedman, Robin Haring, Pirro G. Hysi, Mark M. Iles, Anne E. Justice, Stavroula Kanoni, Vasiliki Lagou, Rui Li, Xin Li, Adam Locke, Chen Lu, Reedik Mägi, John R. B. Perry, Tune H. Pers, Qibin Qi, Marianna Sanna, Ellen M. Schmidt, William R. Scott, Dmitry Shungin, Alexander Teumer, Anna A. E. Vinkhuyzen, Ryan W. Walker, Harm-Jan Westra, Mingfeng Zhang, Weihua Zhang, Jing Hua Zhao, Zhihong Zhu, Uzma Afzal, Tarunveer Singh Ahluwalia, Stephan J. L. Bakker, Claire Bellis, Amélie Bonnefond, Katja Borodulin, Aron S. Buchman, Tommy Cederholm, Audrey C. Choh, Hyung Jin Choi, Joanne E. Curran, Lisette C. P. G. M. de Groot, Philip L. De Jager, Rosalie A. M. Dhonukshe-Rutten, Anke W. Enneman, Elodie Eury, Daniel S. Evans, Tom Forsen, Nele Friedrich, Frédéric Fumeron, Melissa E. Garcia, Simone Gärtner, Bok-Ghee Han, Aki S. Havulinna, Caroline Hayward, Dena Hernandez, Hans Hillege, Till Ittermann, Jack W. Kent, Ivana Kolcic, Tiina Laatikainen, Jari Lahti, Irene Mateo Leach, Christine G. Lee, Jong-Young Lee, Tian Liu, Youfang Liu, Stéphane Lobbens, Marie Loh, Leo-Pekka Lyytikäinen, Carolina Medina-Gomez, Karl Michaëlsson, Mike A. Nalls, Carrie M. Nielson, Laticia Oozageer, Laura Pascoe, Lavinia Paternoster, Ozren Polašek, Samuli Ripatti, Mark A. Sarzynski, Chan Soo Shin, Nina Smolej Narančić, Dominik Spira, Priya Srikanth, Elisabeth Steinhagen-Thiessen, Yun Ju Sung, Karin M. A. Swart, Leena Taittonen, Toshiko Tanaka, Emmi Tikkanen, Nathalie van der Velde, Natasja M. van Schoor, Niek Verweij, Alan F. Wright, Lei Yu, Joseph M. Zmuda, Niina Eklund, Terrence Forrester, Niels Grarup, Anne U. Jackson, Kati Kristiansson, Teemu Kuulasmaa, Johanna Kuusisto, Peter Lichtner, Jian'an Luan, Anubha Mahajan, Satu Männistö, Cameron D. Palmer, Janina S. Ried, Robert A. Scott, Alena Stancáková, Peter J. Wagner, Ayse Demirkan, Angela Döring, Vilmundur Gudnason, Douglas P. Kiel, Brigitte Kühnel, Massimo Mangino, Barbara Mcknight, Cristina Menni, Jeffrey R. O'Connell, Ben A. Oostra, Alan R. Shuldiner, Kijoung Song, Liesbeth Vandenput, Cornelia M. van Duijn, Peter Vollenweider, Charles C. White, Michael Boehnke, Yvonne Boettcher, Richard S. Cooper, Nita G. Forouhi, Christian Gieger, Harald Grallert, Aroon Hingorani, Torben Jørgensen, Pekka Jousilahti, Mika Kivimaki, Meena Kumari, Markku Laakso, Claudia Langenberg, Allan Linneberg, Amy Luke, Colin A. Mckenzie, Aarno Palotie, Oluf Pedersen, Annette Peters, Konstantin Strauch, Bamidele O. Tayo, Nicholas J. Wareham, David A. Bennett, Lars Bertram, John Blangero, Matthias Blüher, Claude Bouchard, Harry Campbell, Nam H. Cho, Steven R. Cummings, Stefan A. Czerwinski, Ilja Demuth, Rahel Eckardt, Johan G. Eriksson, Luigi Ferrucci, Oscar H. Franco, Philippe Froguel, Ron T. Gansevoort, Torben Hansen, Tamara B. Harris, Nicholas Hastie, Markku Heliövaara, Albert Hofman, Joanne M. Jordan, Antti Jula, Mika Kähönen, Eero Kajantie, Paul B. Knekt, Seppo Koskinen, Peter Kovacs, Terho Lehtimäki, Lars Lind, Yongmei Liu, Eric S. Orwoll, Clive Osmond, Markus Perola, Louis Pérusse, Olli T. Raitakari, Tuomo Rankinen, D. C. Rao, Treva K. Rice, Fernando Rivadeneira, Igor Rudan, Veikko Salomaa, Thorkild I. A. Sørensen, Michael Stumvoll, Anke Tönjes, Bradford Towne, Gregory J. Tranah, Angelo Tremblay, André G. Uitterlinden, Pim van der Harst, Erkki Vartiainen, Jorma S. Viikari, Veronique Vitart, Marie-Claude Vohl, Henry Völzke, Mark Walker, Henri Wallaschofski, Sarah Wild, James F. Wilson, Loïc Yengo, D. Timothy Bishop, Ingrid B. Borecki, John C. Chambers, L. Adrienne Cupples, Abbas Dehghan, Panos Deloukas, Ghazaleh Fatemifar, Caroline Fox, Terrence S. Furey, Lude Franke, Jiali Han, David J. Hunter, Juha Karjalainen, Fredrik Karpe, Robert C. Kaplan, Jaspal S. Kooner, Mark I. McCarthy, Joanne M. Murabito, Andrew P. Morris, Julia A. N. Bishop, Kari E. North, Claes Ohlsson, Ken K. Ong, Inga Prokopenko, J. Brent Richards, Eric E. Schadt, Tim D. Spector, Elisabeth Widén, Cristen J. Willer, Jian Yang, Erik Ingelsson, Karen L. Mohlke, Joel N. Hirschhorn, John Andrew Pospisilik, M. Carola Zillikens, Cecilia Lindgren, Tuomas Oskari Kilpeläinen, Ruth J. F. Loos

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