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Profiling the quantitative occupancy of myriad transcription factors across conditions by modeling chromatin accessibility data Luo, Kaixuan; Zhong, Jianling; Safi, Alexias; Hong, Linda K.; Tewari, Alok K.; Song, Lingyun; Reddy, Timothy E.; Ma, Li; Crawford, Gregory E.; Hartemink, Alexander J. Share Save
Enhancer selection dictates gene expression responses in remote organs during tissue regeneration Sun, Fei; Ou, Jianhong; Shoffner, Adam R.; Luan, Yu; Yang, Hongbo; Song, Lingyun; Safi, Alexias; Cao, Jingli; Yue, Feng; Crawford, Gregory E.; Poss, Kenneth D. Share Save
Sex dependent glial-specific changes in the chromatin accessibility landscape in late-onset Alzheimer's disease brains Barrera, Julio; Song, Lingyun; Gamache, Julia E.; Garrett, Melanie E.; Safi, Alexias; Yun, Young; Premasinghe, Ivana; Sprague, Daniel; Chipman, Danielle; Li, Jeffrey; Fradin, Helene; Soldano, Karen; Gordan, Raluca; Ashley-Koch, Allison E.; Crawford, Gregory E.; Chiba-Falek, Ornit Share Save
Targeted long-read sequencing identifies missing disease-causing variation Miller, Danny E.; Sulovari, Arvis; Wang, Tianyun; Loucks, Hailey; Hoekzema, Kendra; Munson, Katherine M.; Lewis, Alexandra P.; Fuerte, Edith P. Almanza; Paschal, Catherine R.; Walsh, Tom; Thies, Jenny; Bennett, James T.; Glass, Ian; Dipple, Katrina M.; Patterson, Karynne; Bonkowski, Emily S.; Nelson, Zoe; Squire, Audrey; Sikes, Megan; Beckman, Erika; Bennett, Robin L.; Earl, Dawn; Lee, Winston; Allikmets, Rando; Perlman, Seth J.; Chow, Penny; Hing, Anne, V; Wenger, Tara L.; Adam, Margaret P.; Sun, Angela; Lam, Christina; Chang, Irene; Zou, Xue; Austin, Stephanie L.; Huggins, Erin; Safi, Alexias; Iyengar, Apoorva K.; Reddy, Timothy E.; Majoros, William H.; Allen, Andrew S.; Crawford, Gregory E.; Kishnani, Priya S.; King, Mary-Claire; Cherry, Tim; Chong, Jessica X.; Bamshad, Michael J.; Nickerson, Deborah A.; Mefford, Heather C.; Doherty, Dan; Eichler, Evan E. Share Save
Integrated chromatin and transcriptomic profiling of patient-derived colon cancer organoids identifies personalized drug targets to overcome oxaliplatin resistance Tung, Kuei-Ling; Chen, Kai-Yuan; Negrete, Marcos; Chen, Tianyi; Safi, Alexias; Aljamal, Abed Alhalim; Song, Lingyun; Crawford, Gregory E.; Ding, Shengli; Hsu, David S.; Shen, Xiling Share Save
Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation Keele, Gregory R.; Quach, Bryan C.; Israel, Jennifer W.; Chappell, Grace A.; Lewis, Lauren; Safi, Alexias; Simon, Jeremy M.; Cotney, Paul; Crawford, Gregory E.; Valdar, William; Rusyn, Ivan; Furey, Terrence S. Share Save
Evaluating Chromatin Accessibility Differences Across Multiple Primate Species Using a Joint Modeling Approach Edsall, Lee E.; Berrio, Alejandro; Majoros, William H.; Swain-Lenz, Devjanee; Morrow, Shauna; Shibata, Yoichiro; Safi, Alexias; Wray, Gregory A.; Crawford, Gregory E.; Allen, Andrew S. Share Save
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Glucocorticoid receptor recruits to enhancers and drives activation by motif-directed binding McDowell, Ian C.; Barrera, Alejandro; D'Ippolito, Anthony M.; Vockley, Christopher M.; Hong, Linda K.; Leichter, Sarah M.; Bartelt, Luke C.; Majoros, William H.; Song, Lingyun; Safi, Alexias; Kocak, D. Dewran; Gersbach, Charles A.; Hartemink, Alexander J.; Crawford, Gregory E.; Engelhardt, Barbara E.; Reddy, Timothy E. Share Save
Evaluation of chromatin accessibility in prefrontal cortex of individuals with schizophrenia Bryois, Julien; Garrett, Melanie E.; Song, Lingyun; Safi, Alexias; Giusti-Rodriguez, Paola; Johnson, Graham D.; Shieh, Annie W.; Buil, Alfonso; Fullard, John F.; Roussos, Panos; Sklar, Pamela; Akbarian, Schahram; Haroutunian, Vahram; Stockmeier, Craig A.; Wray, Gregory A.; White, Kevin P.; Liu, Chunyu; Reddy, Timothy E.; Ashley-Koch, Allison; Sullivan, Patrick F.; Crawford, Gregory E. Share Save
Pre-established Chromatin Interactions Mediate the Genomic Response to Glucocorticoids D'lppolito, Anthony M.; McDowell, Ian C.; Barrera, Alejandro; Hong, Linda K.; Leichter, Sarah M.; Bartelt, Luke C.; Vockley, Christopher M.; Majoros, William H.; Safi, Alexias; Song, Lingyun; Gersbach, Charles A.; Crawford, Gregory E.; Reddy, Timothy E. Share Save
Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights Gusev, Alexander; Mancuso, Nicholas; Won, Hyejung; Kousi, Maria; Finucane, Hilary K.; Reshef, Yakir; Song, Lingyun; Safi, Alexias; McCarroll, Steven; Neale, Benjamin M.; Ophoff, Roel A.; O'Donovan, Michael C.; Crawford, Gregory E.; Geschwind, Daniel H.; Katsanis, Nicholas; Sullivan, Patrick F.; Pasaniuc, Bogdan; Price, Alkes L. Share Save
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Variation in DNA-Damage Responses to an Inhalational Carcinogen (1,3-Butadiene) in Relation to Strain-Specific Differences in Chromatin Accessibility and Gene Transcription Profiles in C57BL/6J and CAST/EiJ Mice Chappell, Grace A.; Israel, Jennifer W.; Simon, Jeremy M.; Pott, Sebastian; Safi, Alexias; Eklund, Karl; Sexton, Kenneth G.; Bodnar, Wanda; Lieb, Jason D.; Crawford, Gregory E.; Rusyn, Ivan; Furey, Terrence S. Share Save
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Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus Yang, Rui; Kerschner, Jenny L.; Gosalia, Nehal; Neems, Daniel; Gorsic, Lidija K.; Safi, Alexias; Crawford, Gregory E.; Kosak, Steven T.; Leir, Shih-Hsing; Harris, Ann Share Save
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Genetic variants and cellular stressors associated with exfoliation syndrome modulate promoter activity of a lncRNA within the LOXL1 locus Hauser, Michael A.; Aboobakar, Inas F.; Liu, Yutao; Miura, Shiroh; Whigham, Benjamin T.; Challa, Pratap; Wheeler, Joshua; Williams, Andrew; Santiago-Turla, Cecelia; Qin, Xuejun; Rautenbach, Robyn M.; Ziskind, Ari; Ramsay, Michele; Uebe, Steffen; Song, Lingyun; Safi, Alexias; Vithana, Eranga N.; Mizoguchi, Takanori; Nakano, Satoko; Kubota, Toshiaki; Hayashi, Ken; Manabe, Shin-ichi; Kazama, Shigeyasu; Mori, Yosai; Miyata, Kazunori; Yoshimura, Nagahisa; Reis, Andre; Crawford, Gregory E.; Pasutto, Francesca; Carmichael, Trevor R.; Williams, Susan E. I.; Ozaki, Mineo; Aung, Tin; Khor, Chiea-Chuen; Stamer, W. Daniel; Ashley-Koch, Allison E.; Allingham, R. Rand Share Save
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