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The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles ( vol 24 , 79 , 2023) Schreiber, Jacob Matthew; Boix, Carles A.; Lee, Jin Wook; Li, Hongyang; Guan, Yuanfang; Chang, Chun-Chieh; Chang, Jen-Chien; Hawkins-Hooker, Alex; Schoelkopf, Bernhard; Schweikert, Gabriele; Carulla, Mateo Rojas; Canakoglu, Arif; Guzzo, Francesco; Nanni, Luca; Masseroli, Marco; Carman, Mark James; Pinoli, Pietro; Hong, Chenyang; Yip, Kevin Y.; Spence, Jefrey P.; Batra, Sanjit Singh; Song, Yun S.; Mahony, Shaun; Zhang, Zheng; Tan, Wuwei; Shen, Yang; Sun, Yuanfei; Shi, Minyi; Adrian, Jessika; Sandstrom, Richard S.; Farrell, Nina P.; Halow, Jessica M.; Lee, Kristen; Jiang, Lixia; Yang, Xinqiong; Epstein, Charles B.; Strattan, J. Seth; Bernstein, Bradley E.; Snyder, Michael P.; Kellis, Manolis; Noble, William S.; Kundaje, Anshul Bharat; ENCODE Imputat Challenge Participants Share Save
Deep learning prediction of ribosome profiling with Translatomer reveals translational regulation and interprets disease variants He, Jialin; Xiong, Lei; Shi, Shaohui; Li, Chengyu; Chen, Kexuan; Fang, Qianchen; Nan, Jiuhong; Ding, Ke; Mao, Yuanhui; Boix, Carles A.; Hu, Xinyang; Kellis, Manolis; Li, Jingyun; Xiong, Xushen Share Save
Transcriptomic and spatial dissection of human ex vivo right atrial tissue reveals proinflammatory microvascular changes in ischemic heart disease Linna-Kuosmanen, Suvi; Schmauch, Eloi; Galani, Kyriakitsa; Ojanen, Johannes; Boix, Carles A.; Ord, Tiit; Toropainen, Anu; Singha, Prosanta K.; Moreau, Pierre R.; Harju, Kristiina; Blazeski, Adriana; Segerstolpe, Asa; Lahtinen, Veikko; Hou, Lei; Kang, Kai; Meibalan, Elamaran; Agudelo, Leandro Z.; Kokki, Hannu; Halonen, Jari; Jalkanen, Juho; Gunn, Jarmo; Macrae, Calum A.; Hollmen, Maija; Hartikainen, Juha E. K.; Kaikkonen, Minna U.; Garcia-Cardena, Guillermo; Tavi, Pasi; Kiviniemi, Tuomas; Kellis, Manolis Share Save
Multitissue H3K27ac profiling of GTEx samples links epigenomic variation to disease Hou, Lei; Xiong, Xushen; Park, Yongjin; Boix, Carles; James, Benjamin; Sun, Na; He, Liang; Patel, Aman; Zhang, Zhizhuo; Molinie, Benoit; Van Wittenberghe, Nicholas; Steelman, Scott; Nusbaum, Chad; Aguet, Francois; Ardlie, Kristin G.; Kellis, Manolis Share Save
The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles Schreiber, Jacob; Boix, Carles; Lee, Jin Wook; Li, Hongyang; Guan, Yuanfang; Chang, Chun-Chieh; Chang, Jen-Chien; Hawkins-Hooker, Alex; Scholkopf, Bernhard; Schweikert, Gabriele; Carulla, Mateo Rojas; Canakoglu, Arif; Guzzo, Francesco; Nanni, Luca; Masseroli, Marco; Carman, Mark James; Pinoli, Pietro; Hong, Chenyang; Yip, Kevin Y.; Spence, Jeffrey P.; Batra, Sanjit Singh; Song, Yun S.; Mahony, Shaun; Zhang, Zheng; Tan, Wuwei; Shen, Yang; Sun, Yuanfei; Shi, Minyi; Adrian, Jessika; Sandstrom, Richard; Farrell, Nina; Halow, Jessica; Lee, Kristen; Jiang, Lixia; Yang, Xinqiong; Epstein, Charles; Strattan, J. Seth; Bernstein, Bradley; Snyder, Michael; Kellis, Manolis; Stafford, William; Kundaje, Anshul Share Save
GENCODE: reference annotation for the human and mouse genomes in 2023 Frankish, Adam; Carbonell-Sala, Silvia; Diekhans, Mark; Jungreis, Irwin; Loveland, Jane E.; Mudge, Jonathan M.; Sisu, Cristina; Wright, James C.; Arnan, Carme; Barnes, If; Banerjee, Abhimanyu; Bennett, Ruth; Berry, Andrew; Bignell, Alexandra; Boix, Carles; Calvet, Ferriol; Cerdan-Velez, Daniel; Cunningham, Fiona; Davidson, Claire; Donaldson, Sarah; Dursun, Cagatay; Fatima, Reham; Giorgetti, Stefano; Giron, Carlos Garcia; Gonzalez, Jose Manuel; Hardy, Matthew; Harrison, Peter W.; Hourlier, Thibaut; Hollis, Zoe; Hunt, Toby; James, Benjamin; Jiang, Yunzhe; Johnson, Rory; Kay, Mike; Lagarde, Julien; Martin, Fergal J.; Gomez, Laura Martinez; Nair, Surag; Ni, Pengyu; Pozo, Fernando; Ramalingam, Vivek; Ruffier, Magali; Schmitt, Bianca M.; Schreiber, Jacob M.; Steed, Emily; Suner, Marie-Marthe; Sumathipala, Dulika; Sycheva, Irina; Uszczynska-Ratajczak, Barbara; Wass, Elizabeth; Yang, Yucheng T.; Yates, Andrew; Zafrulla, Zahoor; Choudhary, Jyoti S.; Gerstein, Mark; Guigo, Roderic; Hubbard, Tim J. P.; Kellis, Manolis; Kundaje, Anshul; Paten, Benedict; Tress, Michael L.; Flicek, Paul Share Save
Neurons burdened by DNA double-strand breaks incite microglia activation through antiviral-like signaling in neurodegeneration Welch, Gwyneth M.; Boix, Carles A.; Schmauch, Eloi; Davila-Velderrain, Jose; Victor, Matheus B.; Dileep, Vishnu; Bozzelli, P. Lorenzo; Su, Qiao; Cheng, Jemmie D.; Lee, Audrey; Leary, Noelle S.; Pfenning, Andreas R.; Kellis, Manolis; Tsai, Li-Huei Share Save
GENCODE 2021 Frankish, Adam; Diekhans, Mark; Jungreis, Irwin; Lagarde, Julien; Loveland, Jane E.; Mudge, Jonathan M.; Sisu, Cristina; Wright, James C.; Armstrong, Joel; Barnes, If; Berry, Andrew; Bignell, Alexandra; Boix, Carles; Carbonell Sala, Silvia; Cunningham, Fiona; Di Domenico, Tomas; Donaldson, Sarah; Fiddes, Ian T.; Giron, Carlos Garcia; Gonzalez, Jose Manuel; Grego, Tiago; Hardy, Matthew; Hourlier, Thibaut; Howe, Kevin L.; Hunt, Toby; Izuogu, Osagie G.; Johnson, Rory; Martin, Fergal J.; Martinez, Laura; Mohanan, Shamika; Muir, Paul; Navarro, Fabio C. P.; Parker, Anne; Pei, Baikang; Pozo, Fernando; Riera, Ferriol Calvet; Ruffier, Magali; Schmitt, Bianca M.; Stapleton, Eloise; Suner, Marie-Marthe; Sycheva, Irina; Uszczynska-Ratajczak, Barbara; Wolf, Maxim Y.; Xu, Jinuri; Yang, Yucheng T.; Yates, Andrew; Zerbino, Daniel; Zhang, Yan; Choudhary, Jyoti S.; Gerstein, Mark; Guigo, Roderic; Hubbard, Tim J. P.; Kellis, Manolis; Paten, Benedict; Tress, Michael L.; Flicek, Paul Share Save
Conserved Epigenetic Regulatory Logic Infers Genes Governing Cell Identity Shim, Woo Jun; Sinniah, Enakshi; Xu, Jun; Vitrinel, Burcu; Alexanian, Michael; Andreoletti, Gaia; Shen, Sophie; Sun, Yuliangzi; Balderson, Brad; Boix, Carles; Peng, Guangdun; Jing, Naihe; Wang, Yuliang; Kellis, Manolis; Tam, Patrick P. L.; Smith, Aaron; Piper, Michael; Christiaen, Lionel; Quan Nguyen; Boden, Mikael; Palpant, Nathan J. Share Save
Single-Cell Transcriptional and Epigenomic Dissection of Human Heart in Health and Coronary Artery Disease Reveals Cell-type-Specific Driver Genes and Pathways Kuosmanen, Suvi Linna; Schmauch, Eloi; Galani, Kyriakitsa; Boix, Carles; Park, Yongjin P.; Hollmen, Maija; Gunn, Jarmo; Kiviniemi, Tuomas O.; Garcia-Cardena, Guillermo; Kellis, Manolis Share Save
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