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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
Standardized annotation of translated open reading frames Mudge, Jonathan M.; Ruiz-Orera, Jorge; Prensner, John R.; Brunet, Marie A.; Calvet, Ferriol; Jungreis, Irwin; Gonzalez, Jose Manuel; Magrane, Michele; Martinez, Thomas F.; Schulz, Jana Felicitas; Yang, Yucheng T.; Alba, M. Mar; Aspden, Julie L.; Baranov, Pavel V.; Bazzini, Ariel A.; Bruford, Elspeth; Martin, Maria Jesus; Calviello, Lorenzo; Carvunis, Anne-Ruxandra; Chen, Jin; Couso, Juan Pablo; Deutsch, Eric W.; Flicek, Paul; Frankish, Adam; Gerstein, Mark; Hubner, Norbert; Ingolia, Nicholas T.; Kellis, Manolis; Menschaert, Gerben; Moritz, Robert L.; Ohler, Uwe; Roucou, Xavier; Saghatelian, Alan; Weissman, Jonathan S.; van Heesch, Sebastiaan Share Save
Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer Ouspenskaia, Tamara; Law, Travis; Clauser, Karl R.; Klaeger, Susan; Sarkizova, Siranush; Aguet, Francois; Li, Bo; Christian, Elena; Knisbacher, Binyamin A.; Le, Phuong M.; Hartigan, Christina R.; Keshishian, Hasmik; Apffel, Annie; Oliveira, Giacomo; Zhang, Wandi; Chen, Sarah; Chow, Yuen Ting; Ji, Zhe; Jungreis, Irwin; Shukla, Sachet A.; Justesen, Sune; Bachireddy, Pavan; Kellis, Manolis; Getz, Gad; Hacohen, Nir; Keskin, Derin B.; Carr, Steven A.; Wu, Catherine J.; Regev, Aviv Share Save
Calcifediol Treatment and Hospital Mortality Due to COVID-19: A Cohort Study Alcala-Diaz, Juan F.; Limia-Perez, Laura; Gomez-Huelgas, Ricardo; Martin-Escalante, Maria D.; Cortes-Rodriguez, Begona; Zambrana-Garcia, Jose L.; Entrenas-Castillo, Marta; Perez-Caballero, Ana I.; Lopez-Carmona, Maria D.; Garcia-Alegria, Javier; Lozano Rodriguez-Mancheno, Aquiles; Arenas-de Larriva, Maria del Sol; Perez-Belmonte, Luis M.; Jungreis, Irwin; Bouillon, Roger; Quesada-Gomez, Jose Manual; Lopez-Miranda, Jose Share Save
Genus-wide characterization of bumblebee genomes provides insights into their evolution and variation in ecological and behavioral traits (vol 38, pg 486, 2021) Sun, Cheng; Huang, Jiaxing; Wang, Yun; Zhao, Xiaomeng; Su, Long; Thomas, Gregg W. C.; Zhao, Mengya; Zhang, Xingtan; Jungreis, Irwin; Kellis, Manolis; Vicario, Saverio; Sharakhov, Igor V.; Bondarenko, Semen M.; Hasselmann, Martin; Kim, Chang N.; Paten, Benedict; Penso-Dolfin, Luca; Wang, Li; Chang, Yuxiao; Gao, Qiang; Ma, Ling; Ma, Lina; Zhang, Zhang; Zhang, Hongbo; Zhang, Huahao; Ruzzante, Livio; Robertson, Hugh M.; Zhu, Yihui; Liu, Yanjie; Yang, Huipeng; Ding, Lele; Wang, Quangui; Ma, Dongna; Xu, Weilin; Liang, Cheng; Itgen, Michael W.; Mee, Lauren; Cao, Gang; Zhang, Ze; Sadd, Ben M.; Hahn, Matthew W.; Schaack, Sarah; Barribeau, Seth M.; Williams, Paul H.; Waterhouse, Robert M.; Mueller, Rachel Lockridge Share Save
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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
Genomic RNA Elements Drive Phase Separation of the SARS-CoV-2 Nucleocapsid Iserman, Christiane; Roden, Christine A.; Boerneke, Mark A.; Sealfon, Rachel S. G.; McLaughlin, Grace A.; Jungreis, Irwin; Fritch, Ethan J.; Hou, Yixuan J.; Ekena, Joanne; Weidmann, Chase A.; Theesfeld, Chandra L.; Kellis, Manolis; Troyanskaya, Olga G.; Baric, Ralph S.; Sheahan, Timothy P.; Weeks, Kevin M.; Gladfelter, Amy S. Share Save
Evidence for secondary-variant genetic burden and non-random distribution across biological modules in a recessive ciliopathy Kousi, Maria; Soylemez, Onuralp; Ozanturk, Aysegul; Mourtzi, Niki; Akle, Sebastian; Jungreis, Irwin; Muller, Jean; Cassa, Christopher A.; Brand, Harrison; Mokry, Jill Anne; Wolf, Maxim Y.; Sadeghpour, Azita; McFadden, Kelsey; Lewis, Richard A.; Talkowski, Michael E.; Dollfus, Helene; Kellis, Manolis; Davis, Erica E.; Sunyaev, Shamil R.; Katsanis, Nicholas Share Save
Genus-Wide Characterization of Bumblebee Genomes Provides Insights into Their Evolution and Variation in Ecological and Behavioral Traits Sun, Cheng; Huang, Jiaxing; Wang, Yun; Zhao, Xiaomeng; Su, Long; Thomas, Gregg W. C.; Zhao, Mengya; Zhang, Xingtan; Jungreis, Irwin; Kellis, Manolis; Vicario, Saverio; Sharakhov, Igor, V; Bondarenko, Semen M.; Hasselmann, Martin; Kim, Chang N.; Paten, Benedict; Penso-Dolfin, Luca; Wang, Li; Chang, Yuxiao; Gao, Qiang; Ma, Ling; Ma, Lina; Zhang, Zhang; Zhang, Hongbo; Zhang, Huahao; Ruzzante, Livio; Robertson, Hugh M.; Zhu, Yihui; Liu, Yanjie; Yang, Huipeng; Ding, Lele; Wang, Quangui; Ma, Dongna; Xu, Weilin; Liang, Cheng; Itgen, Michael W.; Mee, Lauren; Cao, Gang; Zhang, Ze; Sadd, Ben M.; Hahn, Matthew W.; Schaack, Sarah; Barribeau, Seth M.; Williams, Paul H.; Waterhouse, Robert M.; Mueller, Rachel Lockridge Share Save
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Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci Mudge, Jonathan M.; Jungreis, Irwin; Hunt, Toby; Gonzalez, Jose Manuel; Wright, James C.; Kay, Mike; Davidson, Claire; Fitzgerald, Stephen; Seal, Ruth; Tweedie, Susan; He, Liang; Waterhouse, Robert M.; Li, Yue; Bruford, Elspeth; Choudhary, Jyoti S.; Frankish, Adam; Kellis, Manolis Share Save
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A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs McCorkindale, Alexandra L.; Wahle, Philipp; Werner, Sascha; Jungreis, Irwin; Menzel, Peter; Shukla, Chinmay J.; Abreu, Ruben Lopes Pereira; Irizarry, Rafael A.; Meyer, Irmtraud M.; Kellis, Manolis; Zinzen, Robert P. Share Save
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Loose ends: almost one in five human genes still have unresolved coding status (vol 46, pg 7070, 2018) Abascal, Federico; Juan, David; Jungreis, Irwin; Kellis, Manolis; Martinez, Laura; Rigau, Maria; Manuel Rodriguez, Jose; Vazquez, Jesus; Tress, Michael L. Share Save
GENCODE reference annotation for the human and mouse genomes Frankish, Adam; Diekhans, Mark; Ferreira, Anne-Maud; Johnson, Rory; Jungreis, Irwin; Loveland, Jane; Mudge, Jonathan M.; Sisu, Cristina; Wright, James; Armstrong, Joel; Barnes, If; Berry, Andrew; Bignell, Alexandra; Sala, Silvia Carbonell; Chrast, Jacqueline; Cunningham, Fiona; Di Domenico, Tomas; Donaldson, Sarah; Fiddes, Ian T.; Giron, Carlos Garcia; Gonzalez, Jose Manuel; Grego, Tiago; Hardy, Matthew; Hourlier, Thibaut; Hunt, Toby; Izuogu, Osagie G.; Lagarde, Julien; Martin, Fergal J.; Martinez, Laura; Mohanan, Shamika; Muir, Paul; Navarro, Fabio C. P.; Parker, Anne; Pei, Baikang; Pozo, Fernando; Ruffier, Magali; Schmitt, Bianca M.; Stapleton, Eloise; Suner, Marie-Marthe; Sycheva, Irina; Uszczynska-Ratajczak, Barbara; Xu, Jinuri; Yates, Andrew; Zerbino, Daniel; Zhang, Yan; Aken, Bronwen; Choudhary, Jyoti S.; Gerstein, Mark; Guigo, Roderic; Hubbard, Tim J. P.; Kellis, Manolis; Paten, Benedict; Reymond, Alexandre; Tress, Michael L.; Flicek, Paul Share Save
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