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SaveGENCODE: 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 Share Save Share Save Engineered model of t(7;12)(q36;p13) AML recapitulates patient-specific features and gene expression profilesRagusa, Denise; Ciciro, Ylenia; Federico, Concetta; Saccone, Salvatore; Bruno, Francesca; Saeedi, Reza; Sisu, Cristina; Pina, Cristina; Sala, Arturo; Tosi, Sabrina Share Save Differential Expression of RAD51AP1 in Ovarian Cancer: Effects of siRNA In VitroFilipe, Alice; Katopodis, Periklis; Chudasama, Dimple; Kerslake, Rachel; Jeyaneethi, Jeyarooban; Anikin, Vladimir; Silva, Elisabete; Kyrou, Ioannis; Randeva, Harpal S.; Sisu, Cristina; Hall, Marcia; Karteris, Emmanouil Share Save Share Save Share Save GENCODE 2021Frankish, 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 Is There a Link between Bisphenol A (BPA), a Key Endocrine Disruptor, and the Risk for SARS-CoV-2 Infection and Severe COVID-19?Zahra, Aeman; Sisu, Cristina; Silva, Elisabete; Greca, Sophie-Christine De Aguiar; Randeva, Harpal S.; Chatha, Kamaljit; Kyrou, Ioannis; Karteris, Emmanouil Share Save Transcriptional activity and strain-specific history of mouse pseudogenesSisu, Cristina; Muir, Paul; Frankish, Adam; Fiddes, Ian; Diekhans, Mark; Thybert, David; Odom, Duncan T.; Flicek, Paul; Keane, Thomas M.; Hubbard, Tim; Harrow, Jennifer; Gerstein, Mark Share Save Differential expression of mTOR components in endometriosis and ovarian cancer: Effects of rapalogues and dual kinase inhibitors on mTORC1 and mTORC2 stoichiometryRogers-Broadway, Karly-Rai; Kumar, Juhi; Sisu, Cristina; Wander, Gurleen; Mazey, Emily; Jeyaneethi, Jeyarooban; Pados, George; Tsolakidis, Dimitris; Klonos, Eleftherios; Grunt, Thomas; Hall, Marcia; Chatterjee, Jayanta; Karteris, Emmanouil Share Save GENCODE reference annotation for the human and mouse genomesFrankish, 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 Sixteen diverse laboratory mouse reference genomes define strain-specific haplotypes and novel functional lociLilue, Jingtao; Doran, Anthony G.; Fiddes, Ian T.; Abrudan, Monica; Armstrong, Joel; Bennett, Ruth; Chow, William; Collins, Joanna; Collins, Stephan; Czechanski, Anne; Danecek, Petr; Diekhans, Mark; Dolle, Dirk-Dominik; Dunn, Matt; Durbin, Richard; Earl, Dent; Ferguson-Smith, Anne; Flicek, Paul; Flint, Jonathan; Frankish, Adam; Fu, Beiyuan; Gerstein, Mark; Gilbert, James; Goodstadt, Leo; Harrow, Jennifer; Howe, Kerstin; Ibarra-Soria, Ximena; Kolmogorov, Mikhail; Lelliott, Chris J.; Logan, Darren W.; Loveland, Jane; Mathews, Clayton E.; Mott, Richard; Muir, Paul; Nachtweide, Stefanie; Navarro, Fabio C. P.; Odom, Duncan T.; Park, Naomi; Pelan, Sarah; Pham, Son K.; Quail, Mike; Reinholdt, Laura; Romoth, Lars; Shirley, Lesley; Sisu, Cristina; Sjoberg-Herrera, Marcela; Stanke, Mario; Steward, Charles; Thomas, Mark; Threadgold, Glen; Thybert, David; Torrance, James; Wong, Kim; Wood, Jonathan; Yalcin, Binnaz; Yang, Fengtang; Adams, David J.; Paten, Benedict; Keane, Thomas M. Share Save Repeat associated mechanisms of genome evolution and function revealed by the &ITMus caroli&IT and &ITMus pahari&IT genomesThybert, David; Roller, Masa; Navarro, Fabio C. P.; Fiddes, Ian; Streeter, Ian; Feig, Christine; Martin-Galvez, David; Kolmogorov, Mikhail; Janousek, Vaclav; Akanni, Wasiu; Aken, Bronwen; Aldridge, Sarah; Chakrapani, Varshith; Chow, William; Clarke, Laura; Cummins, Carla; Doran, Anthony; Dunn, Matthew; Goodstadt, Leo; Howe, Kerstin; Howell, Matthew; Josselin, Ambre-Aurore; Karn, Robert C.; Laukaitis, Christina M.; Jingtao, Lilue; Martin, Fergal; Muffato, Matthieu; Nachtweide, Stefanie; Quail, Michael A.; Sisu, Cristina; Stanke, Mario; Stefflova, Klara; Van Oosterhout, Cock; Veyrunes, Frederic; Ward, Ben; Yang, Fengtang; Yazdanifar, Golbahar; Zadissa, Amonida; Adams, David J.; Brazma, Alvis; Gerstein, Mark; Paten, Benedict; Pham, Son; Keane, Thomas M.; Odom, Duncan T.; Flicek, Paul Share Save Comparative analysis of pseudogenes across three phylaSisu, Cristina; Pei, Baikang; Leng, Jing; Frankish, Adam; Zhang, Yan; Balasubramanian, Suganthi; Harte, Rachel; Wang, Daifeng; Rutenberg-Schoenberg, Michael; Clark, Wyatt; Diekhans, Mark; Rozowsky, Joel; Hubbard, Tim; Harrow, Jennifer; Gerstein, Mark B. Share Save The GENCODE pseudogene resourcePei, Baikang; Sisu, Cristina; Frankish, Adam; Howald, Cedric; Habegger, Lukas; Mu, Xinmeng Jasmine; Harte, Rachel; Balasubramanian, Suganthi; Tanzer, Andrea; Diekhans, Mark; Reymond, Alexandre; Hubbard, Tim J.; Harrow, Jennifer; Gerstein, Mark B. Share Save Share Save 
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