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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
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Genomic and phenotypic characterization of 404 individuals with neurodevelopmental disorders caused by CTNNB1 variants Kayumi, Sayaka; Perez-Jurado, Luis A.; Palomares, Maria; Rangu, Sneha; Sheppard, Sarah E.; Chung, Wendy K.; Kruer, Michael C.; Kharbanda, Mira; Amor, David J.; McGillivray, George; Cohen, Julie S.; Garcia-Minaur, Sixto; van Eyk, Clare L.; Harper, Kelly; Jolly, Lachlan A.; Webber, Dani L.; Barnett, Christopher P.; Santos-Simarro, Fernando; Pacio-Miguez, Marta; del Pozo, Angela; Bakhtiari, Somayeh; Deardorff, Matthew; Dubbs, Holly A.; Izumi, Kosuke; Grand, Katheryn; Gray, Christopher; Mark, Paul R.; Bhoj, Elizabeth J.; Li, Dong; Ortiz-Gonzalez, Xilma R.; Keena, Beth; Zackai, Elaine H.; Goldberg, Ethan M.; de Nanclares, Guiomar Perez; Pereda, Arrate; Llano-Rivas, Isabel; Arroyo, Ignacio; Fernandez-Cuesta, Maria Angeles; Thauvin-Robinet, Christel; Faivre, Laurence; Garde, Aurore; Mazel, Benoit; Bruel, Ange-Line; Tress, Michael L.; Brilstra, Eva; Fine, Amena Smith; Crompton, Kylie E.; Stegmann, Alexander P. A.; Sinnema, Margje; Stevens, Servi C. J.; Nicolai, Joost; Lesca, Gaetan; Lion-Francois, Laurence; Haye, Damien; Chatron, Nicolas; Piton, Amelie; Nizon, Mathilde; Cogne, Benjamin; Srivastava, Siddharth; Bassetti, Jennifer; Muss, Candace; Gripp, Karen W.; Procopio, Rebecca A.; Millan, Francisca; Morrow, Michelle M.; Assaf, Melissa; Moreno-De-Luca, Andres; Joss, Shelagh; Hamilton, Mark J.; Bertoli, Marta; Foulds, Nicola; McKee, Shane; MacLennan, Alastair H.; Gecz, Jozef; Corbett, Mark A. 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
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The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens Zhou, Naihui; Jiang, Yuxiang; Bergquist, Timothy R.; Lee, Alexandra J.; Kacsoh, Balint Z.; Crocker, Alex W.; Lewis, Kimberley A.; Georghiou, George; Nguyen, Huy N.; Hamid, Md Nafiz; Davis, Larry; Dogan, Tunca; Atalay, Volkan; Rifaioglu, Ahmet S.; Dalkiran, Alperen; Atalay, Rengul Cetin; Zhang, Chengxin; Hurto, Rebecca L.; Freddolino, Peter L.; Zhang, Yang; Bhat, Prajwal; Supek, Fran; Fernandez, Jose M.; Gemovic, Branislava; Perovic, Vladimir R.; Davidovic, Radoslav S.; Sumonja, Neven; Veljkovic, Nevena; Asgari, Ehsaneddin; Mofrad, Mohammad R. K.; Profiti, Giuseppe; Savojardo, Castrense; Martelli, Pier Luigi; Casadio, Rita; Boecker, Florian; Schoof, Heiko; Kahanda, Indika; Thurlby, Natalie; McHardy, Alice C.; Renaux, Alexandre; Saidi, Rabie; Gough, Julian; Freitas, Alex A.; Antczak, Magdalena; Fabris, Fabio; Wass, Mark N.; Hou, Jie; Cheng, Jianlin; Wang, Zheng; Romero, Alfonso E.; Paccanaro, Alberto; Yang, Haixuan; Goldberg, Tatyana; Zhao, Chenguang; Holm, Liisa; Toronen, Petri; Medlar, Alan J.; Zosa, Elaine; Borukhov, Itamar; Novikov, Ilya; Wilkins, Angela; Lichtarge, Olivier; Chi, Po-Han; Tseng, Wei-Cheng; Linial, Michal; Rose, Peter W.; Dessimoz, Christophe; Vidulin, Vedrana; Dzeroski, Saso; Sillitoe, Ian; Das, Sayoni; Lees, Jonathan Gill; Jones, David T.; Wan, Cen; Cozzetto, Domenico; Fa, Rui; Torres, Mateo; Vesztrocy, Alex Warwick; Rodriguez, Jose Manuel; Tress, Michael L.; Frasca, Marco; Notaro, Marco; Grossi, Giuliano; Petrini, Alessandro; Re, Matteo; Valentini, Giorgio; Mesiti, Marco; Roche, Daniel B.; Reeb, Jonas; Ritchie, David W.; Aridhi, Sabeur; Alborzi, Seyed Ziaeddin; Devignes, Marie-Dominique; Koo, Da Chen Emily; Bonneau, Richard; Gligorijevic, Vladimir; Barot, Meet; Fang, Hai; Toppo, Stefano; Lavezzo, Enrico; Falda, Marco; Berselli, Michele; Tosatto, Silvio C. E.; Carraro, Marco; Piovesan, Damiano; Rehman, Hafeez Ur; Mao, Qizhong; Zhang, Shanshan; Vucetic, Slobodan; Black, Gage S.; Jo, Dane; Suh, Erica; Dayton, Jonathan B.; Larsen, Dallas J.; Omdahl, Ashton R.; McGuffin, Liam J.; Brackenridge, Danielle A.; Babbitt, Patricia C.; Yunes, Jeffrey M.; Fontana, Paolo; Zhang, Feng; Zhu, Shanfeng; You, Ronghui; Zhang, Zihan; Dai, Suyang; Yao, Shuwei; Tian, Weidong; Cao, Renzhi; Chandler, Caleb; Amezola, Miguel; Johnson, Devon; Chang, Jia-Ming; Liao, Wen-Hung; Liu, Yi-Wei; Pascarelli, Stefano; Frank, Yotam; Hoehndorf, Robert; Kulmanov, Maxat; Boudellioua, Imane; Politano, Gianfranco; Di Carlo, Stefano; Benso, Alfredo; Hakala, Kai; Ginter, Filip; Mehryary, Farrokh; Kaewphan, Suwisa; Bjorne, Jari; Moen, Hans; Tolvanen, Martti E. E.; Salakoski, Tapio; Kihara, Daisuke; Jain, Aashish; Smuc, Tomislav; Altenhoff, Adrian; Ben-Hur, Asa; Rost, Burkhard; Brenner, Steven E.; Orengo, Christine A.; Jeffery, Constance J.; Bosco, Giovanni; Hogan, Deborah A.; Martin, Maria J.; O'Donovan, Claire; Mooney, Sean D.; Greene, Casey S.; Radivojac, Predrag; Friedberg, Iddo Share Save
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
SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification (vol 28, pg 396, 2018) Tardaguila, Manuel; de la Fuente, Lorena; Marti, Cristina; Pereira, Cecile; Pardo-Palacios, Francisco Jose; del Risco, Hector; Ferrell, Marc; Mellado, Maravillas; Macchietto, Marissa; Verheggen, Kenneth; Edelmann, Mariola; Ezkurdia, Iakes; Vazquez, Jesus; Tress, Michael; Mortazavi, Ali; Martens, Lennart; Rodriguez-Navarro, Susana; Moreno-Manzano, Victoria; Conesa, Ana Share Save
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SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification Tardaguila, Manuel; de la Fuente, Lorena; Marti, Cristina; Pereira, Cecile; Jose Pardo-Palacios, Francisco; del Risco, Hector; Ferrell, Marc; Mellado, Maravillas; Macchietto, Marissa; Verheggen, Kenneth; Edelmann, Mariola; Ezkurdia, Iakes; Vazquez, Jesus; Tress, Michael; Mortazavi, Ali; Martens, Lennart; Rodriguez-Navarro, Susana; Moreno-Manzano, Victoria; Conesa, Ana Share Save
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