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High-throughput annotation of full-length long noncoding RNAs with capture long-read sequencing
Lagarde, Julien, Uszczynska-Ratajczak, Barbara, Carbonell, Silvia, Pérez-Lluch, Sílvia, Abad, Amaya, Davis, Carrie, Gingeras, Thomas R, Frankish, Adam, Harrow, Jennifer, Guigo, Roderic, Johnson, Rory
Published in Nature genetics (01.12.2017)
Published in Nature genetics (01.12.2017)
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Journal Article
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, Carbonell Sala, Silvia, Chrast, Jacqueline, Cunningham, Fiona, Di Domenico, Tomás, Donaldson, Sarah, Fiddes, Ian T, García Girón, Carlos, Gonzalez, Jose Manuel, Grego, Tiago, Hardy, Matthew, Hourlier, Thibaut, Hunt, Toby, Izuogu, Osagie G, Lagarde, Julien, Martin, Fergal J, Martínez, 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, Guigó, Roderic, Hubbard, Tim J P, Kellis, Manolis, Paten, Benedict, Reymond, Alexandre, Tress, Michael L, Flicek, Paul
Published in Nucleic acids research (08.01.2019)
Published in Nucleic acids research (08.01.2019)
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Journal Article
Genetic effects on gene expression across human tissues
Battle, Alexis, Brown, Christopher D, Engelhardt, Barbara E, Montgomery, Stephen B
Published in Nature (London) (12.10.2017)
Published in Nature (London) (12.10.2017)
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Journal Article
LncATLAS database for subcellular localization of long noncoding RNAs
Mas-Ponte, David, Carlevaro-Fita, Joana, Palumbo, Emilio, Hermoso Pulido, Toni, Guigo, Roderic, Johnson, Rory
Published in RNA (Cambridge) (01.07.2017)
Published in RNA (Cambridge) (01.07.2017)
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Journal Article
Integrative transcriptomic analysis suggests new autoregulatory splicing events coupled with nonsense-mediated mRNA decay
Pervouchine, Dmitri, Popov, Yaroslav, Berry, Andy, Borsari, Beatrice, Frankish, Adam, Guigó, Roderic
Published in Nucleic acids research (04.06.2019)
Published in Nucleic acids research (04.06.2019)
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Journal Article
The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease
Astle, William J., Elding, Heather, Jiang, Tao, Allen, Dave, Ruklisa, Dace, Mann, Alice L., Mead, Daniel, Bouman, Heleen, Riveros-Mckay, Fernando, Kostadima, Myrto A., Lambourne, John J., Sivapalaratnam, Suthesh, Downes, Kate, Kundu, Kousik, Bomba, Lorenzo, Berentsen, Kim, Bradley, John R., Daugherty, Louise C., Delaneau, Olivier, Freson, Kathleen, Garner, Stephen F., Grassi, Luigi, Guerrero, Jose, Haimel, Matthias, Janssen-Megens, Eva M., Kaan, Anita, Kamat, Mihir, Kim, Bowon, Mandoli, Amit, Marchini, Jonathan, Martens, Joost H.A., Meacham, Stuart, Megy, Karyn, O’Connell, Jared, Petersen, Romina, Sharifi, Nilofar, Sheard, Simon M., Staley, James R., Tuna, Salih, van der Ent, Martijn, Walter, Klaudia, Wang, Shuang-Yin, Wheeler, Eleanor, Wilder, Steven P., Iotchkova, Valentina, Moore, Carmel, Sambrook, Jennifer, Stunnenberg, Hendrik G., Di Angelantonio, Emanuele, Kaptoge, Stephen, Kuijpers, Taco W., Carrillo-de-Santa-Pau, Enrique, Juan, David, Rico, Daniel, Valencia, Alfonso, Chen, Lu, Ge, Bing, Vasquez, Louella, Kwan, Tony, Garrido-Martín, Diego, Watt, Stephen, Yang, Ying, Guigo, Roderic, Beck, Stephan, Paul, Dirk S., Pastinen, Tomi, Bujold, David, Bourque, Guillaume, Frontini, Mattia, Danesh, John, Roberts, David J., Ouwehand, Willem H., Butterworth, Adam S., Soranzo, Nicole
Published in Cell (17.11.2016)
Published in Cell (17.11.2016)
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Journal Article
Identification of genetic variants associated with alternative splicing using sQTLseekeR
Monlong, Jean, Calvo, Miquel, Ferreira, Pedro G., Guigó, Roderic
Published in Nature communications (20.08.2014)
Published in Nature communications (20.08.2014)
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Journal Article
The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression
Derrien, Thomas, Johnson, Rory, Bussotti, Giovanni, Tanzer, Andrea, Djebali, Sarah, Tilgner, Hagen, Guernec, Gregory, Martin, David, Merkel, Angelika, Knowles, David G., Lagarde, Julien, Veeravalli, Lavanya, Ruan, Xiaoan, Ruan, Yijun, Lassmann, Timo, Carninci, Piero, Brown, James B., Lipovich, Leonard, Gonzalez, Jose M., Thomas, Mark, Davis, Carrie A., Shiekhattar, Ramin, Gingeras, Thomas R., Hubbard, Tim J., Notredame, Cedric, Harrow, Jennifer, Guigó, Roderic
Published in Genome research (01.09.2012)
Published in Genome research (01.09.2012)
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Journal Article
Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells
Chen, Lu, Ge, Bing, Casale, Francesco Paolo, Vasquez, Louella, Kwan, Tony, Garrido-Martín, Diego, Watt, Stephen, Yan, Ying, Kundu, Kousik, Ecker, Simone, Datta, Avik, Richardson, David, Burden, Frances, Mead, Daniel, Mann, Alice L., Fernandez, Jose Maria, Rowlston, Sophia, Wilder, Steven P., Farrow, Samantha, Shao, Xiaojian, Lambourne, John J., Redensek, Adriana, Albers, Cornelis A., Amstislavskiy, Vyacheslav, Ashford, Sofie, Berentsen, Kim, Bomba, Lorenzo, Bourque, Guillaume, Bujold, David, Busche, Stephan, Caron, Maxime, Chen, Shu-Huang, Cheung, Warren, Delaneau, Oliver, Dermitzakis, Emmanouil T., Elding, Heather, Colgiu, Irina, Bagger, Frederik O., Flicek, Paul, Habibi, Ehsan, Iotchkova, Valentina, Janssen-Megens, Eva, Kim, Bowon, Lehrach, Hans, Lowy, Ernesto, Mandoli, Amit, Matarese, Filomena, Maurano, Matthew T., Morris, John A., Pancaldi, Vera, Pourfarzad, Farzin, Rehnstrom, Karola, Rendon, Augusto, Risch, Thomas, Sharifi, Nilofar, Simon, Marie-Michelle, Sultan, Marc, Valencia, Alfonso, Walter, Klaudia, Wang, Shuang-Yin, Frontini, Mattia, Antonarakis, Stylianos E., Clarke, Laura, Yaspo, Marie-Laure, Beck, Stephan, Guigo, Roderic, Rico, Daniel, Martens, Joost H.A., Ouwehand, Willem H., Kuijpers, Taco W., Paul, Dirk S., Stunnenberg, Hendrik G., Stegle, Oliver, Downes, Kate, Pastinen, Tomi, Soranzo, Nicole
Published in Cell (17.11.2016)
Published in Cell (17.11.2016)
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Journal Article
The Genotype-Tissue Expression (GTEx) project
Lonsdale, John, Thomas, Jeffrey, Salvatore, Mike, Phillips, Rebecca, Hasz, Richard, Walters, Gary, Garcia, Fernando, Young, Nancy, Karasik, Ellen, Gillard, Bryan, Ramsey, Kimberley, Magazine, Harold, Syron, John, Fleming, Johnelle, Traino, Heather, Mosavel, Maghboeba, Barker, Laura, Rohrer, Dan, Maxim, Dan, Filkins, Dana, Harbach, Philip, Cortadillo, Eddie, Berghuis, Bree, Turner, Lisa, Hudson, Eric, Robb, James, Branton, Phillip, Korzeniewski, Greg, Shive, Charles, Tabor, David, Groch, Kevin, Nampally, Sreenath, Buia, Steve, Zimmerman, Angela, Smith, Anna, Burges, Robin, Robinson, Karna, Valentino, Kim, Bradbury, Deborah, Diaz-Mayoral, Norma, Kennedy, Mary, Erickson, Kenyon, Ardlie, Kristin, Winckler, Wendy, Getz, Gad, MacArthur, Daniel, Kellis, Manolis, Thomson, Alexander, Gelfand, Ellen, Donovan, Molly, Meng, Yan, Marcus, Yvonne, Basile, Margaret, Zhu, Jun, Tu, Zhidong, Cox, Nancy J, Gamazon, Eric R, Im, Hae Kyung, Konkashbaev, Anuar, Pritchard, Jonathan, Flutre, Timothèe, Wen, Xiaoquan, Dermitzakis, Emmanouil T, Guigo, Roderic, Monlong, Jean, Sammeth, Michael, Koller, Daphne, Battle, Alexis, Mostafavi, Sara, McCarthy, Mark, Rivas, Manual, Rusyn, Ivan, Nobel, Andrew, Wright, Fred, Shabalin, Andrey, Sturcke, Anne, Paschal, Justin, Anderson, James M, Wilder, Elizabeth L, Derr, Leslie K, Green, Eric D, Temple, Gary, Volpi, Simona, Boyer, Joy T, Thomson, Elizabeth J, Guyer, Mark S, Ng, Cathy, Abdallah, Assya, Colantuoni, Deborah, Insel, Thomas R, Koester, Susan E, Little, A Roger, Bender, Patrick K, Lehner, Thomas, Compton, Carolyn C, Vaught, Jimmie B, Sawyer, Sherilyn, Lockhart, Nicole C, Demchok, Joanne, Moore, Helen F
Published in Nature genetics (01.06.2013)
Published in Nature genetics (01.06.2013)
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Journal Article
Discovery of Cancer Driver Long Noncoding RNAs across 1112 Tumour Genomes: New Candidates and Distinguishing Features
Lanzós, Andrés, Carlevaro-Fita, Joana, Mularoni, Loris, Reverter, Ferran, Palumbo, Emilio, Guigó, Roderic, Johnson, Rory
Published in Scientific reports (27.01.2017)
Published in Scientific reports (27.01.2017)
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Journal Article
Landscape of transcription in human cells
Djebali, Sarah, Davis, Carrie A., Merkel, Angelika, Dobin, Alex, Lassmann, Timo, Mortazavi, Ali, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Schlesinger, Felix, Xue, Chenghai, Marinov, Georgi K., Khatun, Jainab, Williams, Brian A., Zaleski, Chris, Rozowsky, Joel, Röder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F., Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T., Bar, Nadav S., Batut, Philippe, Bell, Kimberly, Bell, Ian, Chakrabortty, Sudipto, Chen, Xian, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jacqueline, Duttagupta, Radha, Falconnet, Emilie, Fastuca, Meagan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J., Gao, Hui, Gonzalez, David, Gordon, Assaf, Gunawardena, Harsha, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Luo, Oscar J., Park, Eddie, Persaud, Kimberly, Preall, Jonathan B., Ribeca, Paolo, Risk, Brian, Robyr, Daniel, Sammeth, Michael, Schaffer, Lorian, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Wrobel, John, Yu, Yanbao, Ruan, Xiaoan, Hayashizaki, Yoshihide, Harrow, Jennifer, Gerstein, Mark, Hubbard, Tim, Reymond, Alexandre, Antonarakis, Stylianos E., Hannon, Gregory, Giddings, Morgan C., Ruan, Yijun, Wold, Barbara, Carninci, Piero, Guigó, Roderic, Gingeras, Thomas R.
Published in Nature (London) (06.09.2012)
Published in Nature (London) (06.09.2012)
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Journal Article
GENCODE: The reference human genome annotation for The ENCODE Project
Harrow, Jennifer, Frankish, Adam, Gonzalez, Jose M., Tapanari, Electra, Diekhans, Mark, Kokocinski, Felix, Aken, Bronwen L., Barrell, Daniel, Zadissa, Amonida, Searle, Stephen, Barnes, If, Bignell, Alexandra, Boychenko, Veronika, Hunt, Toby, Kay, Mike, Mukherjee, Gaurab, Rajan, Jeena, Despacio-Reyes, Gloria, Saunders, Gary, Steward, Charles, Harte, Rachel, Lin, Michael, Howald, Cédric, Tanzer, Andrea, Derrien, Thomas, Chrast, Jacqueline, Walters, Nathalie, Balasubramanian, Suganthi, Pei, Baikang, Tress, Michael, Rodriguez, Jose Manuel, Ezkurdia, Iakes, van Baren, Jeltje, Brent, Michael, Haussler, David, Kellis, Manolis, Valencia, Alfonso, Reymond, Alexandre, Gerstein, Mark, Guigó, Roderic, Hubbard, Tim J.
Published in Genome research (01.09.2012)
Published in Genome research (01.09.2012)
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Journal Article
Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs
Tilgner, Hagen, Knowles, David G., Johnson, Rory, Davis, Carrie A., Chakrabortty, Sudipto, Djebali, Sarah, Curado, João, Snyder, Michael, Gingeras, Thomas R., Guigó, Roderic
Published in Genome research (01.09.2012)
Published in Genome research (01.09.2012)
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Journal Article
The tomato genome sequence provides insights into fleshy fruit evolution
Tomato Genome Consortium, Sato, S, Guigó Serra, Roderic, Cámara, Francisco, Gianese, S
Published in Nature (London) (31.05.2012)
Published in Nature (London) (31.05.2012)
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Journal Article
Fast Computation and Applications of Genome Mappability
Derrien, Thomas, Estellé, Jordi, Marco Sola, Santiago, Knowles, David G., Raineri, Emanuele, Guigó, Roderic, Ribeca, Paolo
Published in PloS one (19.01.2012)
Published in PloS one (19.01.2012)
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Journal Article
Assessment of transcript reconstruction methods for RNA-seq
Steijger, Tamara, Abril, Josep F, Engström, Pär G, Kokocinski, Felix, Hubbard, Tim J, Guigó, Roderic, Harrow, Jennifer, Bertone, Paul
Published in Nature methods (01.12.2013)
Published in Nature methods (01.12.2013)
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Journal Article
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia
Puente, Xose S., Pinyol, Magda, Quesada, Víctor, Conde, Laura, Ordóñez, Gonzalo R., Villamor, Neus, Escaramis, Georgia, Jares, Pedro, Beà, Sílvia, González-Díaz, Marcos, Bassaganyas, Laia, Baumann, Tycho, Juan, Manel, López-Guerra, Mónica, Colomer, Dolors, Tubío, José M. C., López, Cristina, Navarro, Alba, Tornador, Cristian, Aymerich, Marta, Rozman, María, Hernández, Jesús M., Puente, Diana A., Freije, José M. P., Velasco, Gloria, Gutiérrez-Fernández, Ana, Costa, Dolors, Carrió, Anna, Guijarro, Sara, Enjuanes, Anna, Hernández, Lluís, Yagüe, Jordi, Nicolás, Pilar, Romeo-Casabona, Carlos M., Himmelbauer, Heinz, Castillo, Ester, Dohm, Juliane C., de Sanjosé, Silvia, Piris, Miguel A., de Alava, Enrique, Miguel, Jesús San, Royo, Romina, Gelpí, Josep L., Torrents, David, Orozco, Modesto, Pisano, David G., Valencia, Alfonso, Guigó, Roderic, Bayés, Mónica, Heath, Simon, Gut, Marta, Klatt, Peter, Marshall, John, Raine, Keiran, Stebbings, Lucy A., Futreal, P. Andrew, Stratton, Michael R., Campbell, Peter J., Gut, Ivo, López-Guillermo, Armando, Estivill, Xavier, Montserrat, Emili, López-Otín, Carlos, Campo, Elías
Published in Nature (London) (07.07.2011)
Published in Nature (London) (07.07.2011)
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Journal Article