Dynamic changes in intron retention are tightly associated with regulation of splicing factors and proliferative activity during B-cell development by Ullrich, Sebastian, Guigó, Roderic

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Genome annotation: From human genetics to biodiversity genomics by Guigó, Roderic

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Modelling and simulating generic RNA-Seq experiments with the flux simulator by Griebel, Thasso, Zacher, Benedikt, Ribeca, Paolo, Raineri, Emanuele, Lacroix, Vincent, Guigó, Roderic, Sammeth, Michael

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Landscape of transcription in human cells by 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.

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Extensive error in the number of genes inferred from draft genome assemblies by Denton, James F, Lugo-Martinez, Jose, Tucker, Abraham E, Schrider, Daniel R, Warren, Wesley C, Hahn, Matthew W

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Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia by 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

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Genome-wide profiling of the cardiac transcriptome after myocardial infarction identifies novel heart-specific long non-coding RNAs by Ounzain, Samir, Micheletti, Rudi, Beckmann, Tal, Schroen, Blanche, Alexanian, Michael, Pezzuto, Iole, Crippa, Stefania, Nemir, Mohamed, Sarre, Alexandre, Johnson, Rory, Dauvillier, Jérôme, Burdet, Frédéric, Ibberson, Mark, Guigó, Roderic, Xenarios, Ioannis, Heymans, Stephane, Pedrazzini, Thierry

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Transcriptome genetics using second generation sequencing in a Caucasian population by Montgomery, Stephen B, Dermitzakis, Emmanouil T, Sammeth, Micha, Gutierrez-Arcelus, Maria, Lach, Radoslaw P, Ingle, Catherine, Nisbett, James, Guigo, Roderic

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Defining functional DNA elements in the human genome by Kellis, Manolis, Wold, Barbara, Snyderd, Michael P., Bernstein, Bradley E., Kundaje, Anshul, Marinov, Georgi K., Ward, Lucas D., Birney, Ewan, Crawford, Gregory E., Dekker, Job, Dunham, Ian, Elnitski, Laura L., Farnham, Peggy J., Feingold, Elise A., Gerstein, Mark, Giddings, Morgan C., Gilbert, David M., Gingeras, Thomas R., Green, Eric D., Guigo, Roderic, Hubbard, Tim, Kent, Jim, Lieb, Jason D., Myerst, Richard M., Pazin, Michael J., Ren, Bing, Stamatoyannopoulos, John A., Weng, Zhiping, White, Kevin P., Hardison, Ross C.

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The European Genome-phenome Archive in 2021 by Freeberg, Mallory Ann, Fromont, Lauren A, D’Altri, Teresa, Romero, Anna Foix, Ciges, Jorge Izquierdo, Jene, Aina, Kerry, Giselle, Moldes, Mauricio, Ariosa, Roberto, Bahena, Silvia, Barrowdale, Daniel, Barbero, Marcos Casado, Fernandez-Orth, Dietmar, Garcia-Linares, Carles, Garcia-Rios, Emilio, Haziza, Frédéric, Juhasz, Bela, Llobet, Oscar Martinez, Milla, Gemma, Mohan, Anand, Rueda, Manuel, Sankar, Aravind, Shaju, Dona, Shimpi, Ashutosh, Singh, Babita, Thomas, Coline, de la Torre, Sabela, Uyan, Umuthan, Vasallo, Claudia, Flicek, Paul, Guigo, Roderic, Navarro, Arcadi, Parkinson, Helen, Keane, Thomas, Rambla, Jordi

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The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs by Johnson, Rory, Guigó, Roderic

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Functional Evolution of Clustered Aquaporin Genes Reveals Insights into the Oceanic Success of Teleost Eggs by Ferré, Alba, Chauvigné, François, Vlasova, Anna, Norberg, Birgitta, Bargelloni, Luca, Guigó, Roderic, Finn, Roderick Nigel, Cerdà, Joan

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Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx by Abascal, Federico, Corvelo, André, Cruz, Fernando, Villanueva-Cañas, José L, Vlasova, Anna, Marcet-Houben, Marina, Martínez-Cruz, Begoña, Cheng, Jade Yu, Prieto, Pablo, Quesada, Víctor, Quilez, Javier, Li, Gang, García, Francisca, Rubio-Camarillo, Miriam, Frias, Leonor, Ribeca, Paolo, Capella-Gutiérrez, Salvador, Rodríguez, José M, Câmara, Francisco, Lowy, Ernesto, Cozzuto, Luca, Erb, Ionas, Tress, Michael L, Rodriguez-Ales, Jose L, Ruiz-Orera, Jorge, Reverter, Ferran, Casas-Marce, Mireia, Soriano, Laura, Arango, Javier R, Derdak, Sophia, Galán, Beatriz, Blanc, Julie, Gut, Marta, Lorente-Galdos, Belen, Andrés-Nieto, Marta, López-Otín, Carlos, Valencia, Alfonso, Gut, Ivo, García, José L, Guigó, Roderic, Murphy, William J, Ruiz-Herrera, Aurora, Marques-Bonet, Tomas, Roma, Guglielmo, Notredame, Cedric, Mailund, Thomas, Albà, M Mar, Gabaldón, Toni, Alioto, Tyler, Godoy, José A

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Enhancers with tissue-specific activity are enriched in intronic regions by Borsari, Beatrice, Villegas-Mirón, Pablo, Pérez-Lluch, Sílvia, Turpin, Isabel, Laayouni, Hafid, Segarra-Casas, Alba, Bertranpetit, Jaume, Guigó, Roderic, Acosta, Sandra

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The genomes of two key bumblebee species with primitive eusocial organization by Sadd, Ben M, Barribeau, Seth M, Bloch, Guy, de Graaf, Dirk C, Dearden, Peter, Elsik, Christine G, Gadau, Jürgen, Grimmelikhuijzen, Cornelis J P, Hasselmann, Martin, Lozier, Jeffrey D, Robertson, Hugh M, Smagghe, Guy, Stolle, Eckart, Van Vaerenbergh, Matthias, Waterhouse, Robert M, Bornberg-Bauer, Erich, Klasberg, Steffen, Bennett, Anna K, Câmara, Francisco, Guigó, Roderic, Hoff, Katharina, Mariotti, Marco, Munoz-Torres, Monica, Murphy, Terence, Santesmasses, Didac, Amdam, Gro V, Beckers, Matthew, Beye, Martin, Biewer, Matthias, Bitondi, Márcia M G, Blaxter, Mark L, Bourke, Andrew F G, Brown, Mark J F, Buechel, Severine D, Cameron, Rossanah, Cappelle, Kaat, Carolan, James C, Christiaens, Olivier, Ciborowski, Kate L, Clarke, David F, Colgan, Thomas J, Collins, David H, Cridge, Andrew G, Dalmay, Tamas, Dreier, Stephanie, du Plessis, Louis, Duncan, Elizabeth, Erler, Silvio, Evans, Jay, Falcon, Tiago, Flores, Kevin, Freitas, Flávia C P, Fuchikawa, Taro, Gempe, Tanja, Hartfelder, Klaus, Hauser, Frank, Helbing, Sophie, Humann, Fernanda C, Irvine, Frano, Jermiin, Lars S, Johnson, Claire E, Johnson, Reed M, Jones, Andrew K, Kadowaki, Tatsuhiko, Kidner, Jonathan H, Koch, Vasco, Köhler, Arian, Kraus, F Bernhard, Lattorff, H Michael G, Leask, Megan, Lockett, Gabrielle A, Mallon, Eamonn B, Antonio, David S Marco, Marxer, Monika, Meeus, Ivan, Moritz, Robin F A, Nair, Ajay, Näpflin, Kathrin, Nissen, Inga, Niu, Jinzhi, Nunes, Francis M F, Oakeshott, John G, Osborne, Amy, Otte, Marianne, Pinheiro, Daniel G, Rossié, Nina, Rueppell, Olav, Santos, Carolina G, Schmid-Hempel, Regula, Schmitt, Björn D, Schulte, Christina, Simões, Zilá L P, Soares, Michelle P M, Swevers, Luc, Winnebeck, Eva C, Wolschin, Florian, Yu, Na, Zdobnov, Evgeny M, Aqrawi, Peshtewani K, Blankenburg, Kerstin P

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Highly accessible AU-rich regions in 3' untranslated regions are hotspots for binding of regulatory factors by Plass, Mireya, Rasmussen, Simon H, Krogh, Anders

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Recent advances in functional genome analysis [version 1; peer review: 2 approved] by Guigo, Roderic, de Hoon, Michiel

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Selenoprotein Gene Nomenclature by Gladyshev, Vadim N., Arnér, Elias S., Berry, Marla J., Brigelius-Flohé, Regina, Bruford, Elspeth A., Burk, Raymond F., Carlson, Bradley A., Castellano, Sergi, Chavatte, Laurent, Conrad, Marcus, Copeland, Paul R., Diamond, Alan M., Driscoll, Donna M., Ferreiro, Ana, Flohé, Leopold, Green, Fiona R., Guigó, Roderic, Handy, Diane E., Hatfield, Dolph L., Hesketh, John, Hoffmann, Peter R., Holmgren, Arne, Hondal, Robert J., Howard, Michael T., Huang, Kaixun, Kim, Hwa-Young, Kim, Ick Young, Köhrle, Josef, Krol, Alain, Kryukov, Gregory V., Lee, Byeong Jae, Lee, Byung Cheon, Lei, Xin Gen, Liu, Qiong, Lescure, Alain, Lobanov, Alexei V., Loscalzo, Joseph, Maiorino, Matilde, Mariotti, Marco, Sandeep Prabhu, K., Rayman, Margaret P., Rozovsky, Sharon, Salinas, Gustavo, Schmidt, Edward E., Schomburg, Lutz, Schweizer, Ulrich, Simonović, Miljan, Sunde, Roger A., Tsuji, Petra A., Tweedie, Susan, Ursini, Fulvio, Whanger, Philip D., Zhang, Yan

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Effect of transcription factor resource sharing on gene expression noise by Das, Dipjyoti, Dey, Supravat, Brewster, Robert C, Choubey, Sandeep

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Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes by Nayfach, Stephen, Bradley, Patrick H, Wyman, Stacia K, Laurent, Timothy J, Williams, Alex, Eisen, Jonathan A, Pollard, Katherine S, Sharpton, Thomas J

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