Sambamba: fast processing of NGS alignment formats by Tarasov, Artem, Vilella, Albert J, Cuppen, Edwin, Nijman, Isaac J, Prins, Pjotr

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EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates by Vilella, Albert J, Severin, Jessica, Ureta-Vidal, Abel, Heng, Li, Durbin, Richard, Birney, Ewan

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Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm by Löytynoja, Ari, Vilella, Albert J, Goldman, Nick

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Simultaneous sequencing of genetic and epigenetic bases in DNA by Füllgrabe, Jens, Gosal, Walraj S., Creed, Páidí, Liu, Sidong, Lumby, Casper K., Morley, David J., Ost, Tobias W. B., Vilella, Albert J., Yu, Shirong, Bignell, Helen, Burns, Philippa, Charlesworth, Tom, Fu, Beiyuan, Fordham, Howerd, Harding, Nicolas J., Gandelman, Olga, Golder, Paula, Hodson, Christopher, Li, Mengjie, Lila, Marjana, Liu, Yang, Mason, Joanne, Mellad, Jason, Monahan, Jack M., Nentwich, Oliver, Palmer, Alexandra, Steward, Michael, Taipale, Minna, Vandomme, Audrey, San-Bento, Rita Santo, Singhal, Ankita, Vivian, Julia, Wójtowicz, Natalia, Williams, Nathan, Walker, Nicolas J., Wong, Nicola C. H., Yalloway, Gary N., Holbrook, Joanna D., Balasubramanian, Shankar

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Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis by Dalloul, Rami A, Long, Julie A, Zimin, Aleksey V, Aslam, Luqman, Beal, Kathryn, Blomberg, Le Ann, Bouffard, Pascal, Burt, David W, Crasta, Oswald, Crooijmans, Richard P M A, Cooper, Kristal, Coulombe, Roger A, De, Supriyo, Delany, Mary E, Dodgson, Jerry B, Dong, Jennifer J, Evans, Clive, Frederickson, Karin M, Flicek, Paul, Florea, Liliana, Folkerts, Otto, Groenen, Martien A M, Harkins, Tim T, Herrero, Javier, Hoffmann, Steve, Megens, Hendrik-Jan, Jiang, Andrew, de Jong, Pieter, Kaiser, Pete, Kim, Heebal, Kim, Kyu-Won, Kim, Sungwon, Langenberger, David, Lee, Mi-Kyung, Lee, Taeheon, Mane, Shrinivasrao, Marcais, Guillaume, Marz, Manja, McElroy, Audrey P, Modise, Thero, Nefedov, Mikhail, Notredame, Cédric, Paton, Ian R, Payne, William S, Pertea, Geo, Prickett, Dennis, Puiu, Daniela, Qioa, Dan, Raineri, Emanuele, Ruffier, Magali, Salzberg, Steven L, Schatz, Michael C, Scheuring, Chantel, Schmidt, Carl J, Schroeder, Steven, Searle, Stephen M J, Smith, Edward J, Smith, Jacqueline, Sonstegard, Tad S, Stadler, Peter F, Tafer, Hakim, Tu, Zhijian Jake, Van Tassell, Curtis P, Vilella, Albert J, Williams, Kelly P, Yorke, James A, Zhang, Liqing, Zhang, Hong-Bin, Zhang, Xiaojun, Zhang, Yang, Reed, Kent M

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Development and application of a next-generation sequencing protocol and bioinformatics pipeline for the comprehensive analysis of the canine immunoglobulin repertoire by Cullen, Jonah N, Martin, Jolyon, Vilella, Albert J, Treeful, Amy, Sargan, David, Bradley, Allan, Friedenberg, Steven G

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Genome-wide DNA polymorphism analyses using VariScan by Hutter, Stephan, Vilella, Albert J, Rozas, Julio

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Ensembl comparative genomics resources by Herrero, Javier, Muffato, Matthieu, Beal, Kathryn, Fitzgerald, Stephen, Gordon, Leo, Pignatelli, Miguel, Vilella, Albert J, Searle, Stephen M J, Amode, Ridwan, Brent, Simon, Spooner, William, Kulesha, Eugene, Yates, Andrew, Flicek, Paul

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eHive: an artificial intelligence workflow system for genomic analysis by Severin, Jessica, Beal, Kathryn, Vilella, Albert J, Fitzgerald, Stephen, Schuster, Michael, Gordon, Leo, Ureta-Vidal, Abel, Flicek, Paul, Herrero, Javier

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RNAcentral: A vision for an international database of RNA sequences by Bateman, Alex, Agrawal, Shipra, Birney, Ewan, Bruford, Elspeth A, Bujnicki, Janusz M, Cochrane, Guy, Cole, James R, Dinger, Marcel E, Enright, Anton J, Gardner, Paul P, Gautheret, Daniel, Griffiths-Jones, Sam, Harrow, Jen, Herrero, Javier, Holmes, Ian H, Huang, Hsien-Da, Kelly, Krystyna A, Kersey, Paul, Kozomara, Ana, Lowe, Todd M, Marz, Manja, Moxon, Simon, Pruitt, Kim D, Samuelsson, Tore, Stadler, Peter F, Vilella, Albert J, Vogel, Jan-Hinnerk, Williams, Kelly P, Wright, Mathew W, Zwieb, Christian

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A high-resolution map of human evolutionary constraint using 29 mammals by Lindblad-Toh, Kerstin, Garber, Manuel, Zuk, Or, Lin, Michael F., Parker, Brian J., Washietl, Stefan, Kheradpour, Pouya, Ernst, Jason, Jordan, Gregory, Mauceli, Evan, Ward, Lucas D., Lowe, Craig B., Holloway, Alisha K., Clamp, Michele, Gnerre, Sante, Alföldi, Jessica, Beal, Kathryn, Chang, Jean, Clawson, Hiram, Cuff, James, Di Palma, Federica, Fitzgerald, Stephen, Flicek, Paul, Guttman, Mitchell, Hubisz, Melissa J., Jaffe, David B., Jungreis, Irwin, Kent, W. James, Kostka, Dennis, Lara, Marcia, Martins, Andre L., Massingham, Tim, Moltke, Ida, Raney, Brian J., Rasmussen, Matthew D., Robinson, Jim, Stark, Alexander, Vilella, Albert J., Wen, Jiayu, Xie, Xiaohui, Zody, Michael C., Worley, Kim C., Kovar, Christie L., Muzny, Donna M., Gibbs, Richard A., Warren, Wesley C., Mardis, Elaine R., Weinstock, George M., Wilson, Richard K., Birney, Ewan, Margulies, Elliott H., Herrero, Javier, Green, Eric D., Haussler, David, Siepel, Adam, Goldman, Nick, Pollard, Katherine S., Pedersen, Jakob S., Lander, Eric S., Kellis, Manolis

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Insights into hominid evolution from the gorilla genome sequence by Scally, Aylwyn, Dutheil, Julien Y., Hillier, LaDeana W., Jordan, Gregory E., Goodhead, Ian, Herrero, Javier, Hobolth, Asger, Lappalainen, Tuuli, Mailund, Thomas, Marques-Bonet, Tomas, McCarthy, Shane, Montgomery, Stephen H., Schwalie, Petra C., Tang, Y. Amy, Ward, Michelle C., Xue, Yali, Yngvadottir, Bryndis, Alkan, Can, Andersen, Lars N., Ayub, Qasim, Ball, Edward V., Beal, Kathryn, Bradley, Brenda J., Chen, Yuan, Clee, Chris M., Fitzgerald, Stephen, Graves, Tina A., Gu, Yong, Heath, Paul, Heger, Andreas, Karakoc, Emre, Kolb-Kokocinski, Anja, Laird, Gavin K., Lunter, Gerton, Meader, Stephen, Mort, Matthew, Mullikin, James C., Munch, Kasper, O’Connor, Timothy D., Phillips, Andrew D., Prado-Martinez, Javier, Rogers, Anthony S., Sajjadian, Saba, Schmidt, Dominic, Shaw, Katy, Simpson, Jared T., Stenson, Peter D., Turner, Daniel J., Vigilant, Linda, Vilella, Albert J., Whitener, Weldon, Zhu, Baoli, Cooper, David N., de Jong, Pieter, Dermitzakis, Emmanouil T., Eichler, Evan E., Flicek, Paul, Goldman, Nick, Mundy, Nicholas I., Ning, Zemin, Odom, Duncan T., Ponting, Chris P., Quail, Michael A., Ryder, Oliver A., Searle, Stephen M., Warren, Wesley C., Wilson, Richard K., Schierup, Mikkel H., Rogers, Jane, Tyler-Smith, Chris, Durbin, Richard

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Comparative and demographic analysis of orang-utan genomes by Locke, Devin P., Hillier, LaDeana W., Warren, Wesley C., Worley, Kim C., Nazareth, Lynne V., Muzny, Donna M., Yang, Shiaw-Pyng, Wang, Zhengyuan, Chinwalla, Asif T., Minx, Pat, Mitreva, Makedonka, Cook, Lisa, Delehaunty, Kim D., Fronick, Catrina, Schmidt, Heather, Fulton, Lucinda A., Fulton, Robert S., Nelson, Joanne O., Magrini, Vincent, Pohl, Craig, Graves, Tina A., Markovic, Chris, Cree, Andy, Dinh, Huyen H., Hume, Jennifer, Kovar, Christie L., Lunter, Gerton, Meader, Stephen, Heger, Andreas, Ponting, Chris P., Marques-Bonet, Tomas, Alkan, Can, Chen, Lin, Cheng, Ze, Kidd, Jeffrey M., Eichler, Evan E., White, Simon, Searle, Stephen, Vilella, Albert J., Chen, Yuan, Flicek, Paul, Ma, Jian, Raney, Brian, Suh, Bernard, Burhans, Richard, Herrero, Javier, Haussler, David, Faria, Rui, Fernando, Olga, Darré, Fleur, Farré, Domènec, Gazave, Elodie, Oliva, Meritxell, Navarro, Arcadi, Roberto, Roberta, Capozzi, Oronzo, Archidiacono, Nicoletta, Valle, Giuliano Della, Purgato, Stefania, Rocchi, Mariano, Konkel, Miriam K., Walker, Jerilyn A., Ullmer, Brygg, Batzer, Mark A., Smit, Arian F. A., Hubley, Robert, Casola, Claudio, Schrider, Daniel R., Hahn, Matthew W., Quesada, Victor, Puente, Xose S., Ordoñez, Gonzalo R., López-Otín, Carlos, Vinar, Tomas, Brejova, Brona, Ratan, Aakrosh, Harris, Robert S., Miller, Webb, Kosiol, Carolin, Lawson, Heather A., Taliwal, Vikas, Martins, André L., Siepel, Adam, RoyChoudhury, Arindam, Ma, Xin, Degenhardt, Jeremiah, Bustamante, Carlos D., Gutenkunst, Ryan N., Mailund, Thomas, Dutheil, Julien Y., Hobolth, Asger, Schierup, Mikkel H., Ryder, Oliver A., Yoshinaga, Yuko, de Jong, Pieter J., Weinstock, George M., Rogers, Jeffrey, Mardis, Elaine R., Gibbs, Richard A., Wilson, Richard K.

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Ensembl 2011 by Flicek, Paul, Amode, M. Ridwan, Barrell, Daniel, Beal, Kathryn, Brent, Simon, Chen, Yuan, Clapham, Peter, Coates, Guy, Fairley, Susan, Fitzgerald, Stephen, Gordon, Leo, Hendrix, Maurice, Hourlier, Thibaut, Johnson, Nathan, Kähäri, Andreas, Keefe, Damian, Keenan, Stephen, Kinsella, Rhoda, Kokocinski, Felix, Kulesha, Eugene, Larsson, Pontus, Longden, Ian, McLaren, William, Overduin, Bert, Pritchard, Bethan, Riat, Harpreet Singh, Rios, Daniel, Ritchie, Graham R.S, Ruffier, Magali, Schuster, Michael, Sobral, Daniel, Spudich, Giulietta, Tang, Y. Amy, Trevanion, Stephen, Vandrovcova, Jana, Vilella, Albert J, White, Simon, Wilder, Steven P, Zadissa, Amonida, Zamora, Jorge, Aken, Bronwen L, Birney, Ewan, Cunningham, Fiona, Dunham, Ian, Durbin, Richard, Fernández-Suarez, Xosé M, Herrero, Javier, Hubbard, Tim J.P, Parker, Anne, Proctor, Glenn, Vogel, Jan, Searle, Stephen M.J

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Genome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer by Murchison, Elizabeth P., Schulz-Trieglaff, Ole B., Ning, Zemin, Alexandrov, Ludmil B., Bauer, Markus J., Fu, Beiyuan, Hims, Matthew, Ding, Zhihao, Ivakhno, Sergii, Stewart, Caitlin, Ng, Bee Ling, Wong, Wendy, Aken, Bronwen, White, Simon, Alsop, Amber, Becq, Jennifer, Bignell, Graham R., Cheetham, R. Keira, Cheng, William, Connor, Thomas R., Cox, Anthony J., Feng, Zhi-Ping, Gu, Yong, Grocock, Russell J., Harris, Simon R., Khrebtukova, Irina, Kingsbury, Zoya, Kowarsky, Mark, Kreiss, Alexandre, Luo, Shujun, Marshall, John, McBride, David J., Murray, Lisa, Pearse, Anne-Maree, Raine, Keiran, Rasolonjatovo, Isabelle, Shaw, Richard, Tedder, Philip, Tregidgo, Carolyn, Vilella, Albert J., Wedge, David C., Woods, Gregory M., Gormley, Niall, Humphray, Sean, Schroth, Gary, Smith, Geoffrey, Hall, Kevin, Searle, Stephen M.J., Carter, Nigel P., Papenfuss, Anthony T., Futreal, P. Andrew, Campbell, Peter J., Yang, Fengtang, Bentley, David R., Evers, Dirk J., Stratton, Michael R.

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TreeFam: 2008 Update by Ruan, Jue, Li, Heng, Chen, Zhongzhong, Coghlan, Avril, Coin, Lachlan James M, Guo, Yiran, Hériché, Jean-Karim, Hu, Yafeng, Kristiansen, Karsten, Li, Ruiqiang, Liu, Tao, Moses, Alan, Qin, Junjie, Vang, Søren, Vilella, Albert J, Ureta-Vidal, Abel, Bolund, Lars, Wang, Jun, Durbin, Richard

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VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data by Vilella, Albert J., Blanco-Garcia, Angel, Hutter, Stephan, Rozas, Julio

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Joining forces in the quest for orthologs by Gabaldón, Toni, Dessimoz, Christophe, Huxley-Jones, Julie, Vilella, Albert J, Sonnhammer, Erik Ll, Lewis, Suzanna

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ncRNA orthologies in the vertebrate lineage by Pignatelli, Miguel, Vilella, Albert J, Muffato, Matthieu, Gordon, Leo, White, Simon, Flicek, Paul, Herrero, Javier

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Considerations for the inclusion of 2x mammalian genomes in phylogenetic analyses by Vilella, Albert J, Birney, Ewan, Flicek, Paul, Herrero, Javier

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