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2. Ensembl 2015

Author

Cunningham, Fiona, Amode, Ridwan M., Barrell, Daniel, Beal, Kathryn, Billis, Konstantinos, Brent, Simon, Carvalho-Silva, Denise, Clapham, Peter, Coates, Guy, Fitzgerald, Stephen, Gil, Laurent, Girón, Carlos García, Gordon, Leo, Hourlier, Thibaut, Hunt, Sarah E., Janacek, Sophie H., Johnson, Nathan, Juettemann, Thomas, Kähäri, Andreas K., Keenan, Stephen, Martin, Fergal J., Maurel, Thomas, McLaren, William, Murphy, Daniel N., Nag, Rishi, Overduin, Bert, Parker, Anne, Patricio, Mateus, Perry, Emily, Pignatelli, Miguel, Riat, Harpreet Singh, Sheppard, Daniel, Taylor, Kieron, Thormann, Anja, Vullo, Alessandro, Wilder, Steven P., Zadissa, Amonida, Aken, Bronwen L., Birney, Ewan, Harrow, Jennifer, Kinsella, Rhoda, Muffato, Matthieu, Ruffier, Magali, Searle, Stephen M.J., Spudich, Giulietta, Trevanion, Stephen J., Yates, Andy, Zerbino, Daniel R., and Flicek, Paul

Published
2015
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3. An integrated encyclopedia of DNA elements in the human genome

Author

Dunham, Ian, Kundaje, Anshul, Aldred, Shelley F., Collins, Patrick J., Davis, Carrie A., Doyle, Francis, Epstein, Charles B., Frietze, Seth, Harrow, Jennifer, Kaul, Rajinder, Khatun, Jainab, Lajoie, Bryan R., Landt, Stephen G., Lee, Bum-Kyu, Pauli, Florencia, Rosenbloom, Kate R., Sabo, Peter, Safi, Alexias, Sanyal, Amartya, Shoresh, Noam, Simon, Jeremy M., Song, Lingyun, Trinklein, Nathan D., Altshuler, Robert C., Birney, Ewan, Brown, James B., Cheng, Chao, Djebali, Sarah, Dong, Xianjun, Ernst, Jason, Furey, Terrence S., Gerstein, Mark, Giardine, Belinda, Greven, Melissa, Hardison, Ross C., Harris, Robert S., Herrero, Javier, Hoffman, Michael M., Iyer, Sowmya, Kellis, Manolis, Kheradpour, Pouya, Lassmann, Timo, Li, Qunhua, Lin, Xinying, Marinov, Georgi K., Merkel, Angelika, Mortazavi, Ali, Parker, Stephen C. J., Reddy, Timothy E., Rozowsky, Joel, Schlesinger, Felix, Thurman, Robert E., Wang, Jie, Ward, Lucas D., Whitfield, Troy W., Wilder, Steven P., Wu, Weisheng, Xi, Hualin S., Yip, Kevin Y., Zhuang, Jiali, Bernstein, Bradley E., Green, Eric D., Gunter, Chris, Snyder, Michael, Pazin, Michael J., Lowdon, Rebecca F., Dillon, Laura A. L., Adams, Leslie B., Kelly, Caroline J., Zhang, Julia, Wexler, Judith R., Good, Peter J., Feingold, Elise A., Crawford, Gregory E., Dekker, Job, Elnitski, Laura, Farnham, Peggy J., Giddings, Morgan C., Gingeras, Thomas R., Guigo, Roderic, Hubbard, Timothy J., Kent, W. James, Lieb, Jason D., Margulies, Elliott H., Myers, Richard M., Stamatoyannopoulos, John A., Tenenbaum, Scott A., Weng, Zhiping, White, Kevin P., Wold, Barbara, Yu, Yanbao, Wrobel, John, Risk, Brian A., Gunawardena, Harsha P., Kuiper, Heather C., Maier, Christopher W., Xie, Ling, Chen, Xian, Mikkelsen, Tarjei S., Gillespie, Shawn, Goren, Alon, Ram, Oren, Zhang, Xiaolan, Wang, Li, Issner, Robbyn, Coyne, Michael J., Durham, Timothy, Ku, Manching, Truong, Thanh, Eaton, Matthew L., Dobin, Alex, Tanzer, Andrea, Lagarde, Julien, Lin, Wei, Xue, Chenghai, Williams, Brian A., Zaleski, Chris, Roder, Maik, Kokocinski, Felix, Abdelhamid, Rehab F., Alioto, Tyler, Antoshechkin, Igor, Baer, Michael T., Batut, Philippe, Bell, Ian, Bell, Kimberly, Chakrabortty, Sudipto, Chrast, Jacqueline, Curado, Joao, Derrien, Thomas, Drenkow, Jorg, Dumais, Erica, Dumais, Jackie, Duttagupta, Radha, Fastuca, Megan, Fejes-Toth, Kata, Ferreira, Pedro, Foissac, Sylvain, Fullwood, Melissa J., Gao, Hui, Gonzalez, David, Gordon, Assaf, Howald, Cedric, Jha, Sonali, Johnson, Rory, Kapranov, Philipp, King, Brandon, Kingswood, Colin, Li, Guoliang, Luo, Oscar J., Park, Eddie, Preall, Jonathan B., Presaud, Kimberly, Ribeca, Paolo, Robyr, Daniel, Ruan, Xiaoan, Sammeth, Michael, Sandhu, Kuljeet Singh, Schaeffer, Lorain, See, Lei-Hoon, Shahab, Atif, Skancke, Jorgen, Suzuki, Ana Maria, Takahashi, Hazuki, Tilgner, Hagen, Trout, Diane, Walters, Nathalie, Wang, Huaien, Hayashizaki, Yoshihide, Reymond, Alexandre, Antonarakis, Stylianos E., Hannon, Gregory J., Ruan, Yijun, Carninci, Piero, Sloan, Cricket A., Learned, Katrina, Malladi, Venkat S., Wong, Matthew C., Barber, Galt P., Cline, Melissa S., Dreszer, Timothy R., Heitner, Steven G., Karolchik, Donna, Kirkup, Vanessa M., Meyer, Laurence R., Long, Jeffrey C., Maddren, Morgan, Raney, Brian J., Grasfeder, Linda L., Giresi, Paul G., Battenhouse, Anna, Sheffield, Nathan C., Showers, Kimberly A., London, Darin, Bhinge, Akshay A., Shestak, Christopher, Schaner, Matthew R., Ki Kim, Seul, Zhang, Zhuzhu Z., Mieczkowski, Piotr A., Mieczkowska, Joanna O., Liu, Zheng, McDaniell, Ryan M., Ni, Yunyun, Rashid, Naim U., Kim, Min Jae, Adar, Sheera, Zhang, Zhancheng, Wang, Tianyuan, Winter, Deborah, Keefe, Damian, Iyer, Vishwanath R., Zheng, Meizhen, Wang, Ping, Gertz, Jason, Vielmetter, Jost, Partridge, E., Varley, Katherine E., Gasper, Clarke, Bansal, Anita, Pepke, Shirley, Jain, Preti, Amrhein, Henry, Bowling, Kevin M., Anaya, Michael, Cross, Marie K., Muratet, Michael A., Newberry, Kimberly M., McCue, Kenneth, Nesmith, Amy S., Fisher-Aylor, Katherine I., Pusey, Barbara, DeSalvo, Gilberto, Parker, Stephanie L., Balasubramanian, Sreeram, Davis, Nicholas S., Meadows, Sarah K., Eggleston, Tracy, Newberry, J. Scott, Levy, Shawn E., Absher, Devin M., Wong, Wing H., Blow, Matthew J., Visel, Axel, Pennachio, Len A., Petrykowska, Hanna M., Abyzov, Alexej, Aken, Bronwen, Barrell, Daniel, Barson, Gemma, Berry, Andrew, Bignell, Alexandra, Boychenko, Veronika, Bussotti, Giovanni, Davidson, Claire, Despacio-Reyes, Gloria, Diekhans, Mark, Ezkurdia, Iakes, Frankish, Adam, Gilbert, James, Gonzalez, Jose Manuel, Griffiths, Ed, Harte, Rachel, Hendrix, David A., Hunt, Toby, Jungreis, Irwin, Kay, Mike, Khurana, Ekta, Leng, Jing, Lin, Michael F., Loveland, Jane, Lu, Zhi, Manthravadi, Deepa, Mariotti, Marco, Mudge, Jonathan, Mukherjee, Gaurab, Notredame, Cedric, Pei, Baikang, Rodriguez, Jose Manuel, Saunders, Gary, Sboner, Andrea, Searle, Stephen, Sisu, Cristina, Snow, Catherine, Steward, Charlie, Tapanari, Electra, Tress, Michael L., van Baren, Marijke J., Washietl, Stefan, Wilming, Laurens, Zadissa, Amonida, Zhang, Zhengdong, Brent, Michael, Haussler, David, Valencia, Alfonso, Addleman, Nick, Alexander, Roger P., Auerbach, Raymond K., Balasubramanian, Suganthi, Bettinger, Keith, Bhardwaj, Nitin, Boyle, Alan P., Cao, Alina R., Cayting, Philip, Charos, Alexandra, Cheng, Yong, Eastman, Catharine, Euskirchen, Ghia, Fleming, Joseph D., Grubert, Fabian, Habegger, Lukas, Hariharan, Manoj, Harmanci, Arif, Iyengar, Sushma, Jin, Victor X., Karczewski, Konrad J., Kasowski, Maya, Lacroute, Phil, Lam, Hugo, Lamarre-Vincent, Nathan, Lian, Jin, Lindahl-Allen, Marianne, Min, Renqiang, Miotto, Benoit, Monahan, Hannah, Moqtaderi, Zarmik, Mu, Xinmeng J., Ouyang, Zhengqing, Patacsil, Dorrelyn, Raha, Debasish, Ramirez, Lucia, Reed, Brian, Shi, Minyi, Slifer, Teri, Witt, Heather, Wu, Linfeng, Xu, Xiaoqin, Yan, Koon-Kiu, Yang, Xinqiong, Struhl, Kevin, Weissman, Sherman M., Penalva, Luiz O., Karmakar, Subhradip, Bhanvadia, Raj R., Choudhury, Alina, Domanus, Marc, Ma, Lijia, Moran, Jennifer, Victorsen, Alec, Auer, Thomas, Centanin, Lazaro, Eichenlaub, Michael, Gruhl, Franziska, Heermann, Stephan, Hoeckendorf, Burkhard, Inoue, Daigo, Kellner, Tanja, Kirchmaier, Stephan, Mueller, Claudia, Reinhardt, Robert, Schertel, Lea, Schneider, Stephanie, Sinn, Rebecca, Wittbrodt, Beate, Wittbrodt, Jochen, Partridge, E. Christopher, Jain, Gaurav, Balasundaram, Gayathri, Bates, Daniel L., Byron, Rachel, Canfield, Theresa K., Diegel, Morgan J., Dunn, Douglas, Ebersol, Abigail K., Frum, Tristan, Garg, Kavita, Gist, Erica, Hansen, R. Scott, Boatman, Lisa, Haugen, Eric, Humbert, Richard, Johnson, Audra K., Johnson, Ericka M., Kutyavin, Tattyana V., Lee, Kristen, Lotakis, Dimitra, Maurano, Matthew T., Neph, Shane J., Neri, Fiedencio V., Nguyen, Eric D., Qu, Hongzhu, Reynolds, Alex P., Roach, Vaughn, Rynes, Eric, Sanchez, Minerva E., Sandstrom, Richard S., Shafer, Anthony O., Stergachis, Andrew B., Thomas, Sean, Vernot, Benjamin, Vierstra, Jeff, Vong, Shinny, Weaver, Molly A., Yan, Yongqi, Zhang, Miaohua, Akey, Joshua M., Bender, Michael, Dorschner, Michael O., Groudine, Mark, MacCoss, Michael J., Navas, Patrick, Stamatoyannopoulos, George, Beal, Kathryn, Brazma, Alvis, Flicek, Paul, Johnson, Nathan, Lukk, Margus, Luscombe, Nicholas M., Sobral, Daniel, Vaquerizas, Juan M., Batzoglou, Serafim, Sidow, Arend, Hussami, Nadine, Kyriazopoulou-Panagiotopoulou, Sofia, Libbrecht, Max W., Schaub, Marc A., Miller, Webb, Bickel, Peter J., Banfai, Balazs, Boley, Nathan P., Huang, Haiyan, Li, Jingyi Jessica, Noble, William Stafford, Bilmes, Jeffrey A., Buske, Orion J., Sahu, Avinash D., Kharchenko, Peter V., Park, Peter J., Baker, Dannon, Taylor, James, and Lochovsky, Lucas

Subjects
Genetic research, Human genome -- Research, Genetic transcription -- Research, Environmental issues, Science and technology, Zoology and wildlife conservation
Abstract

The human genome encodes the blueprint of life, but the function of the vast majority of its nearly three billion bases is unknown. The Encyclopedia of DNA Elements (ENCODE) project has systematically mapped regions of transcription, transcription factor association, chromatin structure and histone modification. These data enabled us to assign biochemical functions for 80% of the genome, in particular outside of the well-studied protein-coding regions. Many discovered candidate regulatory elements are physically associated with one another and with expressed genes, providing new insights into the mechanisms of gene regulation. The newly identified elements also show a statistical correspondence to sequence variants linked to human disease, and can thereby guide interpretation of this variation. Overall, the project provides new insights into the organization and regulation of our genes and genome, and is an expansive resource of functional annotations for biomedical research., Author(s): The ENCODE Project Consortium; Overall coordination (data analysis coordination); Ian Dunham [2]; Anshul Kundaje [3, 82]; Data production leads (data production); Shelley F. Aldred [4]; Patrick J. Collins [4]; [...]

Published
2012
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4. Ensembl 2014

Author

Flicek, Paul, Amode, Ridwan M., Barrell, Daniel, Beal, Kathryn, Billis, Konstantinos, Brent, Simon, Carvalho-Silva, Denise, Clapham, Peter, Coates, Guy, Fitzgerald, Stephen, Gil, Laurent, Girón, Carlos García, Gordon, Leo, Hourlier, Thibaut, Hunt, Sarah, Johnson, Nathan, Juettemann, Thomas, Kähäri, Andreas K., Keenan, Stephen, Kulesha, Eugene, Martin, Fergal J., Maurel, Thomas, McLaren, William M., Murphy, Daniel N., Nag, Rishi, Overduin, Bert, Pignatelli, Miguel, Pritchard, Bethan, Pritchard, Emily, Riat, Harpreet S., Ruffier, Magali, Sheppard, Daniel, Taylor, Kieron, Thormann, Anja, Trevanion, Stephen J., Vullo, Alessandro, Wilder, Steven P., Wilson, Mark, Zadissa, Amonida, Aken, Bronwen L., Birney, Ewan, Cunningham, Fiona, Harrow, Jennifer, Herrero, Javier, Hubbard, Tim J.P., Kinsella, Rhoda, Muffato, Matthieu, Parker, Anne, Spudich, Giulietta, Yates, Andy, Zerbino, Daniel R., and Searle, Stephen M.J.

Published
2014
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5. The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing

Author

Harrison, Peter W, primary, Lopez, Rodrigo, additional, Rahman, Nadim, additional, Allen, Stefan Gutnick, additional, Aslam, Raheela, additional, Buso, Nicola, additional, Cummins, Carla, additional, Fathy, Yasmin, additional, Felix, Eloy, additional, Glont, Mihai, additional, Jayathilaka, Suran, additional, Kadam, Sandeep, additional, Kumar, Manish, additional, Lauer, Katharina B, additional, Malhotra, Geetika, additional, Mosaku, Abayomi, additional, Edbali, Ossama, additional, Park, Young Mi, additional, Parton, Andrew, additional, Pearce, Matt, additional, Estrada Pena, Jose Francisco, additional, Rossetto, Joseph, additional, Russell, Craig, additional, Selvakumar, Sandeep, additional, Sitjà, Xènia Pérez, additional, Sokolov, Alexey, additional, Thorne, Ross, additional, Ventouratou, Marianna, additional, Walter, Peter, additional, Yordanova, Galabina, additional, Zadissa, Amonida, additional, Cochrane, Guy, additional, Blomberg, Niklas, additional, and Apweiler, Rolf, additional

Published
2021
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6. ELIXIR-CONVERGE D8.1 Access to EU tools and project data

Author

Cochrane, Guy, Rajan, Jeena, and Zadissa, Amonida

Subjects
Biomolecular data, COVID-19, European COVID-19 Data Platform, ELIXIR-CONVERGE, COVID-19 Data Portal, ELIXIR
Abstract

Rich and integrated biomolecular data are essential to support the world's scientific research into COVID-19. These data underlie our biological understanding (viral biology, the infection processes and patient response), our ability to identify and track COVID-19 (epidemiology and viral spread) and our capacity to intervene (through public health, therapeutic and vaccine approaches). An early priority of the European COVID-19 Data Platform has been to bring together relevant biomolecular data and the scholarly literature describing these data along with tools, standards and other resources to support operations upon the data. In this deliverable, we report on content-building activities within the Platform that serve, through the COVID-19 Data Portal, to make discoverable and accessible biomolecular data, literature and collections (tools, standards and related resources) relating to COVID-19 (https://www.covid19dataportal.org/). Our content building has resulted to date in over 420,000 biomolecular data records, almost 110,000 literature records and 57 linked collections covering tools, standards and other resources. Data continue to grow in number and diversity. This content has seen heavy exposure to users and two use cases around drug development and bioinformatics illustrate impact.Our work builds upon and demonstrates the important foundations that are provided by well-managed biomolecular data and shows the potential of these data rapidly to be deployed to support urgent scientific challenges., This project has received funding from the European Union's Horizon 2020 Research and Innovation programme under grant agreement No 871075.

Published
2020
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7. Ensembl 2013

Author

Flicek, Paul, Ahmed, Ikhlak, Amode, Ridwan M., Barrell, Daniel, Beal, Kathryn, Brent, Simon, Carvalho-Silva, Denise, Clapham, Peter, Coates, Guy, Fairley, Susan, Fitzgerald, Stephen, Gil, Laurent, García-Girón, Carlos, Gordon, Leo, Hourlier, Thibaut, Hunt, Sarah, Juettemann, Thomas, Kähäri, Andreas K., Keenan, Stephen, Komorowska, Monika, Kulesha, Eugene, Longden, Ian, Maurel, Thomas, McLaren, William M., Muffato, Matthieu, Nag, Rishi, Overduin, Bert, Pignatelli, Miguel, Pritchard, Bethan, Pritchard, Emily, Riat, Harpreet Singh, Ritchie, Graham R. S., Ruffier, Magali, Schuster, Michael, Sheppard, Daniel, Sobral, Daniel, Taylor, Kieron, Thormann, Anja, Trevanion, Stephen, White, Simon, Wilder, Steven P., Aken, Bronwen L., Birney, Ewan, Cunningham, Fiona, Dunham, Ian, Harrow, Jennifer, Herrero, Javier, Hubbard, Tim J. P., Johnson, Nathan, Kinsella, Rhoda, Parker, Anne, Spudich, Giulietta, Yates, Andy, Zadissa, Amonida, and Searle, Stephen M. J.

Published
2013
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8. Ensembl 2012

Author

Flicek, Paul, Amode, M. Ridwan, Barrell, Daniel, Beal, Kathryn, Brent, Simon, Carvalho-Silva, Denise, Clapham, Peter, Coates, Guy, Fairley, Susan, Fitzgerald, Stephen, Gil, Laurent, Gordon, Leo, Hendrix, Maurice, Hourlier, Thibaut, Johnson, Nathan, Kähäri, Andreas K., Keefe, Damian, Keenan, Stephen, Kinsella, Rhoda, Komorowska, Monika, Koscielny, Gautier, Kulesha, Eugene, Larsson, Pontus, Longden, Ian, McLaren, William, Muffato, Matthieu, Overduin, Bert, Pignatelli, Miguel, Pritchard, Bethan, Riat, Harpreet Singh, Ritchie, Graham R. S., Ruffier, Magali, Schuster, Michael, Sobral, Daniel, Tang, Y. Amy, Taylor, Kieron, Trevanion, Stephen, Vandrovcova, Jana, White, Simon, Wilson, Mark, Wilder, Steven P., Aken, Bronwen L., Birney, Ewan, Cunningham, Fiona, Dunham, Ian, Durbin, Richard, Fernández-Suarez, Xosé M., Harrow, Jennifer, Herrero, Javier, Hubbard, Tim J. P., Parker, Anne, Proctor, Glenn, Spudich, Giulietta, Vogel, Jan, Yates, Andy, Zadissa, Amonida, and Searle, Stephen M. J.

Published
2012
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9. The genome of the green anole lizard and a comparative analysis with birds and mammals

Author

Alföldi, Jessica, Di Palma, Federica, Grabherr, Manfred, Williams, Christina, Kong, Lesheng, Mauceli, Evan, Russell, Pamela, Lowe, Craig B., Glor, Richard E., Jaffe, Jacob D., Ray, David A., Boissinot, Stephane, Shedlock, Andrew M., Botka, Christopher, Castoe, Todd A., Colbourne, John K., Fujita, Matthew K., Moreno, Ricardo Godinez, ten Hallers, Boudewijn F., Haussler, David, Heger, Andreas, Heiman, David, Janes, Daniel E., Johnson, Jeremy, de Jong, Pieter J., Koriabine, Maxim Y., Lara, Marcia, Novick, Peter A., Organ, Chris L., Peach, Sally E., Poe, Steven, Pollock, David D., de Queiroz, Kevin, Sanger, Thomas, Searle, Steve, Smith, Jeremy D., Smith, Zachary, Swofford, Ross, Turner-Maier, Jason, Wade, Juli, Young, Sarah, Zadissa, Amonida, Edwards, Scott V., Glenn, Travis C., Schneider, Christopher J., Losos, Jonathan B., Lander, Eric S., Breen, Matthew, Ponting, Chris P., and Lindblad-Toh, Kerstin

Published
2011
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10. Ensembl 2011

Author

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, and Searle, Stephen M. J.

Published
2011
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11. Ensembl’s 10th year

Author

Flicek, Paul, Aken, Bronwen L., Ballester, Benoit, Beal, Kathryn, Bragin, Eugene, Brent, Simon, Chen, Yuan, Clapham, Peter, Coates, Guy, Fairley, Susan, Fitzgerald, Stephen, Fernandez-Banet, Julio, Gordon, Leo, Gräf, Stefan, Haider, Syed, Hammond, Martin, Howe, Kerstin, Jenkinson, Andrew, Johnson, Nathan, Kähäri, Andreas, Keefe, Damian, Keenan, Stephen, Kinsella, Rhoda, Kokocinski, Felix, Koscielny, Gautier, Kulesha, Eugene, Lawson, Daniel, Longden, Ian, Massingham, Tim, McLaren, William, Megy, Karine, Overduin, Bert, Pritchard, Bethan, Rios, Daniel, Ruffier, Magali, Schuster, Michael, Slater, Guy, Smedley, Damian, Spudich, Giulietta, Tang, Y. Amy, Trevanion, Stephen, Vilella, Albert, Vogel, Jan, White, Simon, Wilder, Steven P., Zadissa, Amonida, Birney, Ewan, Cunningham, Fiona, Dunham, Ian, Durbin, Richard, Fernández-Suarez, Xosé M., Herrero, Javier, Hubbard, Tim J., Parker, Anne, Proctor, Glenn, Smith, James, and Searle, Stephen M.

Published
2010
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12. Ensembl 2020

Author

Yates, Andrew D, primary, Achuthan, Premanand, additional, Akanni, Wasiu, additional, Allen, James, additional, Allen, Jamie, additional, Alvarez-Jarreta, Jorge, additional, Amode, M Ridwan, additional, Armean, Irina M, additional, Azov, Andrey G, additional, Bennett, Ruth, additional, Bhai, Jyothish, additional, Billis, Konstantinos, additional, Boddu, Sanjay, additional, Marugán, José Carlos, additional, Cummins, Carla, additional, Davidson, Claire, additional, Dodiya, Kamalkumar, additional, Fatima, Reham, additional, Gall, Astrid, additional, Giron, Carlos Garcia, additional, Gil, Laurent, additional, Grego, Tiago, additional, Haggerty, Leanne, additional, Haskell, Erin, additional, Hourlier, Thibaut, additional, Izuogu, Osagie G, additional, Janacek, Sophie H, additional, Juettemann, Thomas, additional, Kay, Mike, additional, Lavidas, Ilias, additional, Le, Tuan, additional, Lemos, Diana, additional, Martinez, Jose Gonzalez, additional, Maurel, Thomas, additional, McDowall, Mark, additional, McMahon, Aoife, additional, Mohanan, Shamika, additional, Moore, Benjamin, additional, Nuhn, Michael, additional, Oheh, Denye N, additional, Parker, Anne, additional, Parton, Andrew, additional, Patricio, Mateus, additional, Sakthivel, Manoj Pandian, additional, Abdul Salam, Ahamed Imran, additional, Schmitt, Bianca M, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Sycheva, Mira, additional, Szuba, Marek, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Threadgold, Glen, additional, Vullo, Alessandro, additional, Walts, Brandon, additional, Winterbottom, Andrea, additional, Zadissa, Amonida, additional, Chakiachvili, Marc, additional, Flint, Bethany, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, IIsley, Garth, additional, Kostadima, Myrto, additional, Langridge, Nick, additional, Loveland, Jane E, additional, Martin, Fergal J, additional, Morales, Joannella, additional, Mudge, Jonathan M, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Trevanion, Stephen J, additional, Cunningham, Fiona, additional, Howe, Kevin L, additional, Zerbino, Daniel R, additional, and Flicek, Paul, additional

Published
2019
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13. Inference of transcriptional regulation using gene expression data from the bovine and human genomes

Author

McEwan John C, Zadissa Amonida, and Brown Chris M

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Gene expression is in part regulated by sequences in promoters that bind transcription factors. Thus, co-expressed genes may have shared sequence motifs representing putative transcription factor binding sites (TFBSs). However, for agriculturally important animals the genomic sequence is often incomplete. The more complete human genome may be able to be used for this prediction by taking advantage of the expected evolutionary conservation in TFBSs between the species. Results A method of de novo TFBS prediction based on MEME was implemented, tested, and validated on a muscle-specific dataset. Muscle specific expression data from EST library analysis from cattle was used to predict sets of genes whose expression was enriched in muscle and cardiac tissues. The upstream 1500 bases from calculated orthologous genes were extracted from the human reference set. A set of common motifs were discovered in these promoters. Slightly over one third of these motifs were identified as known TFBSs including known muscle specific binding sites. This analysis also predicted several highly statistically significantly overrepresented sites that may be novel TFBS. An independent analysis of the equivalent bovine genomic sequences was also done, this gave less detailed results than the human analysis due to both the quality of orthologue prediction and assembly in promoter regions. However, the most common motifs could be detected in both sets. Conclusion Using promoter sequences from human genes is a useful approach when studying gene expression in species with limited or non-existing genomic sequence. As the bovine genome becomes better annotated it can in turn serve as the reference genome for other agriculturally important ruminants, such as sheep, goat and deer.

Published
2007
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14. Establishment of a pipeline to analyse non-synonymous SNPs in Bos taurus

Author

Schreiber Mark, Morris Chris A, McCulloch Alan F, Dodds Ken G, Cullen Neil G, Manley Tim R, Glass Belinda C, Keane Orla M, Lee Michael A, Warren Jonathan, Zadissa Amonida, Wilson Theresa, and McEwan John C

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Single nucleotide polymorphisms (SNPs) are an abundant form of genetic variation in the genome of every species and are useful for gene mapping and association studies. Of particular interest are non-synonymous SNPs, which may alter protein function and phenotype. We therefore examined bovine expressed sequences for non-synonymous SNPs and validated and tested selected SNPs for their association with measured traits. Results Over 500,000 public bovine expressed sequence tagged (EST) sequences were used to search for coding SNPs (cSNPs). A total of 15,353 SNPs were detected in the transcribed sequences studied, of which 6,325 were predicted to be coding SNPs with the remaining 9,028 SNPs presumed to be in untranslated regions. Of the cSNPs detected, 2,868 were predicted to result in a change in the amino acid encoded. In order to determine the actual number of non-synonymous polymorphic SNPs we designed assays for 920 of the putative SNPs. These SNPs were then genotyped through a panel of cattle DNA pools using chip-based MALDI-TOF mass spectrometry. Of the SNPs tested, 29% were found to be polymorphic with a minor allele frequency >10%. A subset of the SNPs was genotyped through animal resources in order to look for association with age of puberty, facial eczema resistance or meat yield. Three SNPs were nominally associated with resistance to the disease facial eczema (P < 0.01). Conclusion We have identified 15,353 putative SNPs in or close to bovine genes and 2,868 of these SNPs were predicted to be non-synonymous. Approximately 29% of the non-synonymous SNPs were polymorphic and common with a minor allele frequency >10%. Of the SNPs detected in this study, 99% have not been previously reported. These novel SNPs will be useful for association studies or gene mapping.

Published
2006
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15. Gene expression profiling of Naïve sheep genetically resistant and susceptible to gastrointestinal nematodes

Author

Hyndman Dianne L, Wilson Theresa, Zadissa Amonida, Keane Orla M, Greer Gordon J, Baird David B, McCulloch Alan F, Crawford Allan M, and McEwan John C

Subjects
Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

Abstract Background Gastrointestinal nematodes constitute a major cause of morbidity and mortality in grazing ruminants. Individual animals or breeds, however, are known to differ in their resistance to infection. Gene expression profiling allows us to examine large numbers of transcripts simultaneously in order to identify those transcripts that contribute to an animal's susceptibility or resistance. Results With the goal of identifying genes with a differential pattern of expression between sheep genetically resistant and susceptible to gastrointestinal nematodes, a 20,000 spot ovine cDNA microarray was constructed. This array was used to interrogate the expression of 9,238 known genes in duodenum tissue of four resistant and four susceptible female lambs. Naïve animals were used in order to look at genes that were differentially expressed in the absence of infection with gastrointestinal nematodes. Forty one unique known genes were identified that were differentially expressed between the resistant and susceptible animals. Northern blotting of a selection of the genes confirmed differential expression. The differentially expressed genes had a variety of functions, although many genes relating to the stress response and response to stimulus were more highly expressed in the susceptible animals. Conclusion We have constructed the first reported ovine microarray and used this array to examine gene expression in lambs genetically resistant and susceptible to gastrointestinal nematode infection. This study indicates that susceptible animals appear to be generating a hyper-sensitive immune response to non-nematode challenges. The gastrointestinal tract of susceptible animals is therefore under stress and compromised even in the absence of gastrointestinal nematodes. These factors may contribute to the genetic susceptibility of these animals.

Published
2006
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16. Ensembl 2019

Author

Cunningham, Fiona, primary, Achuthan, Premanand, additional, Akanni, Wasiu, additional, Allen, James, additional, Amode, M Ridwan, additional, Armean, Irina M, additional, Bennett, Ruth, additional, Bhai, Jyothish, additional, Billis, Konstantinos, additional, Boddu, Sanjay, additional, Cummins, Carla, additional, Davidson, Claire, additional, Dodiya, Kamalkumar Jayantilal, additional, Gall, Astrid, additional, Girón, Carlos García, additional, Gil, Laurent, additional, Grego, Tiago, additional, Haggerty, Leanne, additional, Haskell, Erin, additional, Hourlier, Thibaut, additional, Izuogu, Osagie G, additional, Janacek, Sophie H, additional, Juettemann, Thomas, additional, Kay, Mike, additional, Laird, Matthew R, additional, Lavidas, Ilias, additional, Liu, Zhicheng, additional, Loveland, Jane E, additional, Marugán, José C, additional, Maurel, Thomas, additional, McMahon, Aoife C, additional, Moore, Benjamin, additional, Morales, Joannella, additional, Mudge, Jonathan M, additional, Nuhn, Michael, additional, Ogeh, Denye, additional, Parker, Anne, additional, Parton, Andrew, additional, Patricio, Mateus, additional, Abdul Salam, Ahamed Imran, additional, Schmitt, Bianca M, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Sparrow, Helen, additional, Stapleton, Eloise, additional, Szuba, Marek, additional, Taylor, Kieron, additional, Threadgold, Glen, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Walts, Brandon, additional, Winterbottom, Andrea, additional, Zadissa, Amonida, additional, Chakiachvili, Marc, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, Kostadima, Myrto, additional, Langridge, Nick, additional, Martin, Fergal J, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Staines, Daniel M, additional, Trevanion, Stephen J, additional, Aken, Bronwen L, additional, Yates, Andrew D, additional, Zerbino, Daniel R, additional, and Flicek, Paul, additional

Published
2018
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17. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Author

Thybert, David, primary, Roller, Maša, additional, Navarro, Fábio C.P., additional, Fiddes, Ian, additional, Streeter, Ian, additional, Feig, Christine, additional, Martin-Galvez, David, additional, Kolmogorov, Mikhail, additional, Janoušek, Václav, additional, Akanni, Wasiu, additional, Aken, Bronwen, additional, Aldridge, Sarah, additional, Chakrapani, Varshith, additional, Chow, William, additional, Clarke, Laura, additional, Cummins, Carla, additional, Doran, Anthony, additional, Dunn, Matthew, additional, Goodstadt, Leo, additional, Howe, Kerstin, additional, Howell, Matthew, additional, Josselin, Ambre-Aurore, additional, Karn, Robert C., additional, Laukaitis, Christina M., additional, Jingtao, Lilue, additional, Martin, Fergal, additional, Muffato, Matthieu, additional, Nachtweide, Stefanie, additional, Quail, Michael A., additional, Sisu, Cristina, additional, Stanke, Mario, additional, Stefflova, Klara, additional, Van Oosterhout, Cock, additional, Veyrunes, Frederic, additional, Ward, Ben, additional, Yang, Fengtang, additional, Yazdanifar, Golbahar, additional, Zadissa, Amonida, additional, Adams, David J., additional, Brazma, Alvis, additional, Gerstein, Mark, additional, Paten, Benedict, additional, Pham, Son, additional, Keane, Thomas M., additional, Odom, Duncan T., additional, and Flicek, Paul, additional

Published
2018
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18. Ensembl 2018

Author

Zerbino, Daniel R, primary, Achuthan, Premanand, additional, Akanni, Wasiu, additional, Amode, M Ridwan, additional, Barrell, Daniel, additional, Bhai, Jyothish, additional, Billis, Konstantinos, additional, Cummins, Carla, additional, Gall, Astrid, additional, Girón, Carlos García, additional, Gil, Laurent, additional, Gordon, Leo, additional, Haggerty, Leanne, additional, Haskell, Erin, additional, Hourlier, Thibaut, additional, Izuogu, Osagie G, additional, Janacek, Sophie H, additional, Juettemann, Thomas, additional, To, Jimmy Kiang, additional, Laird, Matthew R, additional, Lavidas, Ilias, additional, Liu, Zhicheng, additional, Loveland, Jane E, additional, Maurel, Thomas, additional, McLaren, William, additional, Moore, Benjamin, additional, Mudge, Jonathan, additional, Murphy, Daniel N, additional, Newman, Victoria, additional, Nuhn, Michael, additional, Ogeh, Denye, additional, Ong, Chuang Kee, additional, Parker, Anne, additional, Patricio, Mateus, additional, Riat, Harpreet Singh, additional, Schuilenburg, Helen, additional, Sheppard, Dan, additional, Sparrow, Helen, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Walts, Brandon, additional, Zadissa, Amonida, additional, Frankish, Adam, additional, Hunt, Sarah E, additional, Kostadima, Myrto, additional, Langridge, Nicholas, additional, Martin, Fergal J, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Staines, Dan M, additional, Trevanion, Stephen J, additional, Aken, Bronwen L, additional, Cunningham, Fiona, additional, Yates, Andrew, additional, and Flicek, Paul, additional

Published
2017
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19. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomes

Author

Thybert, David, primary, Roller, Maša, additional, Navarro, Fábio C.P., additional, Fiddes, Ian, additional, Streeter, Ian, additional, Feig, Christine, additional, Martin-Galvez, David, additional, Kolmogorov, Mikhail, additional, Janoušek, Václav, additional, Akanni, Wasiu, additional, Aken, Bronwen, additional, Aldridge, Sarah, additional, Chakrapani, Varshith, additional, Chow, William, additional, Clarke, Laura, additional, Cummins, Carla, additional, Doran, Anthony, additional, Dunn, Matthew, additional, Goodstadt, Leo, additional, Howe, Kerstin, additional, Howell, Matthew, additional, Josselin, Ambre-Aurore, additional, Karn, Robert C., additional, Laukaitis, Christina M., additional, Jingtao, Lilue, additional, Martin, Fergal, additional, Muffato, Matthieu, additional, Quail, Michael A., additional, Sisu, Cristina, additional, Stanke, Mario, additional, Stefflova, Klara, additional, Oosterhout, Cock Van, additional, Veyrunes, Frederic, additional, Ward, Ben, additional, Yang, Fengtang, additional, Yazdanifar, Golbahar, additional, Zadissa, Amonida, additional, Adams, David, additional, Brazma, Alvis, additional, Gerstein, Mark, additional, Paten, Benedict, additional, Pham, Son, additional, Keane, Thomas, additional, Odom, Duncan T, additional, and Flicek, Paul, additional

Published
2017
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20. The Ensembl gene annotation system

Author

Aken, Bronwen L., Ayling, Sarah, Barrell, Daniel, Clarke, Laura, Curwen, Valery, Fairley, Susan, Banet, Julio Fernandez, Billis, Konstantinos, Giron, Carlos Garcia, Hourlier, Thibaut, Howe, Kevin, Kähäri, Andreas, Kokocinski, Felix, Martin, Fergal J., Murphy, Daniel N., Nag, Rishi, Ruffier, Magali, Schuster, Michael, Tang, Y. Amy, Vogel, Jan-Hinnerk, White, Simon, Zadissa, Amonida, Flicek, Paul, Searle, Stephen M. J., Aken, Bronwen L., Ayling, Sarah, Barrell, Daniel, Clarke, Laura, Curwen, Valery, Fairley, Susan, Banet, Julio Fernandez, Billis, Konstantinos, Giron, Carlos Garcia, Hourlier, Thibaut, Howe, Kevin, Kähäri, Andreas, Kokocinski, Felix, Martin, Fergal J., Murphy, Daniel N., Nag, Rishi, Ruffier, Magali, Schuster, Michael, Tang, Y. Amy, Vogel, Jan-Hinnerk, White, Simon, Zadissa, Amonida, Flicek, Paul, and Searle, Stephen M. J.

Abstract

The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.

Published
2016
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21. Ensembl 2017

Author

Aken, Bronwen L., primary, Achuthan, Premanand, additional, Akanni, Wasiu, additional, Amode, M. Ridwan, additional, Bernsdorff, Friederike, additional, Bhai, Jyothish, additional, Billis, Konstantinos, additional, Carvalho-Silva, Denise, additional, Cummins, Carla, additional, Clapham, Peter, additional, Gil, Laurent, additional, Girón, Carlos García, additional, Gordon, Leo, additional, Hourlier, Thibaut, additional, Hunt, Sarah E., additional, Janacek, Sophie H., additional, Juettemann, Thomas, additional, Keenan, Stephen, additional, Laird, Matthew R., additional, Lavidas, Ilias, additional, Maurel, Thomas, additional, McLaren, William, additional, Moore, Benjamin, additional, Murphy, Daniel N., additional, Nag, Rishi, additional, Newman, Victoria, additional, Nuhn, Michael, additional, Ong, Chuang Kee, additional, Parker, Anne, additional, Patricio, Mateus, additional, Riat, Harpreet Singh, additional, Sheppard, Daniel, additional, Sparrow, Helen, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Walts, Brandon, additional, Wilder, Steven P., additional, Zadissa, Amonida, additional, Kostadima, Myrto, additional, Martin, Fergal J., additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Staines, Daniel M., additional, Trevanion, Stephen J., additional, Cunningham, Fiona, additional, Yates, Andrew, additional, Zerbino, Daniel R., additional, and Flicek, Paul, additional

Published
2016
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22. The Ensembl gene annotation system

Author

Aken, Bronwen L., primary, Ayling, Sarah, additional, Barrell, Daniel, additional, Clarke, Laura, additional, Curwen, Valery, additional, Fairley, Susan, additional, Fernandez Banet, Julio, additional, Billis, Konstantinos, additional, García Girón, Carlos, additional, Hourlier, Thibaut, additional, Howe, Kevin, additional, Kähäri, Andreas, additional, Kokocinski, Felix, additional, Martin, Fergal J., additional, Murphy, Daniel N., additional, Nag, Rishi, additional, Ruffier, Magali, additional, Schuster, Michael, additional, Tang, Y. Amy, additional, Vogel, Jan-Hinnerk, additional, White, Simon, additional, Zadissa, Amonida, additional, Flicek, Paul, additional, and Searle, Stephen M. J., additional

Published
2016
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23. Ensembl 2016

Author

Yates, Andrew, primary, Akanni, Wasiu, additional, Amode, M. Ridwan, additional, Barrell, Daniel, additional, Billis, Konstantinos, additional, Carvalho-Silva, Denise, additional, Cummins, Carla, additional, Clapham, Peter, additional, Fitzgerald, Stephen, additional, Gil, Laurent, additional, Girón, Carlos García, additional, Gordon, Leo, additional, Hourlier, Thibaut, additional, Hunt, Sarah E., additional, Janacek, Sophie H., additional, Johnson, Nathan, additional, Juettemann, Thomas, additional, Keenan, Stephen, additional, Lavidas, Ilias, additional, Martin, Fergal J., additional, Maurel, Thomas, additional, McLaren, William, additional, Murphy, Daniel N., additional, Nag, Rishi, additional, Nuhn, Michael, additional, Parker, Anne, additional, Patricio, Mateus, additional, Pignatelli, Miguel, additional, Rahtz, Matthew, additional, Riat, Harpreet Singh, additional, Sheppard, Daniel, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Wilder, Steven P., additional, Zadissa, Amonida, additional, Birney, Ewan, additional, Harrow, Jennifer, additional, Muffato, Matthieu, additional, Perry, Emily, additional, Ruffier, Magali, additional, Spudich, Giulietta, additional, Trevanion, Stephen J., additional, Cunningham, Fiona, additional, Aken, Bronwen L., additional, Zerbino, Daniel R., additional, and Flicek, Paul, additional

Published
2015
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24. The BioMart community portal: an innovative alternative to large, centralized data repositories

Author

Smedley, Damian, primary, Haider, Syed, additional, Durinck, Steffen, additional, Pandini, Luca, additional, Provero, Paolo, additional, Allen, James, additional, Arnaiz, Olivier, additional, Awedh, Mohammad Hamza, additional, Baldock, Richard, additional, Barbiera, Giulia, additional, Bardou, Philippe, additional, Beck, Tim, additional, Blake, Andrew, additional, Bonierbale, Merideth, additional, Brookes, Anthony J., additional, Bucci, Gabriele, additional, Buetti, Iwan, additional, Burge, Sarah, additional, Cabau, Cédric, additional, Carlson, Joseph W., additional, Chelala, Claude, additional, Chrysostomou, Charalambos, additional, Cittaro, Davide, additional, Collin, Olivier, additional, Cordova, Raul, additional, Cutts, Rosalind J., additional, Dassi, Erik, additional, Genova, Alex Di, additional, Djari, Anis, additional, Esposito, Anthony, additional, Estrella, Heather, additional, Eyras, Eduardo, additional, Fernandez-Banet, Julio, additional, Forbes, Simon, additional, Free, Robert C., additional, Fujisawa, Takatomo, additional, Gadaleta, Emanuela, additional, Garcia-Manteiga, Jose M., additional, Goodstein, David, additional, Gray, Kristian, additional, Guerra-Assunção, José Afonso, additional, Haggarty, Bernard, additional, Han, Dong-Jin, additional, Han, Byung Woo, additional, Harris, Todd, additional, Harshbarger, Jayson, additional, Hastings, Robert K., additional, Hayes, Richard D., additional, Hoede, Claire, additional, Hu, Shen, additional, Hu, Zhi-Liang, additional, Hutchins, Lucie, additional, Kan, Zhengyan, additional, Kawaji, Hideya, additional, Keliet, Aminah, additional, Kerhornou, Arnaud, additional, Kim, Sunghoon, additional, Kinsella, Rhoda, additional, Klopp, Christophe, additional, Kong, Lei, additional, Lawson, Daniel, additional, Lazarevic, Dejan, additional, Lee, Ji-Hyun, additional, Letellier, Thomas, additional, Li, Chuan-Yun, additional, Lio, Pietro, additional, Liu, Chu-Jun, additional, Luo, Jie, additional, Maass, Alejandro, additional, Mariette, Jerome, additional, Maurel, Thomas, additional, Merella, Stefania, additional, Mohamed, Azza Mostafa, additional, Moreews, Francois, additional, Nabihoudine, Ibounyamine, additional, Ndegwa, Nelson, additional, Noirot, Céline, additional, Perez-Llamas, Cristian, additional, Primig, Michael, additional, Quattrone, Alessandro, additional, Quesneville, Hadi, additional, Rambaldi, Davide, additional, Reecy, James, additional, Riba, Michela, additional, Rosanoff, Steven, additional, Saddiq, Amna Ali, additional, Salas, Elisa, additional, Sallou, Olivier, additional, Shepherd, Rebecca, additional, Simon, Reinhard, additional, Sperling, Linda, additional, Spooner, William, additional, Staines, Daniel M., additional, Steinbach, Delphine, additional, Stone, Kevin, additional, Stupka, Elia, additional, Teague, Jon W., additional, Dayem Ullah, Abu Z., additional, Wang, Jun, additional, Ware, Doreen, additional, Wong-Erasmus, Marie, additional, Youens-Clark, Ken, additional, Zadissa, Amonida, additional, Zhang, Shi-Jian, additional, and Kasprzyk, Arek, additional

Published
2015
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25. Ensembl 2015

Author

Cunningham, Fiona, primary, Amode, M. Ridwan, additional, Barrell, Daniel, additional, Beal, Kathryn, additional, Billis, Konstantinos, additional, Brent, Simon, additional, Carvalho-Silva, Denise, additional, Clapham, Peter, additional, Coates, Guy, additional, Fitzgerald, Stephen, additional, Gil, Laurent, additional, Girón, Carlos García, additional, Gordon, Leo, additional, Hourlier, Thibaut, additional, Hunt, Sarah E., additional, Janacek, Sophie H., additional, Johnson, Nathan, additional, Juettemann, Thomas, additional, Kähäri, Andreas K., additional, Keenan, Stephen, additional, Martin, Fergal J., additional, Maurel, Thomas, additional, McLaren, William, additional, Murphy, Daniel N., additional, Nag, Rishi, additional, Overduin, Bert, additional, Parker, Anne, additional, Patricio, Mateus, additional, Perry, Emily, additional, Pignatelli, Miguel, additional, Riat, Harpreet Singh, additional, Sheppard, Daniel, additional, Taylor, Kieron, additional, Thormann, Anja, additional, Vullo, Alessandro, additional, Wilder, Steven P., additional, Zadissa, Amonida, additional, Aken, Bronwen L., additional, Birney, Ewan, additional, Harrow, Jennifer, additional, Kinsella, Rhoda, additional, Muffato, Matthieu, additional, Ruffier, Magali, additional, Searle, Stephen M.J., additional, Spudich, Giulietta, additional, Trevanion, Stephen J., additional, Yates, Andy, additional, Zerbino, Daniel R., additional, and Flicek, Paul, additional

Published
2014
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26. Erratum: Corrigendum: The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

Author

Wang, Zhuo, primary, Pascual-Anaya, Juan, additional, Zadissa, Amonida, additional, Li, Wenqi, additional, Niimura, Yoshihito, additional, Huang, Zhiyong, additional, Li, Chunyi, additional, White, Simon, additional, Xiong, Zhiqiang, additional, Fang, Dongming, additional, Wang, Bo, additional, Ming, Yao, additional, Chen, Yan, additional, Zheng, Yuan, additional, Kuraku, Shigehiro, additional, Pignatelli, Miguel, additional, Herrero, Javier, additional, Beal, Kathryn, additional, Nozawa, Masafumi, additional, Li, Qiye, additional, Wang, Juan, additional, Zhang, Hongyan, additional, Yu, Lili, additional, Shigenobu, Shuji, additional, Wang, Junyi, additional, Liu, Jiannan, additional, Flicek, Paul, additional, Searle, Steve, additional, Wang, Jun, additional, Kuratani, Shigeru, additional, Yin, Ye, additional, Aken, Bronwen, additional, Zhang, Guojie, additional, and Irie, Naoki, additional

Published
2014
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27. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

Author

Wang, Zhuo, Pascual-Anaya, Juan, Zadissa, Amonida, Li, Wenqi, Niimura, Yoshihito, Huang, Zhiyong, Li, Chunyi, White, Simon, Xiong, Zhiqiang, Fang, Dongming, Wang, Bo, Ming, Yao, Chen, Yan, Zheng, Yuan, Kuraku, Shigehiro, Pignatelli, Miguel, Herrero, Javier, Beal, Kathryn, Nozawa, Masafumi, Li, Qiye, Wang, Juan, Zhang, Hongyan, Yu, Lili, Shigenobu, Shuji, Wang, Junyi, Liu, Jiannan, Flicek, Paul, Searle, Steve, Wang, Jun, Kuratani, Shigeru, Yin, Ye, Aken, Bronwen, Zhang, Guojie, Irie, Naoki, Wang, Zhuo, Pascual-Anaya, Juan, Zadissa, Amonida, Li, Wenqi, Niimura, Yoshihito, Huang, Zhiyong, Li, Chunyi, White, Simon, Xiong, Zhiqiang, Fang, Dongming, Wang, Bo, Ming, Yao, Chen, Yan, Zheng, Yuan, Kuraku, Shigehiro, Pignatelli, Miguel, Herrero, Javier, Beal, Kathryn, Nozawa, Masafumi, Li, Qiye, Wang, Juan, Zhang, Hongyan, Yu, Lili, Shigenobu, Shuji, Wang, Junyi, Liu, Jiannan, Flicek, Paul, Searle, Steve, Wang, Jun, Kuratani, Shigeru, Yin, Ye, Aken, Bronwen, Zhang, Guojie, and Irie, Naoki

Published
2013

28. Repeat associated mechanisms of genome evolution and function revealed by the Mus caroliand Mus paharigenomes

Author

Thybert, David, Roller, Maša, Navarro, Fšábio C.P., Fiddes, Ian, Streeter, Ian, Feig, Christine, Martin-Galvez, David, Kolmogorov, Mikhail, Janoušáášek, Všááclav, 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., and Flicek, Paul

Abstract

Understanding the mechanisms driving lineage-specific evolution in both primates and rodents has been hindered by the lack of sister clades with a similar phylogenetic structure having high-quality genome assemblies. Here, we have created chromosome-level assemblies of the Mus caroliand Mus paharigenomes. Together with the Mus musculusand Rattus norvegicusgenomes, this set of rodent genomes is similar in divergence times to the Hominidae (human-chimpanzee-gorilla-orangutan). By comparing the evolutionary dynamics between the Muridae and Hominidae, we identified punctate events of chromosome reshuffling that shaped the ancestral karyotype of Mus musculusand Mus carolibetween 3 and 6 million yr ago, but that are absent in the Hominidae. Hominidae show between four- and sevenfold lower rates of nucleotide change and feature turnover in both neutral and functional sequences, suggesting an underlying coherence to the Muridae acceleration. Our system of matched, high-quality genome assemblies revealed how specific classes of repeats can play lineage-specific roles in related species. Recent LINE activity has remodeled protein-coding loci to a greater extent across the Muridae than the Hominidae, with functional consequences at the species level such as reproductive isolation. Furthermore, we charted a Muridae-specific retrotransposon expansion at unprecedented resolution, revealing how a single nucleotide mutation transformed a specific SINE element into an active CTCF binding site carrier specifically in Mus caroli, which resulted in thousands of novel, species-specific CTCF binding sites. Our results show that the comparison of matched phylogenetic sets of genomes will be an increasingly powerful strategy for understanding mammalian biology.

Published
2018
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29. The genome of the green anole lizard and a comparative analysis with birds and mammals

Author

Alfoeldi, Jessica, Di Palma, Federica, Grabherr, Manfred, Williams, Christina, Kong, Lesheng, Mauceli, Evan, Russell, Pamela, Lowe, Craig B., Glor, Richard E., Jaffe, Jacob D., Ray, David A., Boissinot, Stephane, Shedlock, Andrew M., Botka, Christopher, Castoe, Todd A., Colbourne, John K., Fujita, Matthew K., Moreno, Ricardo Godinez, ten Hallers, Boudewijn F., Haussler, David, Heger, Andreas, Heiman, David, Janes, Daniel E., Johnson, Jeremy, de Jong, Pieter J., Koriabine, Maxim Y., Lara, Marcia, Novick, Peter A., Organ, Chris L., Peach, Sally E., Poe, Steven, Pollock, David D., de Queiroz, Kevin, Sanger, Thomas, Searle, Steve, Smith, Jeremy D., Smith, Zachary, Swofford, Ross, Turner-Maier, Jason, Wade, Juli, Young, Sarah, Zadissa, Amonida, Edwards, Scott V., Glenn, Travis C., Schneider, Christopher J., Losos, Jonathan B., Lander, Eric S., Breen, Matthew, Ponting, Chris P., Lindblad-Toh, Kerstin, Alfoeldi, Jessica, Di Palma, Federica, Grabherr, Manfred, Williams, Christina, Kong, Lesheng, Mauceli, Evan, Russell, Pamela, Lowe, Craig B., Glor, Richard E., Jaffe, Jacob D., Ray, David A., Boissinot, Stephane, Shedlock, Andrew M., Botka, Christopher, Castoe, Todd A., Colbourne, John K., Fujita, Matthew K., Moreno, Ricardo Godinez, ten Hallers, Boudewijn F., Haussler, David, Heger, Andreas, Heiman, David, Janes, Daniel E., Johnson, Jeremy, de Jong, Pieter J., Koriabine, Maxim Y., Lara, Marcia, Novick, Peter A., Organ, Chris L., Peach, Sally E., Poe, Steven, Pollock, David D., de Queiroz, Kevin, Sanger, Thomas, Searle, Steve, Smith, Jeremy D., Smith, Zachary, Swofford, Ross, Turner-Maier, Jason, Wade, Juli, Young, Sarah, Zadissa, Amonida, Edwards, Scott V., Glenn, Travis C., Schneider, Christopher J., Losos, Jonathan B., Lander, Eric S., Breen, Matthew, Ponting, Chris P., and Lindblad-Toh, Kerstin

Abstract

The evolution of the amniotic egg was one of the great evolutionary innovations in the history of life, freeing vertebrates from an obligatory connection to water and thus permitting the conquest of terrestrial environments(1). Among amniotes, genome sequences are available for mammals and birds(2-4), but not for non-avian reptiles. Here we report the genome sequence of the North American green anole lizard, Anolis carolinensis. We find that A. carolinensis microchromosomes are highly syntenic with chicken microchromosomes, yet do not exhibit the high GC and low repeat content that are characteristic of avian microchromosomes(2). Also, A. carolinensis mobile elements are very young and diverse-more so than in any other sequenced amniote genome. The GC content of this lizard genome is also unusual in its homogeneity, unlike the regionally variable GC content found in mammals and birds(5). We describe and assign sequence to the previously unknown A. carolinensis X chromosome. Comparative gene analysis shows that amniote egg proteins have evolved significantly more rapidly than other proteins. An anole phylogeny resolves basal branches to illuminate the history of their repeated adaptive radiations.

Published
2011
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30. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan

Author

Wang, Zhuo, primary, Pascual-Anaya, Juan, additional, Zadissa, Amonida, additional, Li, Wenqi, additional, Niimura, Yoshihito, additional, Huang, Zhiyong, additional, Li, Chunyi, additional, White, Simon, additional, Xiong, Zhiqiang, additional, Fang, Dongming, additional, Wang, Bo, additional, Ming, Yao, additional, Chen, Yan, additional, Zheng, Yuan, additional, Kuraku, Shigehiro, additional, Pignatelli, Miguel, additional, Herrero, Javier, additional, Beal, Kathryn, additional, Nozawa, Masafumi, additional, Li, Qiye, additional, Wang, Juan, additional, Zhang, Hongyan, additional, Yu, Lili, additional, Shigenobu, Shuji, additional, Wang, Junyi, additional, Liu, Jiannan, additional, Flicek, Paul, additional, Searle, Steve, additional, Wang, Jun, additional, Kuratani, Shigeru, additional, Yin, Ye, additional, Aken, Bronwen, additional, Zhang, Guojie, additional, and Irie, Naoki, additional

Published
2013
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31. GENCODE: The reference human genome annotation for The ENCODE Project

Author

Harrow, Jennifer, primary, Frankish, Adam, additional, Gonzalez, Jose M., additional, Tapanari, Electra, additional, Diekhans, Mark, additional, Kokocinski, Felix, additional, Aken, Bronwen L., additional, Barrell, Daniel, additional, Zadissa, Amonida, additional, Searle, Stephen, additional, Barnes, If, additional, Bignell, Alexandra, additional, Boychenko, Veronika, additional, Hunt, Toby, additional, Kay, Mike, additional, Mukherjee, Gaurab, additional, Rajan, Jeena, additional, Despacio-Reyes, Gloria, additional, Saunders, Gary, additional, Steward, Charles, additional, Harte, Rachel, additional, Lin, Michael, additional, Howald, Cédric, additional, Tanzer, Andrea, additional, Derrien, Thomas, additional, Chrast, Jacqueline, additional, Walters, Nathalie, additional, Balasubramanian, Suganthi, additional, Pei, Baikang, additional, Tress, Michael, additional, Rodriguez, Jose Manuel, additional, Ezkurdia, Iakes, additional, van Baren, Jeltje, additional, Brent, Michael, additional, Haussler, David, additional, Kellis, Manolis, additional, Valencia, Alfonso, additional, Reymond, Alexandre, additional, Gerstein, Mark, additional, Guigó, Roderic, additional, and Hubbard, Tim J., additional

Published
2012
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32. Ensembl's 10th year

Author

Flicek, Paul, primary, Aken, Bronwen L., additional, Ballester, Benoit, additional, Beal, Kathryn, additional, Bragin, Eugene, additional, Brent, Simon, additional, Chen, Yuan, additional, Clapham, Peter, additional, Coates, Guy, additional, Fairley, Susan, additional, Fitzgerald, Stephen, additional, Fernandez-Banet, Julio, additional, Gordon, Leo, additional, Gräf, Stefan, additional, Haider, Syed, additional, Hammond, Martin, additional, Howe, Kerstin, additional, Jenkinson, Andrew, additional, Johnson, Nathan, additional, Kähäri, Andreas, additional, Keefe, Damian, additional, Keenan, Stephen, additional, Kinsella, Rhoda, additional, Kokocinski, Felix, additional, Koscielny, Gautier, additional, Kulesha, Eugene, additional, Lawson, Daniel, additional, Longden, Ian, additional, Massingham, Tim, additional, McLaren, William, additional, Megy, Karine, additional, Overduin, Bert, additional, Pritchard, Bethan, additional, Rios, Daniel, additional, Ruffier, Magali, additional, Schuster, Michael, additional, Slater, Guy, additional, Smedley, Damian, additional, Spudich, Giulietta, additional, Tang, Y. Amy, additional, Trevanion, Stephen, additional, Vilella, Albert, additional, Vogel, Jan, additional, White, Simon, additional, Wilder, Steven P., additional, Zadissa, Amonida, additional, Birney, Ewan, additional, Cunningham, Fiona, additional, Dunham, Ian, additional, Durbin, Richard, additional, Fernández-Suarez, Xosé M., additional, Herrero, Javier, additional, Hubbard, Tim J. P., additional, Parker, Anne, additional, Proctor, Glenn, additional, Smith, James, additional, and Searle, Stephen M. J., additional

Published
2009
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34. Establishment of a pipeline to analyse non-synonymous SNPs in Bos taurus

Author

Lee, Michael A, primary, Keane, Orla M, additional, Glass, Belinda C, additional, Manley, Tim R, additional, Cullen, Neil G, additional, Dodds, Ken G, additional, McCulloch, Alan F, additional, Morris, Chris A, additional, Schreiber, Mark, additional, Warren, Jonathan, additional, Zadissa, Amonida, additional, Wilson, Theresa, additional, and McEwan, John C, additional

Published
2006
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37. The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan (vol 45, pg 701, 2013)

Author

Wang, Zhuo, Pascual-Anaya, Juan, Zadissa, Amonida, Li, Wenqi, Niimura, Yoshihito, Huang, Zhiyong, Li, Chunyi, White, Simon, Xiong, Zhiqiang, Fang, Dongming, Wang, Bo, Ming, Yao, Chen, Yan, Zheng, Yuan, Kuraku, Shigehiro, Pignatelli, Miguel, Herrero, Javier, Beal, Kathryn, Nozawa, Masafumi, Li, Qiye, Wang, Juan, Zhang, Hongyan, Yu, Lili, Shigenobu, Shuji, Wang, Junyi, Liu, Jiannan, Flicek, Paul, Searle, Steve, Wang, Jun, Shigeru Kuratani, Yin, Ye, Aken, Bronwen, Zhang, Guojie, and Irie, Naoki

38. Corrigendum: The draft genomes of soft-shell turtle and green sea turtle yield insights into the development and evolution of the turtle-specific body plan.

Author

Wang, Zhuo, Pascual-Anaya, Juan, Zadissa, Amonida, Li, Wenqi, Niimura, Yoshihito, Huang, Zhiyong, Li, Chunyi, White, Simon, Xiong, Zhiqiang, Fang, Dongming, Wang, Bo, Ming, Yao, Chen, Yan, Zheng, Yuan, Kuraku, Shigehiro, Pignatelli, Miguel, Herrero, Javier, Beal, Kathryn, Nozawa, Masafumi, and Li, Qiye

Subjects
TURTLES, GENOMES
Abstract

A correction to an article on genomes of soft-shell and green sea turtles published in a previous issue of the journal is presented.

Published
2014
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39. Data Mining, Quality and Management in the Life Sciences.

Author

Zadissa A and Apweiler R

Subjects
Data Management, Data Mining, Information Dissemination, Reproducibility of Results, Biological Science Disciplines
Abstract

With the evermore emphasis put on open science and its invaluable benefits to the scientific community, it is no longer the case where a research project simply ends with a scientific publication. The benefits of data sharing and reproducibility of results have taken the centerpiece within the life science research supported by FAIR principles that firmly underline the importance of open data. The current data-intensive multidisciplinary research has also highlighted the significance of how data is mined and managed. Here we describe some of the features adopted by EMBL-EBI data resources to support data mining, data quality, and data management. We also highlight how EMBL-EBI has responded to the current pandemic through its data resources., (© 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Published
2022
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40. Ensembl 2020.

Author

Yates AD, Achuthan P, Akanni W, Allen J, Allen J, Alvarez-Jarreta J, Amode MR, Armean IM, Azov AG, Bennett R, Bhai J, Billis K, Boddu S, Marugán JC, Cummins C, Davidson C, Dodiya K, Fatima R, Gall A, Giron CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Lavidas I, Le T, Lemos D, Martinez JG, Maurel T, McDowall M, McMahon A, Mohanan S, Moore B, Nuhn M, Oheh DN, Parker A, Parton A, Patricio M, Sakthivel MP, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sycheva M, Szuba M, Taylor K, Thormann A, Threadgold G, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Flint B, Frankish A, Hunt SE, IIsley G, Kostadima M, Langridge N, Loveland JE, Martin FJ, Morales J, Mudge JM, Muffato M, Perry E, Ruffier M, Trevanion SJ, Cunningham F, Howe KL, Zerbino DR, and Flicek P

Subjects
Algorithms, Animals, Computer Graphics, Databases, Protein, Genetic Variation, Genome-Wide Association Study, Genomics, Histones metabolism, Humans, Imaging, Three-Dimensional, Internet, Ligands, Search Engine, Software, Species Specificity, Transcriptome, User-Computer Interface, Web Browser, Computational Biology methods, Databases, Genetic, Epigenome, Molecular Sequence Annotation
Abstract

The Ensembl (https://www.ensembl.org) is a system for generating and distributing genome annotation such as genes, variation, regulation and comparative genomics across the vertebrate subphylum and key model organisms. The Ensembl annotation pipeline is capable of integrating experimental and reference data from multiple providers into a single integrated resource. Here, we present 94 newly annotated and re-annotated genomes, bringing the total number of genomes offered by Ensembl to 227. This represents the single largest expansion of the resource since its inception. We also detail our continued efforts to improve human annotation, developments in our epigenome analysis and display, a new tool for imputing causal genes from genome-wide association studies and visualisation of variation within a 3D protein model. Finally, we present information on our new website. Both software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license) and data updates made available four times a year., (© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2020
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41. Ensembl 2019.

Author

Cunningham F, Achuthan P, Akanni W, Allen J, Amode MR, Armean IM, Bennett R, Bhai J, Billis K, Boddu S, Cummins C, Davidson C, Dodiya KJ, Gall A, Girón CG, Gil L, Grego T, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, Kay M, Laird MR, Lavidas I, Liu Z, Loveland JE, Marugán JC, Maurel T, McMahon AC, Moore B, Morales J, Mudge JM, Nuhn M, Ogeh D, Parker A, Parton A, Patricio M, Abdul Salam AI, Schmitt BM, Schuilenburg H, Sheppard D, Sparrow H, Stapleton E, Szuba M, Taylor K, Threadgold G, Thormann A, Vullo A, Walts B, Winterbottom A, Zadissa A, Chakiachvili M, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Yates AD, Zerbino DR, and Flicek P

Subjects
Animals, Computational Biology trends, Humans, Mice, Molecular Sequence Annotation, Software, Databases, Genetic, Genome genetics, Genomics, Vertebrates genetics
Abstract

The Ensembl project (https://www.ensembl.org) makes key genomic data sets available to the entire scientific community without restrictions. Ensembl seeks to be a fundamental resource driving scientific progress by creating, maintaining and updating reference genome annotation and comparative genomics resources. This year we describe our new and expanded gene, variant and comparative annotation capabilities, which led to a 50% increase in the number of vertebrate genomes we support. We have also doubled the number of available human variants and added regulatory regions for many mouse cell types and developmental stages. Our data sets and tools are available via the Ensembl website as well as a through a RESTful webservice, Perl application programming interface and as data files for download.

Published
2019
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42. Ensembl 2018.

Author

Zerbino DR, Achuthan P, Akanni W, Amode MR, Barrell D, Bhai J, Billis K, Cummins C, Gall A, Girón CG, Gil L, Gordon L, Haggerty L, Haskell E, Hourlier T, Izuogu OG, Janacek SH, Juettemann T, To JK, Laird MR, Lavidas I, Liu Z, Loveland JE, Maurel T, McLaren W, Moore B, Mudge J, Murphy DN, Newman V, Nuhn M, Ogeh D, Ong CK, Parker A, Patricio M, Riat HS, Schuilenburg H, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Zadissa A, Frankish A, Hunt SE, Kostadima M, Langridge N, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Aken BL, Cunningham F, Yates A, and Flicek P

Subjects
Animals, Epigenomics, Genome, Human, Genome-Wide Association Study, Genomics, High-Throughput Nucleotide Sequencing, Humans, Molecular Sequence Annotation, Vertebrates genetics, Web Browser, Databases, Genetic, Datasets as Topic, Genome, Information Dissemination
Abstract

The Ensembl project has been aggregating, processing, integrating and redistributing genomic datasets since the initial releases of the draft human genome, with the aim of accelerating genomics research through rapid open distribution of public data. Large amounts of raw data are thus transformed into knowledge, which is made available via a multitude of channels, in particular our browser (http://www.ensembl.org). Over time, we have expanded in multiple directions. First, our resources describe multiple fields of genomics, in particular gene annotation, comparative genomics, genetics and epigenomics. Second, we cover a growing number of genome assemblies; Ensembl Release 90 contains exactly 100. Third, our databases feed simultaneously into an array of services designed around different use cases, ranging from quick browsing to genome-wide bioinformatic analysis. We present here the latest developments of the Ensembl project, with a focus on managing an increasing number of assemblies, supporting efforts in genome interpretation and improving our browser., (© The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2018
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43. Ensembl 2017.

Author

Aken BL, Achuthan P, Akanni W, Amode MR, Bernsdorff F, Bhai J, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Juettemann T, Keenan S, Laird MR, Lavidas I, Maurel T, McLaren W, Moore B, Murphy DN, Nag R, Newman V, Nuhn M, Ong CK, Parker A, Patricio M, Riat HS, Sheppard D, Sparrow H, Taylor K, Thormann A, Vullo A, Walts B, Wilder SP, Zadissa A, Kostadima M, Martin FJ, Muffato M, Perry E, Ruffier M, Staines DM, Trevanion SJ, Cunningham F, Yates A, Zerbino DR, and Flicek P

Subjects
Animals, Data Mining, Evolution, Molecular, Gene Expression Regulation, Genetic Variation, Genome, Human, Humans, Molecular Sequence Annotation, Species Specificity, Vertebrates, Computational Biology methods, Databases, Genetic, Genomics methods, Search Engine, Software, Web Browser
Abstract

Ensembl (www.ensembl.org) is a database and genome browser for enabling research on vertebrate genomes. We import, analyse, curate and integrate a diverse collection of large-scale reference data to create a more comprehensive view of genome biology than would be possible from any individual dataset. Our extensive data resources include evidence-based gene and regulatory region annotation, genome variation and gene trees. An accompanying suite of tools, infrastructure and programmatic access methods ensure uniform data analysis and distribution for all supported species. Together, these provide a comprehensive solution for large-scale and targeted genomics applications alike. Among many other developments over the past year, we have improved our resources for gene regulation and comparative genomics, and added CRISPR/Cas9 target sites. We released new browser functionality and tools, including improved filtering and prioritization of genome variation, Manhattan plot visualization for linkage disequilibrium and eQTL data, and an ontology search for phenotypes, traits and disease. We have also enhanced data discovery and access with a track hub registry and a selection of new REST end points. All Ensembl data are freely released to the scientific community and our source code is available via the open source Apache 2.0 license., (© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2017
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44. Ensembl 2016.

Author

Yates A, Akanni W, Amode MR, Barrell D, Billis K, Carvalho-Silva D, Cummins C, Clapham P, Fitzgerald S, Gil L, Girón CG, Gordon L, Hourlier T, Hunt SE, Janacek SH, Johnson N, Juettemann T, Keenan S, Lavidas I, Martin FJ, Maurel T, McLaren W, Murphy DN, Nag R, Nuhn M, Parker A, Patricio M, Pignatelli M, Rahtz M, Riat HS, Sheppard D, Taylor K, Thormann A, Vullo A, Wilder SP, Zadissa A, Birney E, Harrow J, Muffato M, Perry E, Ruffier M, Spudich G, Trevanion SJ, Cunningham F, Aken BL, Zerbino DR, and Flicek P

Subjects
Animals, Genes, Genetic Variation, Humans, Internet, Mice, Proteins genetics, Rats, Regulatory Sequences, Nucleic Acid, Software, Databases, Genetic, Genomics, Molecular Sequence Annotation
Abstract

The Ensembl project (http://www.ensembl.org) is a system for genome annotation, analysis, storage and dissemination designed to facilitate the access of genomic annotation from chordates and key model organisms. It provides access to data from 87 species across our main and early access Pre! websites. This year we introduced three newly annotated species and released numerous updates across our supported species with a concentration on data for the latest genome assemblies of human, mouse, zebrafish and rat. We also provided two data updates for the previous human assembly, GRCh37, through a dedicated website (http://grch37.ensembl.org). Our tools, in particular the VEP, have been improved significantly through integration of additional third party data. REST is now capable of larger-scale analysis and our regulatory data BioMart can deliver faster results. The website is now capable of displaying long-range interactions such as those found in cis-regulated datasets. Finally we have launched a website optimized for mobile devices providing views of genes, variants and phenotypes. Our data is made available without restriction and all code is available from our GitHub organization site (http://github.com/Ensembl) under an Apache 2.0 license., (© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.)

Published
2016
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