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ORCIDEwan Birney
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2020 – today
- 2024
[j71]Simone Maestri
, Mattia Furlan, Logan Mulroney, Lucia Coscujuela Tarrero, Camilla Ugolini, Fabio Dalla Pozza, Tommaso Leonardi, Ewan Birney, Francesco Nicassio, Mattia Pelizzola:
Benchmarking of computational methods for m6A profiling with Nanopore direct RNA sequencing. Briefings Bioinform. 25(2) (2024)- 2023
- [j70]Loïc Lannelongue, Hans-Erik G. Aronson, Alex Bateman, Ewan Birney, Talia Caplan, Martin Juckes, Johanna R. McEntyre, Andrew D. Morris, Gerry Reilly, Michael Inouye:
GREENER principles for environmentally sustainable computational science. Nat. Comput. Sci. 3(6): 514-521 (2023) - 2022
- [j69]Gaia Cantelli, Alex Bateman, Cath Brooksbank, Anton I. Petrov, Rahuman S. Malik-Sheriff, Michele Ide-Smith, Henning Hermjakob, Paul Flicek, Rolf Apweiler, Ewan Birney, Johanna R. McEntyre:
The European Bioinformatics Institute (EMBL-EBI) in 2021. Nucleic Acids Res. 50(D1): 11-19 (2022) - [j68]Mihaly Varadi, Stephen Anyango, Mandar S. Deshpande, Sreenath Nair, Cindy Natassia, Galabina Yordanova, David Yuan, Oana Stroe, Gemma Wood, Agata Laydon, Augustin Zídek, Tim Green, Kathryn Tunyasuvunakool, Stig Petersen, John Jumper, Ellen Clancy, Richard Green, Ankur Vora, Mira Lutfi, Michael Figurnov, Andrew Cowie, Nicole Hobbs, Pushmeet Kohli, Gerard J. Kleywegt, Ewan Birney, Demis Hassabis, Sameer Velankar:
AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models. Nucleic Acids Res. 50(D1): 439-444 (2022) - 2021
- [j67]Gaia Cantelli, Guy Cochrane, Cath Brooksbank, Ellen M. McDonagh, Paul Flicek, Johanna R. McEntyre, Ewan Birney, Rolf Apweiler:
The European Bioinformatics Institute: empowering cooperation in response to a global health crisis. Nucleic Acids Res. 49(Database-Issue): D29-D37 (2021) - [c7]Ewan Birney:
Big Data in Biology: What the Pandemic has Taught us. ITAT 2021: 19 - 2020
- [j66]Charles E. Cook, Oana Stroe, Guy Cochrane, Ewan Birney, Rolf Apweiler:
The European Bioinformatics Institute in 2020: building a global infrastructure of interconnected data resources for the life sciences. Nucleic Acids Res. 48(Database-Issue): D17-D23 (2020)
2010 – 2019
- 2019
- [j65]Jerome Kelleher, Mike Lin, Carl H. Albach, Ewan Birney, Robert Davies, Marina Gourtovaia, David Glazer, Cristina Y. González, David K. Jackson, Aaron Kemp, John Marshall, Andrew Nowak, Alexander Senf, Jaime M. Tovar-Corona, Alexander Vikhorev, Thomas M. Keane, GA4GH Streaming Task Team:
htsget: a protocol for securely streaming genomic data. Bioinform. 35(1): 119-121 (2019) - [j64]Charles E. Cook, Rodrigo Lopez, Oana Stroe, Guy Cochrane, Cath Brooksbank, Ewan Birney, Rolf Apweiler:
The European Bioinformatics Institute in 2018: tools, infrastructure and training. Nucleic Acids Res. 47(Database-Issue): D15-D22 (2019) - 2018
- [j63]Hannah Verena Meyer, Ewan Birney:
PhenotypeSimulator: A comprehensive framework for simulating multi-trait, multi-locus genotype to phenotype relationships. Bioinform. 34(17): 2951-2956 (2018) - [j62]Charles E. Cook, Mary Todd Bergman, Guy Cochrane, Rolf Apweiler, Ewan Birney:
The European Bioinformatics Institute in 2017: data coordination and integration. Nucleic Acids Res. 46(Database-Issue): D21-D29 (2018) - [j61]Carl Barton, Sandro Morganella, Øyvind Ødegård-Fougner, Stephanie Alexander, Jonas Ries, Tomas W. Fitzgerald, Jan Ellenberg, Ewan Birney:
ChromoTrace: Computational reconstruction of 3D chromosome configurations for super-resolution microscopy. PLoS Comput. Biol. 14(3) (2018) - 2017
- [j60]Gautier Koscielny, Peter An, Denise Carvalho-Silva, Jennifer A. Cham, Luca Fumis, Rippa Gasparyan, Samiul Hasan, Nikiforos Karamanis, Michael Maguire, Eliseo Papa, Andrea Pierleoni, Miguel Pignatelli, Theo Platt, Francis Rowland, Priyanka Wankar, A. Patrícia Bento, Tony Burdett, Antonio Fabregat, Simon A. Forbes, Anna Gaulton, Cristina Yenyxe González, Henning Hermjakob, Anne Hersey, Steven Jupe, Senay Kafkas, Maria Keays, Catherine Leroy, Francisco-Javier Lopez, María P. Magariños, James Malone, Johanna R. McEntyre, Alfonso Muñoz-Pomer Fuentes, Claire O'Donovan, Irene Papatheodorou, Helen E. Parkinson, Barbara Palka, Justin E. Paschall, Robert Petryszak, Naruemon Pratanwanich, Sirarat Sarntivijai, Gary Saunders, Konstantinos Sidiropoulos, Thomas Smith, Zbyslaw Sondka, Oliver Stegle, Y. Amy Tang, Edward Turner, Brendan W. Vaughan, Olga Vrousgou, Xavier Watkins, Maria Jesus Martin, Philippe Sanseau, Jessica Vamathevan, Ewan Birney, Jeffrey Barrett, Ian Dunham:
Open Targets: a platform for therapeutic target identification and validation. Nucleic Acids Res. 45(Database-Issue): D985-D994 (2017) - 2016
- [j59]Daniel R. Zerbino, Nathan Johnson, Thomas Juettemann, Daniel Sheppard, Steven P. Wilder, Ilias Lavidas, Michael Nuhn, Emily Perry, Quentin Raffaillac-Desfosses, Daniel Sobral, Damian Keefe, Stefan Gräf, Ikhlak Ahmed, Rhoda Kinsella, Bethan Pritchard, Simon Brent, M. Ridwan Amode, Anne Parker, Stephen J. Trevanion, Ewan Birney, Ian Dunham, Paul Flicek:
Ensembl regulation resources. Database J. Biol. Databases Curation 2016 (2016) - [j58]Charles E. Cook, Mary Todd Bergman, Robert D. Finn, Guy Cochrane, Ewan Birney, Rolf Apweiler:
The European Bioinformatics Institute in 2016: Data growth and integration. Nucleic Acids Res. 44(Database-Issue): 20-26 (2016) - [j57]Andrew D. Yates, Wasiu A. Akanni, M. Ridwan Amode, Daniel Barrell, Konstantinos Billis, Denise Carvalho-Silva, Carla A. Cummins, Peter Clapham, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Nathan Johnson, Thomas Juettemann, Stephen Keenan, Ilias Lavidas, Fergal J. Martin, Thomas Maurel, William M. McLaren, Daniel N. Murphy, Rishi Nag, Michael Nuhn, Anne Parker, Mateus Patricio, Miguel Pignatelli, Matthew Rahtz, Harpreet Singh Riat, Daniel Sheppard, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Steven P. Wilder, Amonida Zadissa, Ewan Birney, Jennifer L. Harrow, Matthieu Muffato, Emily Perry, Magali Ruffier, Giulietta Spudich, Stephen J. Trevanion, Fiona Cunningham, Bronwen L. Aken, Daniel R. Zerbino, Paul Flicek:
Ensembl 2016. Nucleic Acids Res. 44(Database-Issue): 710-716 (2016) - 2015
- [j56]Fiona Cunningham, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Konstantinos Billis, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Nathan Johnson, Thomas Juettemann, Andreas K. Kähäri, Stephen Keenan, Fergal J. Martin, Thomas Maurel, William M. McLaren, Daniel N. Murphy, Rishi Nag, Bert Overduin, Anne Parker, Mateus Patricio, Emily Perry, Miguel Pignatelli, Harpreet Singh Riat, Daniel Sheppard, Kieron R. Taylor, Anja Thormann, Alessandro Vullo, Steven P. Wilder, Amonida Zadissa, Bronwen L. Aken, Ewan Birney, Jennifer L. Harrow, Rhoda Kinsella, Matthieu Muffato, Magali Ruffier, Stephen M. J. Searle, Giulietta Spudich, Stephen J. Trevanion, Andy Yates, Daniel R. Zerbino, Paul Flicek:
Ensembl 2015. Nucleic Acids Res. 43(Database-Issue): 662-669 (2015) - [i2]Ian Dunham, Eugene Kulesha, Valentina Iotchkova, Sandro Morganella, Ewan Birney:
FORGE: A tool to discover cell specific enrichments of GWAS associated SNPs in regulatory regions. F1000Research 4: 18 (2015) - [i1]Camilla L. C. Ip, Matthew Loose, John R. Tyson, Mariateresa de Cesare, Bonnie L. Brown, Miten Jain, Richard M. Leggett, David A. Eccles, Vadim Zalunin, John M. Urban, Paolo Piazza, Rory J. Bowden, Benedict Paten, Solomon Mwaigwisya, Elizabeth M. Batty, Jared T. Simpson, Terrance P. Snutch, Ewan Birney, David Buck, Sara Goodwin, Hans J. Jansen, Justin O'Grady, Hugh E. Olsen, MinION Analysis, Reference Consortium:
MinION Analysis and Reference Consortium: Phase 1 data release and analysis. F1000Research 4: 1075 (2015) - 2014
- [j55]Simon Jupp, James Malone, Jerven T. Bolleman, Marco Brandizi, Mark Davies, Leyla J. García, Anna Gaulton, Sebastien Gehant, Camille Laibe, Nicole Redaschi, Sarala M. Wimalaratne, Maria Jesus Martin, Nicolas Le Novère, Helen E. Parkinson, Ewan Birney, Andrew M. Jenkinson:
The EBI RDF platform: linked open data for the life sciences. Bioinform. 30(9): 1338-1339 (2014) - [j54]Catherine Brooksbank, Mary Todd Bergman, Rolf Apweiler, Ewan Birney, Janet M. Thornton:
The European Bioinformatics Institute's data resources 2014. Nucleic Acids Res. 42(Database-Issue): 18-25 (2014) - [j53]David Croft, Antonio Fabregat Mundo, Robin Haw, Marija Milacic, Joel Weiser, Guanming Wu, Michael Caudy, Phani V. Garapati, Marc Gillespie, Maulik R. Kamdar, Bijay Jassal, Steven Jupe, Lisa Matthews, Bruce May, Stanislav Palatnik, Karen Rothfels, Veronica Shamovsky, Heeyeon Song, Mark Williams, Ewan Birney, Henning Hermjakob, Lincoln Stein, Peter D'Eustachio:
The Reactome pathway knowledgebase. Nucleic Acids Res. 42(Database-Issue): 472-477 (2014) - [j52]Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Konstantinos Billis, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Nathan Johnson, Thomas Juettemann, Andreas Kähäri, Stephen Keenan, Eugene Kulesha, Fergal J. Martin, Thomas Maurel, William M. McLaren, Daniel N. Murphy, Rishi Nag, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Emily Pritchard, Harpreet Singh Riat, Magali Ruffier, Daniel Sheppard, Kieron R. Taylor, Anja Thormann, Stephen J. Trevanion, Alessandro Vullo, Steven P. Wilder, Mark Wilson, Amonida Zadissa, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Jennifer L. Harrow, Javier Herrero, Tim J. P. Hubbard, Rhoda Kinsella, Matthieu Muffato, Anne Parker, Giulietta Spudich, Andy Yates, Daniel R. Zerbino, Stephen M. J. Searle:
Ensembl 2014. Nucleic Acids Res. 42(Database-Issue): 749-755 (2014) - 2013
- [j51]Paul Flicek, Ikhlak Ahmed, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil, Carlos García-Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Thomas Juettemann, Andreas Kähäri, Stephen Keenan, Monika Komorowska, Eugene Kulesha, Ian Longden, Thomas Maurel, William M. McLaren, Matthieu Muffato, Rishi Nag, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Emily Pritchard, Harpreet Singh Riat, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sheppard, Daniel Sobral, Kieron R. Taylor, Anja Thormann, Stephen J. Trevanion, Simon White, Steven P. Wilder, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Jennifer L. Harrow, Javier Herrero, Tim J. P. Hubbard, Nathan Johnson, Rhoda Kinsella, Anne Parker, Giulietta Spudich, Andy Yates, Amonida Zadissa, Stephen M. J. Searle:
Ensembl 2013. Nucleic Acids Res. 41(Database-Issue): 48-55 (2013) - [j50]Jie Wang, Jiali Zhuang, Sowmya Iyer, Xin-Ying Lin, Melissa C. Greven, Bong-Hyun Kim, Jill Moore, Brian G. Pierce, Xianjun Dong, Daniel Virgil, Ewan Birney, Jui-Hung Hung, Zhiping Weng:
Factorbook.org: a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. Nucleic Acids Res. 41(Database-Issue): 171-176 (2013) - [j49]Nick Goldman, Paul Bertone, Siyuan Chen, Christophe Dessimoz, Emily M. LeProust, Botond Sipos, Ewan Birney:
Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nat. 494(7435): 77-80 (2013) - 2012
- [j48]Marcel H. Schulz, Daniel R. Zerbino, Martin Vingron, Ewan Birney:
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinform. 28(8): 1086-1092 (2012) - [j47]Clara Amid, Ewan Birney, Lawrence Bower, Ana Cerdeño-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Richard Gibson, Neil Goodgame, Christopher I. Hunter, Mikyung Jang, Rasko Leinonen, Xin Liu, Arnaud Oisel, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Stéphane Rivière, Marc Rossello, Alexander Senf, Dimitriy Smirnov, Petra ten Hoopen, Daniel Vaughan, Robert Vaughan, Vadim Zalunin, Guy Cochrane:
Major submissions tool developments at the European nucleotide archive. Nucleic Acids Res. 40(Database-Issue): 43-47 (2012) - [j46]Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Denise Carvalho-Silva, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Laurent Gil, Leo Gordon, Maurice Hendrix, Thibaut Hourlier, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Monika Komorowska, Gautier Koscielny, Eugene Kulesha, Pontus Larsson, Ian Longden, William M. McLaren, Matthieu Muffato, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Harpreet Singh Riat, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sobral, Y. Amy Tang, Kieron R. Taylor, Stephen J. Trevanion, Jana Vandrovcova, Simon White, Mark Wilson, Steven P. Wilder, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suárez, Jennifer L. Harrow, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, Giulietta Spudich, Jan Vogel, Andy Yates, Amonida Zadissa, Stephen M. J. Searle:
Ensembl 2012. Nucleic Acids Res. 40(Database-Issue): 84-90 (2012) - [j45]Paul J. Kersey, Daniel M. Staines, Daniel Lawson, Eugene Kulesha, Paul S. Derwent, Jay C. Humphrey, Daniel S. T. Hughes, Stephen Keenan, Arnaud Kerhornou, Gautier Koscielny, Nicholas Langridge, Mark D. McDowall, Karine Megy, Uma Maheswari, Michael Nuhn, Michael Paulini, Helder Pedro, Iliana Toneva, Derek Wilson, Andrew D. Yates, Ewan Birney:
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species. Nucleic Acids Res. 40(Database-Issue): 91-97 (2012) - 2011
- [j44]Rasko Leinonen, Ruth Akhtar, Ewan Birney, Lawrence Bower, Ana Cerdeño-Tárraga, Ying Cheng, Iain Cleland, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Mikyung Jang, Nima Pakseresht, Sheila Plaister, Rajesh Radhakrishnan, Kethi Reddy, Siamak Sobhany, Petra ten Hoopen, Robert Vaughan, Vadim Zalunin, Guy Cochrane:
The European Nucleotide Archive. Nucleic Acids Res. 39(Database-Issue): 28-31 (2011) - [j43]David Croft, Gavin O'Kelly, Guanming Wu, Robin Haw, Marc Gillespie, Lisa Matthews, Michael Caudy, Phani V. Garapati, Gopal Gopinath, Bijay Jassal, Steven Jupe, Irina Kalatskaya, Shahana Mahajan, Bruce May, Nelson Ndegwa, Esther Schmidt, Veronica Shamovsky, Christina K. Yung, Ewan Birney, Henning Hermjakob, Peter D'Eustachio, Lincoln Stein:
Reactome: a database of reactions, pathways and biological processes. Nucleic Acids Res. 39(Database-Issue): 691-697 (2011) - [j42]Paul Flicek, M. Ridwan Amode, Daniel Barrell, Kathryn Beal, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Leo Gordon, Maurice Hendrix, Thibaut Hourlier, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Eugene Kulesha, Pontus Larsson, Ian Longden, William M. McLaren, Bert Overduin, Bethan Pritchard, Harpreet Singh Riat, Daniel Rios, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sobral, Giulietta Spudich, Y. Amy Tang, Stephen J. Trevanion, Jana Vandrovcova, Albert J. Vilella, Simon White, Steven P. Wilder, Amonida Zadissa, Jorge Zamora, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suárez, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, Jan Vogel, Stephen M. J. Searle:
Ensembl 2011. Nucleic Acids Res. 39(Database-Issue): 800-806 (2011) - 2010
- [j41]Bijay Jassal, Steven Jupe, Michael Caudy, Ewan Birney, Lincoln Stein, Henning Hermjakob, Peter D'Eustachio:
The systematic annotation of the three main GPCR families in Reactome. Database J. Biol. Databases Curation 2010 (2010) - [j40]Damian Smedley, Paul N. Schofield, Chao-Kung Chen, Vassilis Aidinis, Crysanthi Ainali, Jonathan B. L. Bard, Rudi Balling, Ewan Birney, Andrew Blake, Erik Bongcam-Rudloff, Anthony J. Brookes, Gianni Cesareni, Christina Chandras, Janan T. Eppig, Paul Flicek, Georgios V. Gkoutos, Simon Greenaway, Michael Gruenberger, Jean-Karim Hériché, Andrew Lyall, Ann-Marie Mallon, Dawn Muddyman, Florian Reisinger, Martin Ringwald, Nadia A. Rosenthal, Klaus Schughart, Morris A. Swertz, Gudmundur A. Thorisson, Michael Zouberakis, John M. Hancock:
Finding and sharing: new approaches to registries of databases and services for the biomedical sciences. Database J. Biol. Databases Curation 2010 (2010) - [j39]Daniel Rios, William M. McLaren, Yuan Chen, Ewan Birney, Arne Stabenau, Paul Flicek, Fiona Cunningham:
A database and API for variation, dense genotyping and resequencing data. BMC Bioinform. 11: 238 (2010) - [j38]Rasko Leinonen, Ruth Akhtar, Ewan Birney, James K. Bonfield, Lawrence Bower, Matthew Corbett, Ying Cheng, Fehmi Demiralp, Nadeem Faruque, Neil Goodgame, Richard Gibson, Gemma Hoad, Christopher I. Hunter, Mikyung Jang, Steven Leonard, Quan Lin, Rodrigo Lopez, Michael Maguire, Hamish McWilliam, Sheila Plaister, Rajesh Radhakrishnan, Siamak Sobhany, Guy Slater, Petra ten Hoopen, Franck Valentin, Robert Vaughan, Vadim Zalunin, Daniel R. Zerbino, Guy Cochrane:
Improvements to services at the European Nucleotide Archive. Nucleic Acids Res. 38(Database-Issue): 39-45 (2010) - [j37]Paul Flicek, Bronwen L. Aken, Benoît Ballester, Kathryn Beal, Eugene Bragin, Simon Brent, Yuan Chen, Peter Clapham, Guy Coates, Susan Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Kerstin Howe, Andrew M. Jenkinson, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Gautier Koscielny, Eugene Kulesha, Daniel Lawson, Ian Longden, Tim Massingham, William M. McLaren, Karine Megy, Bert Overduin, Bethan Pritchard, Daniel Rios, Magali Ruffier, Michael Schuster, Guy Slater, Damian Smedley, Giulietta Spudich, Y. Amy Tang, Stephen J. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, Steven P. Wilder, Amonida Zadissa, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosé M. Fernández-Suárez, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, James A. Smith, Stephen M. J. Searle:
Ensembl's 10th year. Nucleic Acids Res. 38(Database-Issue): 557-562 (2010) - [j36]Paul J. Kersey, Daniel Lawson, Ewan Birney, Paul S. Derwent, Matthias Haimel, Javier Herrero, Stephen Keenan, Arnaud Kerhornou, Gautier Koscielny, Andreas Kähäri, Rhoda Kinsella, Eugene Kulesha, Uma Maheswari, Karine Megy, Michael Nuhn, Glenn Proctor, Daniel M. Staines, Franck Valentin, Albert J. Vilella, Andy Yates:
Ensembl Genomes: Extending Ensembl across the taxonomic space. Nucleic Acids Res. 38(Database-Issue): 563-569 (2010) - [j35]Phil Wilkinson, Jitka Sengerova, Raffaele Matteoni, Chao-Kung Chen, Gaetan Soulat, Abel Ureta-Vidal, Sabine Fessele, Michael Hagn, Marzia Massimi, Karen Pickford, Richard H. Butler, Susan Marschall, Ann-Marie Mallon, Amanda J. Pickard, Marcello Raspa, Ferdinando Scavizzi, Martin Fray, Vanessa Larrigaldie, Johan Leyritz, Ewan Birney, Glauco P. Tocchini-Valentini, Steve D. M. Brown, Yann Herault, Lluis Montoliu, Martin Hrabé de Angelis, Damian Smedley:
EMMA - mouse mutant resources for the international scientific community. Nucleic Acids Res. 38(Database-Issue): 570-576 (2010)
2000 – 2009
- 2009
- [j34]Benedict Paten, Javier Herrero, Kathryn Beal, Ewan Birney:
Sequence progressive alignment, a framework for practical large-scale probabilistic consistency alignment. Bioinform. 25(3): 295-301 (2009) - [j33]Guy Cochrane, Ruth Akhtar, James K. Bonfield, Lawrence Bower, Fehmi Demiralp, Nadeem Faruque, Richard Gibson, Gemma Hoad, Tim J. P. Hubbard, Christopher I. Hunter, Mikyung Jang, Szilveszter Juhos, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Sheila Plaister, Rajesh Radhakrishnan, Stephen Robinson, Siamak Sobhany, Petra ten Hoopen, Robert Vaughan, Vadim Zalunin, Ewan Birney:
Petabyte-scale innovations at the European Nucleotide Archive. Nucleic Acids Res. 37(Database-Issue): 19-25 (2009) - [j32]Daniel Lawson, Peter Arensburger, Peter Atkinson, Nora J. Besansky, Robert V. Bruggner, Ryan Butler, Kathryn S. Campbell, George K. Christophides, Scott Christley, Emmanuel Dialynas, Martin Hammond, Catherine A. Hill, Nathan Konopinski, Neil F. Lobo, Robert M. MacCallum, Gregory R. Madey, Karine Megy, Jason Meyer, Seth Redmond, David W. Severson, Eric O. Stinson, Pantelis Topalis, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, Frank H. Collins:
VectorBase: a data resource for invertebrate vector genomics. Nucleic Acids Res. 37(Database-Issue): 583-587 (2009) - [j31]Lisa Matthews, Gopal Gopinath, Marc Gillespie, Michael Caudy, David Croft, Bernard de Bono, Phani V. Garapati, Jill Hemish, Henning Hermjakob, Bijay Jassal, Alexander Kanapin, Suzanna Lewis, Shahana Mahajan, Bruce May, Esther Schmidt, Imre Vastrik, Guanming Wu, Ewan Birney, Lincoln Stein, Peter D'Eustachio:
Reactome knowledgebase of human biological pathways and processes. Nucleic Acids Res. 37(Database-Issue): 619-622 (2009) - [j30]Tim J. P. Hubbard, Bronwen L. Aken, Sarah C. Ayling, Benoît Ballester, Kathryn Beal, Eugene Bragin, Simon Brent, Yuan Chen, Peter Clapham, Laura Clarke, Guy Coates, Susan Fairley, Stephen Fitzgerald, Julio Fernandez-Banet, Leo Gordon, Stefan Gräf, Syed Haider, Martin Hammond, Richard C. G. Holland, Kevin L. Howe, Andrew M. Jenkinson, Nathan Johnson, Andreas Kähäri, Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, Ian Longden, Karine Megy, Patrick Meidl, Bert Overduin, Anne Parker, Bethan Pritchard, Daniel Rios, Michael Schuster, Guy Slater, Damian Smedley, William Spooner, Giulietta Spudich, Stephen J. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, Steven P. Wilder, Arek Zadissa, Ewan Birney, Fiona Cunningham, Val Curwen, Richard Durbin, Xosé M. Fernández-Suárez, Javier Herrero, Arek Kasprzyk, Glenn Proctor, James A. Smith, Stephen M. J. Searle, Paul Flicek:
Ensembl 2009. Nucleic Acids Res. 37(Database-Issue): 690-697 (2009) - [j29]Florian Gnad, Mario Oroshi, Ewan Birney, Matthias Mann:
MAPU 2.0: high-accuracy proteomes mapped to genomes. Nucleic Acids Res. 37(Database-Issue): 902-906 (2009) - 2008
- [j28]Andrew M. Jenkinson, Mario Albrecht, Ewan Birney, Hagen Blankenburg, Thomas A. Down, Robert D. Finn, Henning Hermjakob, Tim J. P. Hubbard, Rafael C. Jiménez, Philip Jones, Andreas Kähäri, Eugene Kulesha, José R. Macías, Gabrielle A. Reeves, Andreas Prlic:
Integrating biological data - the Distributed Annotation System. BMC Bioinform. 9(S-8) (2008) - [j27]Guy Cochrane, Ruth Akhtar, Philippe Aldebert, Nicola Althorpe, Alastair Baldwin, Kirsty Bates, Sumit Bhattacharyya, James K. Bonfield, Lawrence Bower, Paul Browne, Matias Castro, Tony Cox, Fehmi Demiralp, Ruth Y. Eberhardt, Nadeem Faruque, Gemma Hoad, Mikyung Jang, Tamara Kulikova, Alberto Labarga, Rasko Leinonen, Steven Leonard, Quan Lin, Rodrigo Lopez, Dariusz Lorenc, Hamish McWilliam, Gaurab Mukherjee, Francesco Nardone, Sheila Plaister, Stephen Robinson, Siamak Sobhany, Robert Vaughan, Dan Wu, Weimin Zhu, Rolf Apweiler, Tim J. P. Hubbard, Ewan Birney:
Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Res. 36(Database-Issue): 5-12 (2008) - [j26]Elspeth A. Bruford, Michael J. Lush, Mathew W. Wright, Tam P. Sneddon, Sue Povey, Ewan Birney:
The HGNC Database in 2008: a resource for the human genome. Nucleic Acids Res. 36(Database-Issue): 445-448 (2008) - [j25]Paul Flicek, Bronwen L. Aken, Kathryn Beal, Benoît Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Fiona Cunningham, Tim Cutts, Thomas A. Down, S. C. Dyer, T. Eyre, Stephen Fitzgerald, Julio Fernandez-Banet, Stefan Gräf, Syed Haider, Martin Hammond, Richard C. G. Holland, Kevin L. Howe, Kerstin Howe, Nathan Johnson, Andrew M. Jenkinson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, Ian Longden, Karine Megy, Patrick Meidl, Bert Overduin, Anne Parker, Bethan Pritchard, Andreas Prlic, S. Rice, Daniel Rios, Michael Schuster, Ian Sealy, Guy Slater, Damian Smedley, Giulietta Spudich, Stephen J. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, M. Wood, Ewan Birney, Tony Cox, Val Curwen, Richard Durbin, Xosé M. Fernández-Suárez, Javier Herrero, Tim J. P. Hubbard, Arek Kasprzyk, Glenn Proctor, James A. Smith, Abel Ureta-Vidal, Stephen M. J. Searle:
Ensembl 2008. Nucleic Acids Res. 36(Database-Issue): 707-714 (2008) - [j24]Xosé M. Fernández-Suárez, Ewan Birney:
Advanced Genomic Data Mining. PLoS Comput. Biol. 4(9) (2008) - [c6]Florian Reisinger, Manuel Corpas, John M. Hancock, Henning Hermjakob, Ewan Birney, Pascal Kahlem:
ENFIN - An Integrative Structure for Systems Biology. DILS 2008: 132-143 - 2007
- [j23]Fiona G. G. Nielsen, Stefan Gräf, Xinmin Zhang, Stefan Kurtz, Sergei Denissov, Roland Green, Ewan Birney, Paul Flicek, Martijn A. Huynen, Henk Stunnenberg:
Optimising oligonucleotide array design for ChIP-on-chip. BMC Bioinform. 8(S-8) (2007) - [j22]Bernard de Bono, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Gopal Gopinath, David Croft, Marc Gillespie, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Guanming Wu, Ewan Birney, Lincoln Stein:
Reactome: An integrated expert model of human molecular processes and access toolkit. J. Integr. Bioinform. 4(3) (2007) - [j21]Daniel Lawson, Peter Arensburger, Peter Atkinson, Nora J. Besansky, Robert V. Bruggner, Ryan Butler, Kathryn S. Campbell, George K. Christophides, Scott Christley, Emmanuel Dialynas, David B. Emmert, Martin Hammond, Catherine A. Hill, Ryan C. Kennedy, Neil F. Lobo, Robert M. MacCallum, Gregory R. Madey, Karine Megy, Seth Redmond, Susan Russo, David W. Severson, Eric O. Stinson, Pantelis Topalis, Evgeni M. Zdobnov, Ewan Birney, William M. Gelbart, Fotis C. Kafatos, Christos Louis, Frank H. Collins:
VectorBase: a home for invertebrate vectors of human pathogens. Nucleic Acids Res. 35(Database-Issue): 503-505 (2007) - [j20]Tim J. P. Hubbard, Bronwen L. Aken, Kathryn Beal, Benoît Ballester, Mario Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Fiona Cunningham, Tim Cutts, Thomas A. Down, S. C. Dyer, Stephen Fitzgerald, Julio Fernandez-Banet, Stefan Gräf, Syed Haider, Martin Hammond, Javier Herrero, Richard C. G. Holland, Kevin L. Howe, Kerstin Howe, Nathan Johnson, Andreas Kähäri, Damian Keefe, Felix Kokocinski, Eugene Kulesha, Daniel Lawson, Ian Longden, Craig Melsopp, Karine Megy, Patrick Meidl, Bert Overduin, Anne Parker, Andreas Prlic, S. Rice, Daniel Rios, Michael Schuster, Ian Sealy, Jessica Severin, Guy Slater, Damian Smedley, Giulietta Spudich, Stephen J. Trevanion, Albert J. Vilella, Jan Vogel, Simon White, M. Wood, Tony Cox, Val Curwen, Richard Durbin, Xosé M. Fernández-Suárez, Paul Flicek, Arek Kasprzyk, Glenn Proctor, Stephen M. J. Searle, James A. Smith, Abel Ureta-Vidal, Ewan Birney:
Ensembl 2007. Nucleic Acids Res. 35(Database-Issue): 610-617 (2007) - [c5]Stefan Gräf, Fiona G. G. Nielsen, Stefan Kurtz, Martijn A. Huynen, Ewan Birney, Henk Stunnenberg, Paul Flicek:
Optimized design and assessment of whole genome tiling arrays. ISMB/ECCB (Supplement of Bioinformatics) 2007: 195-204 - 2006
- [j19]Ewan Birney, T. Daniel Andrews, Mario Cáccamo, Yuan Chen, Laura Clarke, Guy Coates, Tony Cox, Fiona Cunningham, Val Curwen, Tim Cutts, Thomas A. Down, Richard Durbin, Xosé M. Fernández-Suárez, Paul Flicek, Stefan Gräf, Martin Hammond, Javier Herrero, Kevin L. Howe, Vivek Iyer, Kerstin Jekosch, Andreas Kähäri, Arek Kasprzyk, Damian Keefe, Felix Kokocinski, Eugene Kulesha, D. London, Ian Longden, Craig Melsopp, Patrick Meidl, Bert Overduin, Anne Parker, Glenn Proctor, Andreas Prlic, Mark Rae, Daniel Rios, Seth Redmond, Michael Schuster, Ian Sealy, Stephen M. J. Searle, Jessica Severin, Guy Slater, Damian Smedley, James A. Smith, Arne Stabenau, Jim Stalker, Stephen J. Trevanion, Abel Ureta-Vidal, Jan Vogel, Simon White, Cara Woodwark, Tim J. P. Hubbard:
Ensembl 2006. Nucleic Acids Res. 34(Database-Issue): 556-561 (2006) - [c4]Andreas Prlic, Ewan Birney, Tony Cox, Thomas A. Down, Robert D. Finn, Stefan Gräf, David K. Jackson, Andreas Kähäri, Eugene Kulesha, Roger Pettett, James A. Smith, Jim Stalker, Tim J. P. Hubbard:
The Distributed Annotation System for Integration of Biological Data. DILS 2006: 195-203 - [c3]Esther Schmidt, Ewan Birney, David Croft, Bernard de Bono, Peter D'Eustachio, Marc Gillespie, Gopal Gopinath, Bijay Jassal, Suzanna Lewis, Lisa Matthews, Lincoln Stein, Imre Vastrik, Guanming Wu:
Reactome - A Knowledgebase of Biological Pathways. OTM Workshops (1) 2006: 710-719 - 2005
- [j18]Guy St. C. Slater, Ewan Birney:
Automated generation of heuristics for biological sequence comparison. BMC Bioinform. 6: 31 (2005) - [j17]Eduardo Eyras, Alexandre Reymond, Robert Castelo, Jacqueline M. Bye, Francisco Camara, Paul Flicek, Elizabeth J. Huckle, Genis Parra, David D. Shteynberg, Carine Wyss, Jane Rogers, Stylianos E. Antonarakis, Ewan Birney, Roderic Guigó, Michael R. Brent:
Gene finding in the chicken genome. BMC Bioinform. 6: 131 (2005) - [j16]G. Joshi-Tope, Marc Gillespie, Imre Vastrik, Peter D'Eustachio, Esther Schmidt, Bernard de Bono, Bijay Jassal, Gopal R. Gopinath, G. R. Wu, Lisa Matthews, Suzanna Lewis, Ewan Birney, Lincoln Stein:
Reactome: a knowledgebase of biological pathways. Nucleic Acids Res. 33(Database-Issue): 428-432 (2005) - [j15]Tim J. P. Hubbard, D. Andrews, Mario Cáccamo, Graham Cameron, Yuan Chen, Michele E. Clamp, Laura Clarke, Guy Coates, Tony Cox, Fiona Cunningham, Val Curwen, Tim Cutts, Thomas A. Down, Richard Durbin, Xosé M. Fernández-Suárez, James G. R. Gilbert, Martin Hammond, Javier Herrero, H. Hotz, Kevin L. Howe, Vivek Iyer, Kerstin Jekosch, Andreas Kähäri, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Felix Kokocinski, D. London, Ian Longden, Graham P. McVicker, Craig Melsopp, Patrick Meidl, Simon C. Potter, Glenn Proctor, Mark Rae, Daniel Rios, Michael Schuster, Stephen M. J. Searle, Jessica Severin, Guy Slater, Damian Smedley, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, R. Storey, Stephen J. Trevanion, Abel Ureta-Vidal, Jan Vogel, Simon White, Cara Woodwark, Ewan Birney:
Ensembl 2005. Nucleic Acids Res. 33(Database-Issue): 447-453 (2005) - 2004
- [j14]Ewan Birney, Michele E. Clamp:
Biological database design and implementation. Briefings Bioinform. 5(1): 31-38 (2004) - [j13]Ewan Birney, T. Daniel Andrews, Paul Bevan, Mario Cáccamo, Graham Cameron, Yuan Chen, Laura Clarke, Guy Coates, Tony Cox, James A. Cuff, Val Curwen, Tim Cutts, Thomas A. Down, Richard Durbin, Eduardo Eyras, Xosé M. Fernández-Suárez, Paul J. Gane, B. Gibbins, James G. R. Gilbert, Martin Hammond, H. Hotz, Vivek Iyer, Andreas Kähäri, Kerstin Jekosch, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Heikki Lehväslaiho, Graham P. McVicker, Craig Melsopp, Patrick Meidl, Emmanuel Mongin, Roger Pettett, Simon C. Potter, Glenn Proctor, Mark Rae, Stephen M. J. Searle, Guy Slater, Damian Smedley, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, R. Storey, Abel Ureta-Vidal, Cara Woodwark, Michele E. Clamp, Tim J. P. Hubbard:
Ensembl 2004. Nucleic Acids Res. 32(Database-Issue): 468-470 (2004) - 2003
- [j12]Michele E. Clamp, T. Daniel Andrews, Daniel Barker, Paul Bevan, Graham Cameron, Yuan Chen, Laura Clarke, Tony Cox, James A. Cuff, Val Curwen, Thomas A. Down, Richard Durbin, Eduardo Eyras, James G. R. Gilbert, Martin Hammond, Tim J. P. Hubbard, Arek Kasprzyk, Damian Keefe, Heikki Lehväslaiho, Vivek Iyer, Craig Melsopp, Emmanuel Mongin, Roger Pettett, Simon C. Potter, Alistair G. Rust, Esther Schmidt, Stephen M. J. Searle, Guy Slater, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, Elia Stupka, Abel Ureta-Vidal, Imre Vastrik, Ewan Birney:
Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res. 31(1): 38-42 (2003) - [j11]Catherine Brooksbank, Evelyn Camon, Midori A. Harris, Michele Magrane, Maria Jesus Martin, Nicola J. Mulder, Claire O'Donovan, Helen E. Parkinson, Mary Ann Tuli, Rolf Apweiler, Ewan Birney, Alvis Brazma, Kim Henrick, Rodrigo Lopez, Guenter Stoesser, Peter Stoehr, Graham Cameron:
The European Bioinformatics Institute's data resources. Nucleic Acids Res. 31(1): 43-50 (2003) - 2002
- [j10]Tim J. P. Hubbard, Daniel Barker, Ewan Birney, Graham Cameron, Yuan Chen, Laura Clarke, Tony Cox, James A. Cuff, Val Curwen, Thomas A. Down, Richard Durbin, Eduardo Eyras, James G. R. Gilbert, Martin Hammond, Lukasz Huminiecki, Arek Kasprzyk, Heikki Lehväslaiho, Philip Lijnzaad, Craig Melsopp, Emmanuel Mongin, Roger Pettett, Matthew R. Pocock, Simon C. Potter, Alistair G. Rust, Esther Schmidt, Stephen M. J. Searle, Guy Slater, James A. Smith, William Spooner, Arne Stabenau, Jim Stalker, Elia Stupka, Abel Ureta-Vidal, Imre Vastrik, Michele E. Clamp:
The Ensembl genome database project. Nucleic Acids Res. 30(1): 38-41 (2002) - [j9]Alex Bateman, Ewan Birney, Lorenzo Cerutti, Richard Durbin, Laurence Ettwiller, Sean R. Eddy, Sam Griffiths-Jones, Kevin L. Howe, Mhairi Marshall, Erik L. L. Sonnhammer:
The Pfam Protein Families Database. Nucleic Acids Res. 30(1): 276-280 (2002) - 2001
- [j8]Ewan Birney:
Hidden Markov models in biological sequence analysis. IBM J. Res. Dev. 45(3): 449-454 (2001) - [j7]Rolf Apweiler, Terri K. Attwood, Amos Bairoch, Alex Bateman, Ewan Birney, Margaret Biswas, Philipp Bucher, Lorenzo Cerutti, Florence Corpet, Michael D. R. Croning, Richard Durbin