Scientific Publications

Citing Ensembl

If you've used Ensembl in your work, please cite the most recent overview article and the Ensembl release you retrieved your data from (currently 113). References for the specific genome assembly can be found on the More information and statistics page for a species (eg human). For more specialised aspects of our system, further articles are listed below.

Citing Ensembl Data

Since release 25, all Ensembl releases have been archived as fully functional sites for about three years. This makes it possible to accurately cite data being referred to in a paper, even though the main Ensembl site is being continuously updated (currently release 113 - October 2024). For more information see the list of current archives.

Publications

Peter W Harrison, M Ridwan Amode, Olanrewaju Austine-Orimoloye, Andrey G Azov, Matthieu Barba, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Lahcen I Campbell, Manuel Carbajo Martinez, Mehrnaz Charkhchi, Kapeel Chougule, Alexander Cockburn, Claire Davidson, Nishadi H De Silva, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Dionysios Grigoriadis, Gurpreet S Ghattaoraya, Jose Gonzalez Martinez, Tatiana A Gurbich, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Disha Lodha, Diego Marques-Coelho, Gareth Maslen, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Piližota, Daniel Poppleton, Irina Prosovetskaia, Shriya Raj, José G Pérez-Silva, Ahamed Imran Abdul Salam, Shradha Saraf, Nuno Saraiva-Agostinho, Dan Sheppard, Swati Sinha, Botond Sipos, Vasily Sitnik, William Stark, Emily Steed, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Doreen Ware, Elizabeth Wass, Natalie L Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jon Keatley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, Guy Naamati, John Tate, Stephen J Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E Hunt, Fiona Cunningham, Sarah Dyer, Robert D Finn, Fergal J Martin, and Andrew D Yates
Ensembl 2024
Nucleic Acids Res. 2024, 52(D1):D891–D899
PMID: 37953337
10.1093/nar/gkad1049
Fergal J Martin, M Ridwan Amode, Alisha Aneja, Olanrewaju Austine-Orimoloye, Andrey G Azov, If Barnes, Arne Becker, Ruth Bennett, Andrew Berry, Jyothish Bhai, Simarpreet Kaur Bhurji, Alexandra Bignell, Sanjay Boddu, Paulo R Branco Lins, Lucy Brooks, Shashank Budhanuru Ramaraju, Mehrnaz Charkhchi, Alexander Cockburn, Luca Da Rin Fiorretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron, Thiago Genez, Gurpreet S Ghattaoraya, Jose Gonzalez Martinez, Cristi Guijarro, Matthew Hardy, Zoe Hollis, Thibaut Hourlier, Toby Hunt, Mike Kay, Vinay Kaykala, Tuan Le, Diana Lemos, Diego Marques-Coelho, José Carlos Marugán, Gabriela Alejandra Merino, Louisse Paola Mirabueno, Aleena Mushtaq, Syed Nakib Hossain, Denye N Ogeh, Manoj Pandian Sakthivel, Anne Parker, Malcolm Perry, Ivana Piližota, Irina Prosovetskaia, José G Pérez-Silva, Ahamed Imran Abdul Salam, Nuno Saraiva-Agostinho, Helen Schuilenburg, Dan Sheppard, Swati Sinha, Botond Sipos, William Stark, Emily Steed, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Likhitha Surapaneni, Kyösti Sutinen, Michal Szpak, Francesca Floriana Tricomi, David Urbina-Gómez, Andres Veidenberg, Thomas A Walsh, Brandon Walts, Elizabeth Wass, Natalie Willhoft, Jamie Allen, Jorge Alvarez-Jarreta, Marc Chakiachvili, Bethany Flint, Stefano Giorgetti, Leanne Haggerty, Garth R Ilsley, Jane E Loveland, Benjamin Moore, Jonathan M Mudge, John Tate, David Thybert, Stephen J Trevanion, Andrea Winterbottom, Adam Frankish, Sarah E Hunt, Magali Ruffier, Fiona Cunningham, Sarah Dyer, Robert D Finn, Kevin L Howe, Peter W Harrison, Andrew D Yates, and Paul Flicek
Ensembl 2023
Nucleic Acids Res. 2023, 51(D1):D933-D941
PMID: 36318249
doi:10.1093/nar/gkac958
Fiona Cunningham , James E. Allen, Jamie Allen, Jorge Alvarez-Jarreta, M. Ridwan Amode, Irina M. Armean , Olanrewaju Austine-Orimoloye, Andrey G. Azov, If Barnes, Ruth Bennett, Andrew Berry, Jyothish Bhai, Alexandra Bignell, Konstantinos Billis , Sanjay Boddu, Lucy Brooks, Mehrnaz Charkhchi, Carla Cummins , Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Sarah Donaldson, Bilal El Houdaigui, Tamara El Naboulsi, Reham Fatima, Carlos Garcia Giron , Thiago Genez, Jose Gonzalez Martinez, Cristina Guijarro-Clarke, Arthur Gymer, Matthew Hardy, Zoe Hollis, Thibaut Hourlier , Toby Hunt, Thomas Juettemann , Vinay Kaikala, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, José Carlos Marugán, Shamika Mohanan, Aleena Mushtaq, Marc Naven, Denye N. Ogeh, Anne Parker, Andrew Parton, Malcolm Perry, Ivana Piliˇzota, Irina Prosovetskaia, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M. Schmitt, Helen Schuilenburg, Dan Sheppard, José G. Pérez-Silva, William Stark, Emily Steed, Kyösti Sutinen, Ranjit Sukumaran, Dulika Sumathipala, Marie-Marthe Suner, Michal Szpak, Anja Thormann, Francesca Floriana Tricomi, David Urbina-G ́omez, Andres Veidenberg, Thomas A. Walsh, Brandon Walts, Natalie Willhoft, Andrea Winterbottom, Elizabeth Wass, Marc Chakiachvili, Bethany Flint, Adam Frankish , Stefano Giorgetti, Leanne Haggerty, Sarah E. Hunt , Garth R. IIsley, Jane E. Loveland , Fergal J. Martin , Benjamin Moore, Jonathan M. Mudge, Matthieu Muffato, Emily Perry , Magali Ruffier , John Tate, David Thybert, Stephen J. Trevanion, Sarah Dyer, Peter W. Harrison , Kevin L. Howe , Andrew D. Yates , Daniel R. Zerbino and Paul Flicek
Ensembl 2022.
Nucleic Acids Res. 2022, vol. 50(1):D988-D995
PubMed PMID: 34791404.
doi:10.1093/nar/gkab1049
Kevin L Howe, Premanand Achuthan, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Mehrnaz Charkhchi, Carla Cummins, Luca Da Rin Fioretto, Claire Davidson, Kamalkumar Dodiya, Bilal El Houdaigui, Reham Fatima, Astrid Gall, Carlos Garcia Giron, Tiago Grego, Cristina Guijarro-Clarke, Leanne Haggerty, Anmol Hemrom, Thibaut Hourlier, Osagie G Izuogu, Thomas Juettemann, Vinay Kaikala, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Gonzalez Martinez, José Carlos Marugán, Thomas Maurel, Aoife C McMahon, Shamika Mohanan, Benjamin Moore, Matthieu Muffato, Denye N Oheh, Dimitrios Paraschas, Anne Parker, Andrew Parton, Irina Prosovetskaia, Manoj P Sakthivel, Ahamed I Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, Emily Steed, Michal Szpak, Marek Szuba, Kieron Taylor, Anja Thormann, Glen Threadgold, Brandon Walts, Andrea Winterbottom, Marc Chakiachvili, Ameya Chaubal, Nishadi De Silva, Bethany Flint, Adam Frankish, Sarah E Hunt, Garth R IIsley, Nick Langridge, Jane E Loveland, Fergal J Martin, Jonathan M Mudge, Joanella Morales, Emily Perry, Magali Ruffier, John Tate, David Thybert, Stephen J Trevanion, Fiona Cunningham, Andrew D Yates, Daniel R Zerbino, Paul Flicek
Ensembl 2021.
Nucleic Acids Res. 2021, vol. 49(1):884–891
PubMed PMID: 33137190.
doi:10.1093/nar/gkaa942
Andrew D Yates, Premanand Achuthan, Wasiu Akanni, James Allen, Jamie Allen, Jorge Alvarez-Jarreta, M Ridwan Amode, Irina M Armean, Andrey G Azov, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, José Carlos Marugán, Carla Cummins, Claire Davidson, Kamalkumar Dodiya, Reham Fatima, Astrid Gall, Carlos Garcia Giro´n, Laurent Gil, Tiago Grego, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G Izuogu, Sophie H Janacek, Thomas Juettemann, Mike Kay, Ilias Lavidas, Tuan Le, Diana Lemos, Jose Gonzalez Martinez, Thomas Maurel, Mark McDowall, Aoife McMahon, Shamika Mohanan, Benjamin Moore, Michael Nuhn, Denye N Oheh, Anne Parker, Andrew Parton, Mateus Patricio, Manoj Pandian Sakthivel, Ahamed Imran Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, Mira Sycheva, Marek Szuba, Kieron Taylor, Anja Thormann, Glen Threadgold, Alessandro Vullo, Brandon Walts, Andrea Winterbottom, Amonida Zadissa, Marc Chakiachvili, Bethany Flint, Adam Frankish, Sarah E Hunt, Garth IIsley, Myrto Kostadima, Nick Langridge, Jane E Loveland, Fergal J Martin, Joannella Morales, Jonathan M Mudge, Matthieu Muffato, Emily Perry, Magali Ruffier, Stephen J Trevanion, Fiona Cunningham, Kevin L Howe, Daniel R Zerbino, Paul Flicek
Ensembl 2020.
PubMed PMID: 31691826.
doi:10.1093/nar/gkz966
Fiona Cunningham, Premanand Achuthan, Wasiu Akanni, James Allen, M. Ridwan Amode, Irina Armean, Ruth Bennett, Jyothish Bhai, Konstantinos Billis, Sanjay Boddu, Carla Cummins, Claire Davidson, Kamalkumar Jayantilal Dodiya, Astrid Gall, Carlos García Giro´n, Laurent Gil, Tiago Grego, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Mike Kay, Matthew R. Laird, Ilias Lavidas, Zhicheng Liu, Jane E. Loveland, José C Marugán, Thomas Maurel, Aoife C MacMahon, Benjamin Moore, Joannella Morales, Jonathan M Mudge, Michael Nuhn, Denye Ogeh, Anne Parker, Andrew Parton, Mateus Patricio, Ahamed Imran Abdul Salam, Bianca M Schmitt, Helen Schuilenburg, Dan Sheppard, Helen Sparrow, Eloise Stapleton, Marek Szuba, Kieron Taylor, Glen Threadgold, Anja Thormann, Alessandro Vullo, Brandon Walts, Andrea Winterbottom, Amonida Zadissa, Marc Chakiachvili, Adam Frankish, Sarah E. Hunt, Myrto Kostadima, Nicholas Langridge, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Dan M. Staines, Stephen J. Trevanion, Bronwen L. Aken, Andrew Yates, Daniel Zerbino, Paul Flicek
Ensembl 2019.
PubMed PMID: 30407521.
doi:10.1093/nar/gky1113
Sarah E Hunt, William McLaren, Laurent Gil, Anja Thormann, Helen Schuilenburg, Dan Sheppard, Andrew Parton, Irina M Armean, Stephen J Trevanion, Paul Flicek, Fiona Cunningham
Ensembl variation resources
Database Volume 2018
doi:10.1093/database/bay119
William Spooner, William McLaren, Timothy Slidel, Donna K. Finch, Robin Butler, Jamie Campbell, Laura Eghobamien, David Rider, Christine Mione Kiefer, Matthew J. Robinson, Colin Hardman, Fiona Cunningham, Tristan Vaughan, Paul Flicek and Catherine Chaillan Huntington
Haplosaurus computes protein haplotypes for use in precision drug design.
Nature Communications 9:4128(2018)
doi:10.1038/s41467-018-06542-1
Daniel R. Zerbino, Premanand Achuthan, Wasiu Akanni, M. Ridwan Amode, Daniel Barrell, Jyothish Bhai, Konstantinos Billis, Carla Cummins, Astrid Gall, Carlos García Giro´n, Laurent Gil, Leo Gordon, Leanne Haggerty, Erin Haskell, Thibaut Hourlier, Osagie G. Izuogu, Sophie H. Janacek, Thomas Juettemann, Jimmy Kiang To, Matthew R. Laird, Ilias Lavidas, Zhicheng Liu, Jane E. Loveland, Thomas Maurel, William McLaren, Benjamin Moore, Jonathan Mudge, Daniel N. Murphy, Victoria Newman, Michael Nuhn, Denye Ogeh, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Helen Schuilenburg, Dan Sheppard, Helen Sparrow, Kieron Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Amonida Zadissa, Adam Frankish, Sarah E. Hunt, Myrto Kostadima, Nicholas Langridge, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Dan M. Staines, Stephen J. Trevanion, Bronwen L. Aken, Fiona Cunningham, Andrew Yates, Paul Flicek
Ensembl 2018.
Nucleic Acids Res. 2018 46 Database issue:D754–D761.
PubMed PMID: 29155950.
doi:10.1093/nar/gkx1098
Bronwen L. Aken, Premanand Achuthan, Wasiu Akanni, M. Ridwan Amode, Friederike Bernsdorff, Jyothish Bhai, Konstantinos Billis, Denise Carvalho-Silva, Carla Cummins, Peter Clapham, Laurent Gil, Carlos García Girón, Leo Gordon, Thibaut Hourlier, Sarah E. Hunt, Sophie H. Janacek, Thomas Juettemann, Stephen Keenan, Matthew R. Laird, Ilias Lavidas, Thomas Maurel, William McLaren, Benjamin Moore, Daniel N. Murphy, Rishi Nag, Victoria Newman, Michael Nuhn, Chuang Kee Ong, Anne Parker, Mateus Patricio, Harpreet Singh Riat, Daniel Sheppard, Helen Sparrow, Kieron Taylor, Anja Thormann, Alessandro Vullo, Brandon Walts, Steven P. Wilder, Amonida Zadissa, Myrto Kostadima, Fergal J. Martin, Matthieu Muffato, Emily Perry, Magali Ruffier, Daniel M. Staines, Stephen J. Trevanion, Fiona Cunningham, Andrew Yates, Daniel R. Zerbino, Paul Flicek.
Ensembl 2017.
Nucleic Acids Res. 2017 45 Database issue:D635-D642.
PubMed PMID: 27899575; PubMed CentralPMCID: PMC5210575.
doi:10.1093/nar/gkw1104
Magali Ruffier, Andreas Kähäri, Monika Komorowska, Stephen Keenan, Matthew Laird, Ian Longden, Glenn Proctor, Steve Searle, Daniel Staines, Kieron Taylor, Alessandro Vullo, Andrew Yates, Daniel Zerbino, Paul Flicek
Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation
Database 2017, bax020
doi: 10.1093/database/bax020
Bronwen L. Aken, Sarah Ayling, Daniel Barrell1, Laura Clarke, Valery Curwen, Susan Fairley, Julio Fernandez Banet, Konstantinos Billis, Carlos Garcín Girón, Thibaut Hourlier, Kevin Howe, Andreas Kähäri, Felix Kokocinski, Fergal J. Martin, Daniel N. Murphy, Rishi Nag, Magali Ruffier, Michael Schuster, Y. Amy Tang, Jan-Hinnerk Vogel, Simon White, Amonida Zadissa, Paul Flicek and Stephen M. J. Searle
The Ensembl gene annotation system
Database 2016, baw093
doi: 10.1093/database/baw093
William McLaren, Laurent Gil, Sarah Hunt, Harpreet Riat, Graham Ritchie, Anja Thormann, Paul Flicek, Fiona Cunningham
The Ensembl Variant Effect Predictor
Genome Biology 2016, 17:122,
doi: 10.1186/s13059-016-0974-4
Miguel Pignatelli, Albert J. Vilella, Matthieu Muffato, Leo Gordon, Simon White, Paul Flicek, Javier Herrero
ncRNA orthologies in the vertebrate lineage.
Database (Oxford) 2016 pii:bav127.
PubMed PMID: 26896847; PubMed Central PMCID: PMC4761110
doi:10.1093/database/bav127.
Javier Herrero, Matthieu Muffato, Kathryn Beal, Stephen Fitzgerald, Leo Gordon, Miguel Pignatelli, Albert J. Vilella, Stephen M Searle, Ridwan Amode, Simon Brent, William Spooner, Eugene Kulesha, Andrew Yates, Paul Flicek
Ensembl comparative genomics resources.
Database (Oxford) 2016 pii:bav096.
PubMed PMID: 26896847; PubMed Central PMCID: PMC4761110
doi:10.1093/database/bav096.
Daniel R Zerbino, Nathan Johnson, Thomas Juetteman, Dan Sheppard, Steven P. Wilder, Ilias Lavidas, Michael Nuhn, Emily Perry, Quentin Raffaillac-Desfosses, Daniel Sobral, Damian Keefe, Stefan Grä, Ikhlak Ahmed, Rhoda Kinsella, Bethan Pritchard, Simon Brent, Ridwan Amode, Anne Parker, Stephen Trevanion, Ewan Birney, Ian Dunham, Paul Flicek
Ensembl regulation resources.
Database (Oxford) 2016 pii:bav119.
PubMed PMID: 26888907; PubMed Central PMCID: PMC4756621.
doi:10.1093/database/bav119.
Andrew Yates, Wasiu Akanni, M. Ridwan Amode, Daniel Barrell, Konstantinos Billis, Denise Carvalho-Silva, Carla Cummins, Peter Clapham, Stephen Fitzgerald, Laurent Gil1 Carlos Garcín 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 McLaren, Daniel N. Murphy, Rishi Nag, Michael Nuhn, Anne Parker, Mateus Patricio, Miguel Pignatelli, Matthew Rahtz, Harpreet Singh Riat, Daniel Sheppard, Kieron Taylor, Anja Thormann, Alessandro Vullo, Steven P. Wilder, Amonida Zadissa, Ewan Birney, Jennifer 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. 2016 44 Database issue:D710-6.
PubMed PMID: 26687719; PubMed CentralPMCID: PMC4702834.
doi:10.1093/nar/gkv1157
Daniel R Zerbino, Steven P Wilder, Nathan Johnson, Thomas Juettemann and Paul R Flicek
The Ensembl Regulatory Build
Genome Biology (2015) 16:56
doi:10.1186/s13059-015-0621-5
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 Garcín 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 McLaren, Daniel N. Murphy, Rishi Nag, Bert Overduin, Anne Parker, Mateus Patricio, Emily Perry, Miguel Pignatelli, Harpreet Singh Riat, Daniel Sheppard, Kieron Taylor, Anja Thormann, Alessandro Vullo, Steven P. Wilder, Amonida Zadissa, Bronwen L. Aken, Ewan Birney, Jennifer Harrow, Rhoda Kinsella, Matthieu Muffato, Magali Ruffier, Stephen M.J. Searle, Giulietta Spudich, Stephen J. Trevanion, Andy Yates, Daniel R. Zerbino and Paul Flicek
Ensembl 2015
Nucleic Acids Research 2015 43 Database issue:D662-D669
doi: 10.1093/nar/gku1010
Andrew Yates, Kathryn Beal, Stephen Keenan, William McLaren, Miguel Pignatelli, Graham R. S. Ritchie, Magali Ruffier, Kieron Taylor, Alessandro Vullo, Paul Flicek
The Ensembl REST API: Ensembl Data for Any Language
Bioinformatics 2014 31: 143-14
doi: 10.1093/bioinformatics/btu613
Zerbino DR, Johnson N, Juettemann T, Wilder SP, Flicek P.
WiggleTools: parallel processing of large collections of genome-wide datasets for visualization and statistical analysis.
Bioinformatics 2014 30:1008-9
doi: 10.1093/bioinformatics/btt73731
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 Hunt, Nathan Johnson, Thomas Juettemann, Andreas K. 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 S. Riat, Magali Ruffier, Daniel Sheppard, Kieron Taylor, Anja Thormann, Stephen J. Trevanion, Alessandro Vullo, Steven P. Wilder, Mark Wilson, Amonida Zadissa, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Jennifer Harrow, Javier Herrero, Tim J.P. Hubbard, Rhoda Kinsella, Matthieu Muffato, Anne Parker, Giulietta Spudich, Andy Yates, Daniel R. Zerbino, and Stephen M.J. Searle
Ensembl 2014
Nucleic Acids Research 2014 42 Database issue:D749-D755
doi: 10.1093/nar/gkt1196
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 Garcia-Girón, Leo Gordon, Thibaut Hourlier, Sarah Hunt, Thomas Juettemann, Andreas Kähäri, Stephen Keenan, Monika Komorowska, Eugene Kulesha, Ian Longden, Thomas Maurel, William McLaren, Mattieu 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 Taylor, Anja Thormann, Stephen Trevanion, Simon White, Steven P. Wilder, Bronwen L. Aken, Ewan Birney, Fiona Cunningham, Ian Dunham, Jennifer Harrow, Javier Herrero, Tim J. P. Hubbard, Nathan Johnson, Rhoda Kinsella, Anne Parker, Giulietta Spudich, Andy Yates, Amonida Zadissa and Stephen M. J. Searle
Ensembl 2013
Nucleic Acids Research 2013 41 Database issue:D48-D55
doi: 10.1093/nar/gks1236
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 McLaren, Mattieu Muffato, Bert Overduin, Miguel Pignatelli, Bethan Pritchard, Harpreet Singh Riat, Graham R. S. Ritchie, Magali Ruffier, Michael Schuster, Daniel Sobral, Y. Amy Tang, Kieron Taylor, Stephen 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 Harrow, Javier Herrero, Tim J. P. Hubbard, Anne Parker, Glenn Proctor, Giulietta Spudich, Jan Vogel, Andy Yates, Amonida Zadissa and Stephen M. J. Searle
Ensembl 2012
Nucleic Acids Research 2012 40 Database issue:D84-D90
doi:10.1093/nar/gkr991
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 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 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 and Stephen M. J. Searle
Ensembl 2011
Nucleic Acids Research 2011 39 Database issue:D800-D806
doi:10.1093/nar/gkq1064
Kinsella RJ, Kähäri A, Haider S, Zamora J, Proctor G, Spudich G, Almeida-King J, Staines D, Derwent P, Kerhornou A, Kersey P, Flicek P. Ensembl BioMarts: a hub for data retrieval across taxonomic space.
Database (Oxford). Vol. 2011 Published online Jul 23, 2011
McLaren W, Pritchard B, Rios D, Chen Y, Flicek P, Cunningham F.
Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor.
BMC Bioinformatics26(16):2069-70(2010)
doi:10.1093/bioinformatics/btq330
BMC Bioinformatics - Ensembl Update 2010
- Jessica Severin, Kathryn Beal, Albert J Vilella, Stephen Fitzgerald, Michael Schuster, Leo Gordon, Abel Ureta-Vidal, Paul Flicek, Javier Herrero
  eHive: An Artificial Intelligence workflow system for genomic analysis
  BMC Bioinformatics 2010, 11:240 (11 May 2010) [Abstract]
- Yuan Chen, Fiona Cunningham, Daniel Rios, William M McLaren, James A Smith, Bethan Pritchard, Giulietta M Spudich, Simon Brent, Eugene Kulesha, Pablo Marin-Garcia, Damian Smedley, Ewan Birney, Paul Flicek
  Ensembl variation resources
  BMC Bioinformatics 2010, 11:293 (11 May 2010) [Abstract]
- 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 Bioinformatics 2010, 11:238 (11 May 2010) [Abstract]
- Benoît Ballester, Nathan Johnson, Glenn Proctor, Paul Flicek
  Consistent annotation of gene expression arrays
  BMC Bioinformatics 2010, 11:294 (11 May 2010) [Abstract]
- Giulietta M Spudich, Xosé M Fernández-Suárez
  Touring Ensembl: A practical guide to genome browsing
  BMC Bioinformatics 2010, 11:295 (11 May 2010) [Abstract]
- Anne Parker, Eugene Bragin, Simon Brent, Bethan Pritchard, James A Smith, Stephen Trevanion
  Using caching and optimization techniques to improve performance of the Ensembl website
  BMC Bioinformatics 2010, 11:239 (11 May 2010) [Abstract]
Paul Flicek, Bronwen L. Aken, Benoit 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 Jenkinson, Nathan Johnson, Andreas Kähäri Damian Keefe, Stephen Keenan, Rhoda Kinsella, Felix Kokocinski, Gautier Koscielny, Eugene Kulesha, Daniel Lawson, Ian Longden, Tim Massingham, William McLaren, Karyn Megy, Bert Overduin, Bethan Pritchard, Daniel Rios, Magali Ruffier, Michael Schuster, Guy Slater, Damian Smedley, Giulietta Spudich, Y. Amy Tang, Stephen Trevanion, Albert Vilella, Jan Vogel, Simon White, Steven P. Wilder, Amonida Zadissa, Ewan Birney, Fiona Cunningham, Ian Dunham, Richard Durbin, Xosée M. Fernández-Suarez, Javier Herrero ,Tim J. P. Hubbard, Anne Parker, Glenn Proctor, James Smith, and Stephen M. J. Searle
Ensembl's 10th year
Nucleic Acids Research 2010 38 Database issue:D557-D562
doi:10.1093/nar/gkp972
Xosé M. Fernández-Suárez and Michael K. Schuster
Using the Ensembl Genome Server to Browse Genomic Sequence Data.
UNIT 1.15 in Current Protocols in Bioinformatics, Jun 2010.
www.ncbi.nlm.nih.gov/pubmed/20521244
Giulietta M Spudich and Xosé M Fernández-Suárez
Touring Ensembl: A practical guide to genome browsing
BMC Genomics 2010, 11:295 (11 May 2010)
www.biomedcentral.com/1471-2164/11/295
T. J. P. Hubbard, B. L. Aken, S. Ayling, B. Ballester, K. Beal, E. Bragin, S. Brent, Y. Chen, P. Clapham, L. Clarke, G. Coates, S. Fairley, S. Fitzgerald, J. Fernandez-Banet, L. Gordon, S. Gräf, S. Haider, M. Hammond, R. Holland, K. Howe, A. Jenkinson, N. Johnson, A. Kähäri, D. Keefe, S. Keenan, R. Kinsella, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard, D. Rios, M. Schuster, G. Slater, D. Smedley, W. Spooner, G. Spudich, S. Trevanion, A. Vilella, J. Vogel, S. White, S. Wilder, A. Zadissa, E. Birney, F. Cunningham, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, J. Herrero, A. Kasprzyk, G. Proctor, J. Smith, S. Searle and P. Flicek
Ensembl 2009
Nucleic Acids Research 2009 37 Database issue:D690-D697
doi:10.1093/nar/gkn828
A.J. Vilella, J. Severin, A. Ureta-Vidal, R. Durbin, L. Heng and E. Birney
EnsemblCompara GeneTrees: Analysis of complete, duplication-aware phylogenetic trees in vertebrates.
Genome Research 2009 19:327-335
doi:10.1101/gr.073585.107
P. Flicek, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer, T. Eyre, S. Fitzgerald, J. Fernandez-Banet, S. Gräf, S. Haider, M. Hammond, R. Holland, K. L. Howe, K. Howe, N. Johnson, A. Jenkinson, A. Kähäri, D. Keefe, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, K. Megy, P. Meidl, B. Overduin, A. Parker, B. Pritchard, A. Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, G. Slater, D. Smedley, G. Spudich, S. Trevanion, A. J. Vilella, J. Vogel, S. White, M. Wood, E. Birney, T. Cox, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, J. Herrero, T. J. P. Hubbard, A. Kasprzyk, G. Proctor, J. Smith, A. Ureta-Vidal and S. Searle.
Ensembl 2008
Nucleic Acids Research 2008 36 Database issue:D707-14.
doi:10.1093/nar/gkm988
B. Paten, J. Herrero, S. Fitzgerald, K. Beal, P. Flicek, I. Holmes and E. Birney
Genome-wide nucleotide-level mammalian ancestor reconstruction
Genome Research 2008 18:1829-1843
doi:10.1101/gr.076521.108
B. Paten, J. Herrero, K. Beal, S. Fitzgerald and E. Birney
Enredo and Pecan: Genome-wide mammalian consistency-based multiple alignment with paralogs
Genome Research 2008 18: 1814-1828
doi:10.1101/gr.076554.108
Giulietta Spudich, Xosé M. Fernández-Suárez and Ewan Birney
Genome Browsing with Ensembl: a practical overview
Brief Funct Genomic Proteomic, 2007 Sept; 6: 202-219
T. J. P. Hubbard, B. L. Aken, K. Beal, B. Ballester, M. Caccamo, Y. Chen, L. Clarke, G. Coates, F. Cunningham, T. Cutts, T. Down, S. C. Dyer, S. Fitzgerald, J. Fernandez-Banet, S. Graf, S. Haider, M. Hammond, J. Herrero, R. Holland, K. Howe, K. Howe, N. Johnson, A. Kahari, D. Keefe, F. Kokocinski, E. Kulesha, D. Lawson, I. Longden, C. Melsopp, K. Megy, P. Meidl, B. Overduin, A. Parker, A. Prlic, S. Rice, D. Rios, M. Schuster, I. Sealy, J. Severin, G. Slater, D. Smedley, G. Spudich, S. Trevanion, A. Vilella, J. Vogel, S. White, M. Wood, T. Cox, V. Curwen, R. Durbin, X. M. Fernandez-Suarez, P. Flicek, A. Kasprzyk, G. Proctor, S. Searle, J. Smith, A. Ureta-Vidal and E. Birney
Ensembl 2007
Nucleic Acids Research. 2007 Vol. 35, Database issue:D610-D617.
doi:10.1093/nar/gkl996
E. Birney, D. Andrews, M. Caccamo, Y. Chen, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, P. Flicek, S. Gräf, M. Hammond, J. Herrero, K. Howe, V. Iyer, K. Jekosch, A. Kähäri, A. Kasprzyk, D. Keefe, F. Kokocinski, E. Kulesha, D. London, I. Longden, C. Melsopp, P. Meidl, B. Overduin, A. Parker, G. Proctor, A. Prlic, M. Rae, D. Rios, S. Redmond, M. Schuster, I. Sealy, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, A. Stabenau, J. Stalker, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark and T. J. P. Hubbard
Ensembl 2006
Nucleic Acids Research 2006 Jan 1;34 Database issue:D556-D561.
doi:10.1093/nar/gkj133
Guy St. C. Slater and Ewan Birney
Automated generation of heuristics for biological sequence comparison.
BMC Bioinformatics. 2005 Feb 15;6(1):31
doi:10.1186/1471-2105-6-31
T. Hubbard, D. Andrews, M. Caccamo, G. Cameron, Y. Chen, M. Clamp, L. Clarke, G. Coates, T. Cox, F. Cunningham, V. Curwen, T. Cutts, T. Down, R. Durbin, X. M. Fernandez-Suarez, J. Gilbert, M. Hammond, J. Herrero, H. Hotz, K. Howe, V. Iyer, K. Jekosch, A. Kahari, A. Kasprzyk, D. Keefe, S. Keenan, F. Kokocinsci, D. London, I. Longden, G. McVicker, C. Melsopp, P. Meidl, S. Potter, G. Proctor, M. Rae, D. Rios, M. Schuster, S. Searle, J. Severin, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, S. Trevanion, A. Ureta-Vidal, J. Vogel, S. White, C. Woodwark and E. Birney
Ensembl 2005
Nucleic Acids Research 2005 Jan 1;33 Database issue:D447-D453.
doi:10.1093/nar/gki138
J. L. Ashurst, C.-K. Chen, J. G. R. Gilbert, K. Jekosch, S. Keenan, P. Meidl, S. M. Searle, J. Stalker, R. Storey, S. Trevanion, L. Wilming and T. Hubbard
The Vertebrate Genome Annotation (Vega) database.
Nucleic Acids Res. 2005 Jan 1;33 Database issue:D459-D465.
doi:10.1093/nar/gki135
International Chicken Genome Sequencing Consortium.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution.
Nature 2004 432(7018):695-716.
doi:10.1038/nature03154
International Human Genome Sequencing Consortium.
Finishing the euchromatic sequence of the human genome
Nature. 2004 Oct 21;431(7011):931-945.
doi:10.1038/nature03001
Martin P. Hammond and Ewan Birney
Genome information resources - developments at Ensembl
Trends Genetics 2004 20(6):268-272.
doi:10.1016/j.tig.2004.04.002
Genome Research Ensembl Special

The May 2004 issue of Genome Research includes an Ensembl special covering detailed aspects of the Ensembl web site, the underlying scalable database system for storing genome sequence and annotation information, as well as the automated genome analysis and annotation pipeline.
- Ewan Birney, T. Daniel Andrews, Paul Bevan, Mario Caccamo, Yuan Chen, Laura Clarke, Guy Coates, James Cuff, Val Curwen, Tim Cutts, Thomas Down, Eduardo Eyras, Xose M. Fernandez-Suarez, Paul Gane, Brian Gibbins, James Gilbert, Martin Hammond, Hans-Rudolf Hotz, Vivek Iyer, Kerstin Jekosch, Andreas Kahari, Arek Kasprzyk, Damian Keefe, Stephen Keenan, Heikki Lehvaslaiho, Graham McVicker, Craig Melsopp, Patrick Meidl, Emmanuel Mongin, Roger Pettett, Simon Potter, Glenn Proctor, Mark Rae, Steve Searle, Guy Slater, Damian Smedley, James Smith, Will Spooner, Arne Stabenau, James Stalker, Roy Storey, Abel Ureta-Vidal, K. Cara Woodwark, Graham Cameron, Richard Durbin, Anthony Cox, Tim Hubbard and Michele Clamp
  An Overview of Ensembl
  Genome Research 2004 14(5):925-928.
  doi:10.1101/gr.1860604
- Arne Stabenau, Graham McVicker, Craig Melsopp, Glenn Proctor, Michele Clamp and Ewan Birney
  The Ensembl Core Software Libraries
  Genome Research 2004 14(5):929-933.
  doi:10.1101/gr.1857204
- Simon C. Potter, Laura Clarke, Val Curwen, Stephen Keenan, Emmanuel Mongin, Stephen M.J. Searle, Arne Stabenau, Roy Storey and Michele Clamp
  The Ensembl Analysis Pipeline
  Genome Research 2004 14(5):934-941.
  doi:10.1101/gr.1859804
- Val Curwen, Eduardo Eyras, T. Daniel Andrews, Laura Clarke, Emmanuel Mongin, Steven M.J. Searle and Michele Clamp
  The Ensembl Automatic Gene Annotation System
  Genome Research 2004 14(5):942-950.
  doi:10.1101/gr.1858004
- James Stalker, Brian Gibbins, Patrick Meidl, James Smith, William Spooner, Hans-Rudolf Hotz and Antony V. Cox
  The Ensembl Web Site: Mechanics of a Genome Browser
  Genome Research 2004 14(5):951-955.
  doi:10.1101/gr.1863004
- Stephen B. Montgomery, Tamara Astakhova, Mikhail Bilenky, Ewan Birney, Tony Fu, Maik Hassel, Craig Melsopp, Marcin Rak, A. Gordon Robertson, Monica Sleumer, Asim S. Siddiqui and Steven J.M. Jones
  Sockeye: A 3D Environment for Comparative Genomics
  Genome Research 2004 14(5):956-962.
  doi:10.1101/gr.1890304
- Stephen M.J. Searle, James Gilbert, Vivek Iyer and Michele Clamp
  The Otter Annotation System
  Genome Research 2004 14(5):963-970.
  doi:10.1101/gr.1864804
- James A. Cuff, Guy M.P. Coates, Tim J.R. Cutts and Mark Rae
  The Ensembl Computing Architecture
  Genome Research 2004 14(5):971-975.
  doi:10.1101/gr.1866304
- Eduardo Eyras, Mario Caccamo, Val Curwen and Michele Clamp
  ESTGenes: Alternative Splicing From ESTs in Ensembl
  Genome Research 2004 14(5):976-987.
  doi:10.1101/gr.1862204
- Ewan Birney, Michele Clamp and Richard Durbin
  GeneWise and Genomewise
  Genome Research 2004 14(5):988-995.
  doi:10.1101/gr.1865504
Rat Genome Sequencing Project Consortium.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution.
Nature. 2004 428(6982):493-521.
doi:10.1038/nature02426
Emmanuel Mongin, Christos Louis, Robert A. Holt, Ewan Birney and Frank H. Collins
The Anopheles gambiae genome: an update.
Trends in Parasitology 2004 20(2):49-52.
doi:10.1016/j.pt.2003.11.003
Arek Kasprzyk, Damian Keefe, Damian Smedley, Darin London, William Spooner, Craig Melsopp, Martin Hammond, Philippe Rocca-Serra, Tony Cox and Ewan Birney
EnsMart: A Generic System for Fast and Flexible Access to Biological Data.
Genome Research 2004 14(1):160-169.
doi:10.1101/gr.1645104
E. Birney, D. Andrews, P. Bevan, M. Caccamo, G. Cameron, Y. Chen, L. Clarke, G. Coates, T. Cox, J. Cuff, V. Curwen, T. Cutts, T. Down, R. Durbin, E. Eyras, X. M. Fernandez-Suarez, P. Gane, B. Gibbins, J. Gilbert, M. Hammond, H. Hotz, V. Iyer, A. Kahari, K. Jekosch, A. Kasprzyk, D. Keefe, S. Keenan, H. Lehvaslaiho, G. McVicker, C. Melsopp, P. Meidl, E. Mongin, R. Pettett, S. Potter, G. Proctor, M. Rae, S. Searle, G. Slater, D. Smedley, J. Smith, W. Spooner, A. Stabenau, J. Stalker, R. Storey, A. Ureta-Vidal, C. Woodwark, M. Clamp and T. Hubbard
Ensembl 2004
Nucleic Acids Research 2004 32 Database issue:D468-70.
[Abstract] [Full text]
M. Clamp, D. Andrews, D. Barker, P. Bevan, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, T. Hubbard, A. Kasprzyk, D. Keefe, H. Lehvaslaiho, V. Iyer, C. Melsopp, E. Mongin, R. Pettett, S. Potter, A. Rust, E. Schmidt, S. Searle, G. Slater, J. Smith, W. Spooner, A. Stabenau, J. Stalker, E. Stupka, A. Ureta-Vidal, I. Vastrik and E. Birney
Ensembl 2002: accommodating comparative genomics.
Nucleic Acids Research 2003 31(1):38-42.
[Abstract] [Full text]
Mouse Genome Sequencing Consortium.
Initial sequencing and comparative analysis of the mouse genome.
Nature. 2002 Dec 5;420(6915):520-562.
doi:10.1038/nature01262
T. Hubbard, D. Barker, E. Birney, G. Cameron, Y. Chen, L. Clark, T. Cox, J. Cuff, V. Curwen, T. Down, R. Durbin, E. Eyras, J. Gilbert, M. Hammond, L. Huminiecki, A. Kasprzyk, H. Lehvaslaiho, P. Lijnzaad, C. Melsopp, E. Mongin, R. Pettett, M. Pocock, S. Potter, A. Rust, E. Schmidt, S. Searle, G. Slater, J. Smith, W. Spooner, A. Stabenau, J. Stalker, E. Stupka, A. Ureta-Vidal, I. Vastrik and M. Clamp.
The Ensembl genome database project.
Nucleic Acids Research 2002 30(1):38-41.
[Abstract] [Full text]