Scientific publications (and how to cite us)

Citing Ensembl Genomes

To cite the use of Ensembl Genomes, please quote this paper:

Paul Julian Kersey, James E. Allen, Irina Armean, Sanjay Boddu, Bruce J. Bolt, Denise Carvalho-Silva, Mikkel Christensen, Paul Davis, Lee J. Falin, Christoph Grabmueller, Jay Humphrey, Arnaud Kerhornou, Julia Khobova, Naveen K. Aranganathan, Nicholas Langridge, Ernesto Lowy, Mark D. McDowall, Uma Maheswari, Michael Nuhn, Chuang Kee Ong, Bert Overduin, Michael Paulini1, Helder Pedro1, Emily Perry, Giulietta Spudich, Electra Tapanari, Brandon Walts, Gareth Williams, Marcela Tello–Ruiz, Joshua Stein, Sharon Wei, Doreen Ware, Daniel M. Bolser, Kevin L. Howe, Eugene Kulesha, Daniel Lawson, Gareth Maslen and Daniel M. Staines
Ensembl Genomes 2016: more genomes, more complexity
Nucleic Acids Research, 2015
doi: 10.1093/nar/gkv1209

Citing Ensembl BioMarts

To cite the use of Ensembl BioMarts, please quote this paper:

R. J. Kinsella, A. Kähäri, S. Haider, J. Zamora, G. Proctor, G. Spudich, J. Almeida-King, D. Staines, P. Derwent, A. Kerhornou, P. Kersey, P. Flicek
Ensembl BioMarts: a hub for data retrieval across taxonomic space
Database: the journal of biological databases and curation 2011
PMID: 21785142
doi:10.1093/database/bar030

Other publications associated with the Ensembl Genomes project

Paul Julian Kersey, James E. Allen, Mikkel Christensen, Paul Davis, Lee J.Falin, Christoph Grabmueller, Daniel Seth Toney Hughes, Jay Humphrey, Arnaud Kerhornou, Julia Khobova, Nicholas Langridge, Mark D. McDowall, Uma Maheswari, Gareth Maslen, Michael Nuhn, Chuang Kee Ong, Michael Paulini, Helder Pedro, Iliana Toneva, Mary Ann Tuli, Brandon Walts, Gareth Williams, Derek Wilson, Ken Youens-Clark, Marcela K. Monaco, Joshua Stein, Xuehong Wei, Doreen Ware, Daniel M. Bolser, Kevin Lee Howe, Eugene Kulesha, Daniel Lawson and Daniel Michael Staines
Ensembl Genomes 2013: scaling up access to genome-wide data
Nucleic acids research 2014, 42 (D1): D546-D552
PMID: 24163254
doi:10.1093/nar/gkt979

Marcela K Monaco, Joshua Stein, Sushma Naithani, Sharon Wei, Palitha Dharmawardhana, Sunita Kumari, Vindhya Amarasinghe, Ken Youens-Clark, James Thomason, Justin Preece, Shiran Pasternak, Andrew Olson, Yinping Jiao, Zhenyuan Lu, Dan Bolser, Arnaud Kerhornou, Dan Staines, Brandon Walts, Guanming Wu, Peter D’Eustachio, Robin Haw, David Croft, Paul J Kersey, Lincoln Stein, Pankaj Jaiswal, Doreen Ware.
Gramene 2013: comparative plant genomics resources
Nucleic Acids Reseach2014, 42 (D1): D1193-D1199
PMID: 24217918
doi: 10.1093/nar/gkt1110

Todd W Harris, Joachim Baran, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J Chen, Paul Davis, James Done, Christian Grove, Kevin Howe, Ranjana Kishore, Raymond Lee, Yuling Li, Hans-Michael Muller, Cecilia Nakamura, Philip Ozersky, Michael Paulini, Daniela Raciti, Gary Schindelman, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, JD Wong, Karen Yook, Tim Schedl, Jonathan Hodgkin, Matthew Berriman, Paul Kersey, John Spieth, Lincoln Stein, Paul W Sternberg
WormBase 2014: new views of curated biology
Nucleic Acids Reseach 2014, 42 (D1): D789-D793
PMID: 24194605
doi: 10.1093/nar/gkt1063

Dana Nayduch, Lee W. Cohnstaedt, Christopher Saski, Daniel Lawson, Paul Kersey, Mark Fife, and Simon Carpenter
Studying Culicoides vectors of BTV in the post-genomic era: Resources, bottlenecks to progress and future directions
Virus Research 2013
PMID: 24355835
doi:/10.1016/j.virusres.2013.12.009

Keith R Bradnam, Joseph N Fass, Anton Alexandrov, Paul Baranay, Michael Bechner, İnanç Birol, Sébastien Boisvert10, Jarrod A Chapman, Guillaume Chapuis, Rayan Chikhi, Hamidreza Chitsaz, Wen-Chi Chou, Jacques Corbeil, Cristian Del Fabbro, T Roderick Docking, Richard Durbin, Dent Earl, Scott Emrich, Pavel Fedotov, Nuno A Fonseca, Ganeshkumar Ganapathy, Richard A Gibbs, Sante Gnerre, Élénie Godzaridis, Steve Goldstein, Matthias Haimel, Giles Hall, David Haussler, Joseph B Hiatt, Isaac Y Ho, Jason Howard, Martin Hunt, Shaun D Jackman, David B Jaffe, Erich Jarvis, Huaiyang Jiang, Sergey Kazakov, Paul J Kersey, Jacob O Kitzman, James R Knight, Sergey Koren, Tak-Wah Lam, Dominique Lavenier, François Laviolette, Yingrui Li, Zhenyu Li, Binghang Liu, Yue Liu, Ruibang Luo, Iain MacCallum, Matthew D MacManes, Nicolas Maillet, Sergey Melnikov, Bruno Miguel Vieira, Delphine Naquin, Zemin Ning, Thomas D Otto, Benedict Paten, Octávio S Paulo, Adam M Phillippy, Francisco Pina-Martins, Michael Place, Dariusz Przybylski, Xiang Qin, Carson Qu, Filipe J Ribeiro, Stephen Richards, Daniel S Rokhsar, J Graham Ruby, Simone Scalabrin, Michael C Schatz, David C Schwartz, Alexey Sergushichev, Ted Sharpe, Timothy I Shaw, Jay Shendure, Yujian Shi, Jared T Simpson, Henry Song, Fedor Tsarev, Francesco Vezzi, Riccardo Vicedomini, Jun Wang, Kim C Worley, Shuangye Yin, Siu-Ming Yiu, Jianying Yuan, Guojie Zhang, Hao Zhang, Shiguo Zhou, Ian F Korf.
Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species
GigaScience 2013, 2:10
PMID: 23870653
doi:10.1186/2047-217X-2-10

Rachel Brenchley, Manuel Spannagl, Matthias Pfeifer, Gary LA Barker, Rosalinda D’Amore, Alexandra M Allen, Neil McKenzie, Melissa Kramer, Arnaud Kerhornou, Dan Bolser, Suzanne Kay, Darren Waite, Martin Trick, Ian Bancroft, Yong Gu, Naxin Huo, Ming-Cheng Luo, Sunish Sehgal, Bikram Gill, Sharyar Kianian, Olin Anderson, Paul Kersey, Jan Dvorak, W Richard McCombie, Anthony Hall, Klaus FX Mayer, Keith J Edwards, Michael W Bevan, Neil Hall.
Analysis of the bread wheat genome using whole-genome shotgun sequencing
Nature 2012, 491, 705–710
PMID: 23192148
doi:10.1038/nature11650

Paul J. Kersey, Daniel M. Staines, Daniel Lawson, Eugene Kulesha, Paul Derwent, Jay C. Humphrey, Daniel S. T. Hughes, Stephan 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 Yates and Ewan Birney.
Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species
Nucleic Acids Research 2012, 40 (D1): D91-D97
PMID: 22067447
doi:10.1093/nar/gkr895

Baerenfaller K, Bastow R, Benyon J, Brady S, Brendel V, Donaldson S, Dooley R, Forster M,
Friesner J, Gifford D, Grotewold E, et al.
Taking the next step: Building an Arabidopsis Information Portal
The Plant Cell 2012, 24(6): 2248–2256
PMID: 22751211
doi:10.1105/tpc.112.100669

J. Chan, R. Kishore, P. Sternberg, K. Van Auken.
The Gene Ontology: enhancements for 2011
Nucleic Acids Research 2012, 40 (D1): D559-D564
PMID: 22102568
doi:10.1093/nar/gkr1028

K. Howe, P. Davis, M. Paullini, M.A. Tuli, G. Williams, K. Yook, R. Durbin, P. Kersey, P. Sternberg
WormBase: Annotating many nematode genomes
Worm 2012, 1:1
PMID: 24058818
doi:10.4161/worm.19574

K. Yook, T.W. Harris, T. Bieri, A. Cabunoc, J. Chan, W.J. Chen, P. Davis, N. de la Cruz, A. Duong, R. Fang, U. Ganesan, C. Grove, K. Howe, S. Kadam, R. Kishore, R. Lee, Y. Li, H.M. Muller, C. Nakamura, B. Nash, P. Ozersky, M. Paulini, D. Raciti, A. Rangarajan, G. Schindelman, X. Shi, E.M. Schwarz, M. Ann Tuli, K. Van Auken, D. Wang, X. Wang, G. Williams, J. Hodgkin, M. Berriman, R. Durbin, P. Kersey, J. Spieth, L. Stein, P.W. Sternberg
WormBase 2012: more genomes, more data, new website
Nucleic acids research 2012, 40 (D1): D735-D741
PMID: 22067452
doi:10.1093/nar/gkr954

V. Wood, M.A. Harris, M.D. McDowall, K. Rutherford, B.W. Vaughan, D.M. Staines, M. Aslett, A. Lock, J. Bähler, P.J. Kersey, S.G. Oliver
PomBase: a comprehensive online resource for fission yeast
Nucleic acids research 2012, 40 (D1): D695-D699
PMID: 22039153
doi:10.1093/nar/gkr853

X. Gan, O. Stegle, J. Behr, J.G. Steffen, P. Drewe, K.L. Hildebrand, R. Lyngsoe, S.J. Schultheiss, E.J. Osborne, V.T. Sreedharan, A. Kahles, R. Bohnert, G. Jean, P. Derwent, P. Kersey, E.J. Belfield, N.P. Harberd, E. Kemen, C. Toomajian, P.X. Kover, R.M. Clark, G. Rätsch, R. Mott
Multiple reference genomes and transcriptomes for Arabidopsis thaliana
Nature 2011, 477 (7365): 419-423
PMID: 21874022
doi:10.1038/nature10414

R.J. Kinsella, A. Kähäri, S. Haider, J. Zamora, G. Proctor, G. Spudich, J. Almeida-King, D. Staines, P. Derwent, A. Kerhornou, P. Kersey, P. Flicek
Ensembl BioMarts: a hub for data retrieval across taxonomic space
Database: the journal of biological databases and curation 2011
PMID: 21785142
doi:10.1093/database/bar030

K. Youens-Clark, E. Buckler, T. Casstevens, C. Chen, G. DeClerck, P. Derwent, P. Dharmawardhana, P. Jaiswal, P. Kersey, A.S. Karthikeyan, J. Lu, S.R. McCouch, L. Ren, W. Spooner, J.C. Stein, J. Thomason, S. Wei, D. Ware
Gramene database in 2010: updates and extensions
Nucleic acids research 2011, 39 (suppl 1): D1085-D1094
PMID: 21076153
doi:10.1093/nar/gkq1148

International Arabidopsis Informatics Consortium
An international bioinformatics infrastructure to underpin the Arabidopsis community
Plant Cell 2010, 22 (8): 2530-2536
PMID: 20807877
doi:10.1105/tpc.110.078519

P.J. Kersey, D. Lawson, E. Birney, P.S. Derwent, M. Haimel, J. Herrero, S. Keenan, A. Kerhornou, G. Koscielny, A. Kähäri, R.J. Kinsella, E. Kulesha, U. Maheswari, K. Megy, M. Nuhn, G. Proctor, D. Staines, F. Valentin, A.J. Vilella, A. Yates
Ensembl Genomes: extending Ensembl across the taxonomic space
Nucleic acids research 2010, 38 (suppl 1): D563-D569
PMID: 19884133
doi:10.1093/nar/gkp871

A list of publications linked to the Ensembl project is available here.