EUROPEAN MOLECULAR BIOLOGY LABORATORY United Kingdom

http://www.ebi.ac.uk

The European Bioinformatics Institute (EBI) is an academic research institute located on the Wellcome Trust Genome Campus in Hinxton near Cambridge (UK), part of the European Molecular Biology Laboratory (EMBL).

The EBI's mission:

  • To provide freely available data and bioinformatics services to all facets of the scientific community in ways that promote scientific progress
  • To contribute to the advancement of biology through basic investigator-driven research in bioinformatics
  • To provide advanced bioinformatics training to scientists at all levels, from PhD students to independent investigators
  • To help disseminate cutting-edge technologies to industry

Prof. Paul Kersey

Dr. Paul Kersey leads the Ensembl Genomes team at the EBI, which provides services for genome-scale data from non-vertebrate species, primarily through the use of the Ensembl software platform. The team integrates data from across the taxonomic space, and collaborates closely with particular groups involved in genome annotation and the development of domain-specific resources. The team particulates in the WormBase, VectorBase and PomBase consortia (developing resources for nematodes, insect vectors of human pathogens, and the model fungus fission yeast) respectively, and coordinates the PhytoPath project (for plant pathogens), and the EC FP7 consortia Microme (focused on microbial pathways) and transPLANT (focused on plant genomics). Particular areas of interest include genome assembly, comparative genomics and variation.

Publications

WormBase 2012: more genomes, more data, new website Karen Yook, Todd W Harris, Tamberlyn Bieri, Abigail Cabunoc, Juancarlos Chan, Wen J Chen, Paul Davis, Norie de la Cruz, Adrian Duong, Ruihua Fang, Uma Ganesan, Christian Grove, Kevin Howe, Snehalata Kadam, Ranjana Kishore, Raymond Lee, Yuling Li, Hans-Michael Muller, Cecilia Nakamura, Bill Nash, Philip Ozersky, Michael Paulini, Daniela Raciti, Arun Rangarajan, Gary Schindelman, Xiaoqi Shi, Erich M Schwarz, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Jonathan Hodgkin, Matthew Berriman, Richard Durbin, Paul Kersey, John Spieth, Lincoln Stein, Paul W Sternberg Nucleic Acids Research 40 D735-D741 2012.

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species Paul J Kersey, Daniel M Staines, Daniel Lawson, Eugene Kulesha, Paul Derwent, Jay C Humphrey, Daniel ST 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, Ewan Birney Nucleic Acids Research 40 D91-97 2012.

PomBase: a comprehensive online resource for fission yeast Valerie Wood, Midori A Harris, Mark D McDowall, Kim Rutherford, Brendan W Vaughan, Daniel M Staines, Martin Aslett, Antonia Lock, Jürg Bähler, Paul J Kersey, Stephen G Oliver Nucleic Acids Research 40 D695-699 2012.

Assemblathon 1: A competitive assessment of de novo short read assembly methods Dent A Earl, Keith Bradnam, John St John, Aaron Darling, Dawei Lin, Joseph Faas, Hung On Ken Yu, Buffalo Vince, Daniel R Zerbino, Mark Diekhans, Ngan Nguyen, Pramila Nuwantha, Ariyaratne Wing-Kin Sung, Zemin Ning, Matthias Haimel, Jared T Simpson, Nuno A Fronseca, İnanç Birol, T Roderick Docking, Isaac Y Ho, Daniel S Rokhsar, Rayan Chikhi, Dominique Lavenier, Guillaume Chapuis, Delphine Naquin, Nicolas Maillet, Michael C Schatz, David R Kelly, Adam M Phillippy, Sergey Koren, Shiaw-Pyng Yang, Wei Wu, Wen-Chi Chou, Anuj Srivastava, Timothy I Shaw, J Graham Ruby, Peter Skewes-Cox, Miguel Betegon, Michelle T Dimon, Victor Solovyev, Petr Kosarev, Denis Vorobyev, Ricardo Ramirez-Gonzalez, Richard Leggett, Dan MacLean, Fangfang Xia, Ruibang Luo, L Zhenyu, Yinlong Xie, Binghang Liu, Sante Gnerre, Iain MacCallum, Dariusz Przybylski, Filipe J Ribeiro, Shuangye Yin, Ted Sharpe, Giles Hall, Paul J Kersey, Richard Durbin, Shaun D Jackman, Jarrod A Chapman, Xiaoqiu Huang, Joseph L DeRisi, Mario Caccamo, Yingrui Li, David B Jaffe, Richard Green, David Haussler, Ian Korf, Benedict Paten Genome Res. 2011. 21: 2224-2241

Multiple reference genomes and transcriptomes for Arabidopsis thaliana Xiangchao Gan, Oliver Stegle, Jonas Behr, Joshua G Steffen, Philipp Drewe, Katie L Hildebrand, Rune Lyngsoe, Sebastian J Schultheiss, Edward J Osborne, Vipin T Sreedharan, André Kahles, Regina Bohnert, Géraldine Jean, Paul Derwent, Paul Kersey, Eric J Belfield, Nicholas P Harberd, Eric Kemen, Christopher Toomajian, Paula X Kover, Richard M Clark, Gunnar Rätsch, Richard Mott Nature 2011. 477:419-423.

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