John Frederick William Birney (known as Ewan) (born 6 December 1972)  is joint director with Rolf Apweiler of the European Bioinformatics Institute (EBI), part of the European Molecular Biology Laboratory (EMBL) in Hinxton, Cambridgeshire. He also serves as non-executive director of Genomics England, chair of the Global Alliance for Genomics and Health (GA4GH) and honorary professor of Bioinformatics at the University of Cambridge. Birney has made significant contributions to genomics, through his development of innovative bioinformatics and computational biology tools. He was previously an associate faculty member at the Wellcome Trust Sanger Institute..
Birney was educated at Eton College as an Oppidan Scholar. Before going to university, Birney completed a gap year internship at Cold Spring Harbor Laboratory supervised by James Watson and Adrian Krainer. He managed a sweepstake known as GeneSweep, for the genomics community, taking bets on estimates of the total number of genes (and noncoding or "junk" DNA) in the human genome.
Birney completed his Bachelor of Arts degree in Biochemistry at Balliol College, Oxford in 1996 followed by a PhD at the Wellcome Trust Sanger Institute, supervised by Richard Durbin at St John's College, Cambridge. His doctoral research used dynamic programming, finite-state machines and probabilistic automatons for sequence alignment.
Birney is one of the founders of the Ensembl genome browser and other databases, and has played a role in the sequencing of the Human Genome in 2000 and the analysis of genome function in the ENCODE project. He has played a role in annotating the genome sequences of the human, mouse, chicken and several other organisms. His research group focuses on genomic algorithms and inter-individual differences in human and other animals.
Birney is known for his role in the ENCODE consortium. Prior to the ENCODE project, Birney has been involved in creation of a number of widely used bioinformatics and computational biology tools, either directly (PairWise, GeneWise, GenomeWise,), or in collaboration with students and postdocs, e.g. Exonerate (with Guy Slater), Enredo (Javier Herrero), Pecan (Benedict Paten), the Velvet assembler (Daniel Zerbino ) and CRAM (Markus Hsi-Yang Fritz, Rasko Leinonen and Vadim Zalunin). Birney has also contributed to several other projects including the Pfam database, InterPro, BioPerl, and HMMER and Ensembl toolkits.
(As of 2015), Birney's research group focuses on genomic algorithms and studying inter individual differences, in both human and other species. He has supervised several PhD students and postdoctoral researchers that have worked in his laboratory. His research has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC) the Wellcome Trust and the European Union.
In 2002, Birney was named as one of the MIT Technology Review TR100 top 100 innovators in the world under the age of 35.
In 2003, he gave the inaugural Francis Crick Lecture at the Royal Society:
In 2005, he was awarded the Overton Prize by the International Society for Computational Biology (ISCB) for his advocacy of open source bioinformatics, contributions to the BioPerl community and leadership of the Ensembl genome annotation project..
In 2005 Birney was awarded the Benjamin Franklin Award in Bioinformatics:
As expressed by his nominators, Birney has been a significant force in Open Source in Bioinformatics and science. He has been a strong advocate for making genome information freely available to all. His work co-leading the Ensembl project has made high-quality genome annotation available freely over the web, preventing a class system of labs which can and cannot afford to pay subscription fees to proprietary data. The project has worked hard to make the data available in a variety of ways to make the data accessible and easily available for mining. The Ensembl project has been open-source from the outset, enabling researchers and corporations alike to reuse and extend the software system. Birney has been an advocate of open science as well. Along with Sean Eddy, he criticised journal decisions to allow papers to be published without releasing the genome sequence data at the same time. He is also the author of the freely available Wise package of tools, which are important parts of genome annotation pipelines. He serves as a co-leader of the open-source bioinformatics toolkit Bioperl and also co-founded and currently serves as president of the Open Bioinformatics foundation, an organisation that support the development of several bioinformatics toolkits.
He was awarded membership of the European Molecular Biology Organization (EMBO) in 2012 and elected a Fellow of the Royal Society (FRS) in 2014. His certificate of election and candidature reads:
Ewan has grown to be a force in genomics due to his innovation in genome analysis, both algorithmic and integrative analyses. He wrote the first error tolerant, splice aware protein alignment program, used in the human and subsequent genome analysis; he co-authored one of the first and most widely used short read assemblers. In terms of data integration, Ewan has led the analysis in many genomic consortia, in particular ENCODE, leading the integration of many genomic assays; for example making robust predictions of enhancers, promoters, and their integration with disease associated regions. He also co-developed many widely used bioinformatics resources.
In 2014, Birney was awarded an Honorary Doctor of Science (DSc) degree from Brunel University London.
In 2015, Birney was elected a Fellow of the Academy of Medical Sciences (FMedSci).