Birney was educated at Eton College as an Oppidan Scholar where he studied GCE Advanced Levels in Maths, Biology, Chemistry and Art. Before going to university, Birney completed a gap year internship at Cold Spring Harbor Laboratory supervised by James Watson and Adrian Krainer. He acted as a bookmaker to the genomics community, taking bets on estimates of the total number of genes (and so-called "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 as postgraduate student of St John's College, Cambridge. During his university education he completed an internship in financial services in the City of London for the Swiss Bank Corporation.
Birney is one of the founders of the Ensembl genome browser and other databases, and has played a key role in many large-scale genomics projects, notably 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 animal species.
Birney is known for his role in the ENCODE consortium. Prior to the ENCODE project, Birney has been involved in the 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 postdocs that have worked in his laboratory. This research has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC) the Wellcome Trust and the European Union. Birney is also a consultant to Oxford Nanopore Technologies and on the scientific advisory board of The Genome Analysis Centre (TGAC) in Norwich.
Birney has won several awards: In 2003, he gave the inaugural Francis Crick Lecture at the Royal Society:
The inaugural Francis Crick Lecture was awarded to Birney, for his leading role in establishing international standards for software used in genome informatics, and in making research data and software openly available to the research community. The lecture, entitled 'Being human: what our genome tells us' took place at the Royal Society on 4 December 2003.
In 2005, Birney was awarded the Overton Prize by the International Society for Computational Biology (ISCB):
Dr. Ewan Birney of the European Molecular Biology Laboratory (EMBL) European Bioinformatics Institute (EBI), was awarded the 2005 Overton Prize in honour of his advocacy of open source bioinformatics, and his generous contributions to the BioPerl community. Perhaps even more important to biology is his leadership of the Ensembl genome annotation project, providing rapid and accurate computational annotations for eukaryotic genomes.
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.
Birney was 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 2015, Birney was elected a Fellow of the Academy of Medical Sciences (FMedSci). His citation on election reads:
Associate Director of the European Bioinformatics Institute, Dr Ewan Birney has been a prominent leader in genomics internationally for many years and led the ENCODE project. He is a polymath who has drawn from diverse fields, such as speech recognition, computer science and human genetics, to develop world-leading research programmes in population and comparative genomics.
His influence on genomics has been profound, and he has contributed new tools and concepts that have been far ahead of their time. His central position in genomics/bioinformatics in Europe and indeed the world gives him a deep understanding of the impact of genomics technologies on future healthcare and health economics.
In 2014, Birney was awarded an Honorary Doctor of Science (DSc) degree from Brunel University London in recognition of his service to science. In 2002, Birney was named as one of the MIT Technology Review TR100 top 100 innovators in the world under the age of 35: Birney was also awarded EMBO Membership in 2012.
Birney is married to Barley Birney (née Laycock) with two children. He appeared on a special Christmas edition of University Challenge in 2014 representing Balliol College, Oxford with Charlotte Higgins and Alan Beith.