[13][31] Before going to University, Birney completed a gap year internship at Cold Spring Harbor Laboratory supervised by James Watson[14][32] and Adrian Krainer.

[13][14][35] He completed his PhD at the Sanger Institute, supervised by Richard Durbin[6] while he was a postgraduate student at St John's College, Cambridge.

[6] While he was a student he completed internships in the office of the Mayor of Baltimore and also in financial services on valuation of options for the Swiss Bank Corporation.[31][32][when?]

[5][41][52][53][54][55][56] 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,[57] GeneWise,[58] GenomeWise,[59]), or in collaboration with students and postdocs, e.g. Exonerate[60] (with Guy Slater), Enredo (Javier Herrero[61]), Pecan (Benedict Paten[62]), the Velvet assembler (Daniel Zerbino[63] ) and CRAM (Markus Hsi-Yang Fritz,[64] Rasko Leinonen[65] and Vadim Zalunin).

[71] As of 2015[update], Birney's research group focuses on genomic algorithms and studying inter individual differences, in both human and other species.

[85] Birney serves as a consultant to Oxford Nanopore Technologies[86] and on the scientific advisory board of the Earlham Institute (formerly TGAC) in Norwich.

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.

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.

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