John Frederick William Birney (known as Ewan Birney)
(born 6 December 1972)
is joint director of EMBL's European Bioinformatics Institute
The European Bioinformatics Institute (EMBL-EBI) is an Intergovernmental Organization (IGO) which, as part of the European Molecular Biology Laboratory (EMBL) family, focuses on research and services in bioinformatics. It is located on the Well ...
(EMBL-EBI), in Hinxton, Cambridgeshire
Cambridgeshire (abbreviated Cambs.) is a Counties of England, county in the East of England, bordering Lincolnshire to the north, Norfolk to the north-east, Suffolk to the east, Essex and Hertfordshire to the south, and Bedfordshire and North ...
and deputy director general of the European Molecular Biology Laboratory
The European Molecular Biology Laboratory (EMBL) is an intergovernmental organization dedicated to molecular biology research and is supported by 27 member states, two prospect states, and one associate member state. EMBL was created in 1974 and ...
(EMBL). He also serves as non-executive director of Genomics England, chair of the Global Alliance for Genomics and Health (GA4GH) and honorary professor
Honorary titles (professor, reader, lecturer) in academia may be conferred on persons in recognition of contributions by a non-employee or by an employee beyond regular duties. This practice primarily exists in the UK and Germany, as well as in m ...
of bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
at the University of Cambridge
, mottoeng = Literal: From here, light and sacred draughts.
Non literal: From this place, we gain enlightenment and precious knowledge.
, established =
, other_name = The Chancellor, Masters and Schola ...
. Birney has made significant contributions to genomics
Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...
, through his development of innovative bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
and computational biology
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has fo ...
tools.[ He previously served as an associate faculty member at the ]Wellcome Trust Sanger Institute
The Wellcome Sanger Institute, previously known as The Sanger Centre and Wellcome Trust Sanger Institute, is a non-profit British genomics and genetics research institute, primarily funded by the Wellcome Trust.
It is located on the Wellcome G ...
.
Education
Birney was educated at Eton College
Eton College () is a public school in Eton, Berkshire, England. It was founded in 1440 by Henry VI under the name ''Kynge's College of Our Ladye of Eton besyde Windesore'',Nevill, p. 3 ff. intended as a sister institution to King's College, C ...
as an Oppidan Scholar
An Oppidan Scholar is a boy at Eton College who has distinguished himself academically.
Features
Oppidan scholarships
A scholarship is a form of financial aid awarded to students for further education. Generally, scholarships are awarded b ...
. Before going to university, Birney completed a gap year internship at Cold Spring Harbor Laboratory supervised by James Watson
James Dewey Watson (born April 6, 1928) is an American molecular biologist, geneticist, and zoologist. In 1953, he co-authored with Francis Crick the academic paper proposing the double helix structure of the DNA molecule. Watson, Crick and ...
and Adrian Krainer.
Birney completed his Bachelor of Arts
Bachelor of arts (BA or AB; from the Latin ', ', or ') is a bachelor's degree awarded for an undergraduate program in the arts, or, in some cases, other disciplines. A Bachelor of Arts degree course is generally completed in three or four years ...
degree in Biochemistry
Biochemistry or biological chemistry is the study of chemical processes within and relating to living organisms. A sub-discipline of both chemistry and biology, biochemistry may be divided into three fields: structural biology, enzymology and ...
at the University of Oxford
, mottoeng = The Lord is my light
, established =
, endowment = £6.1 billion (including colleges) (2019)
, budget = £2.145 billion (2019–20)
, chancellor ...
in 1996, where he was an undergraduate student at Balliol College, Oxford
Balliol College () is one of the constituent colleges of the University of Oxford in England. One of Oxford's oldest colleges, it was founded around 1263 by John I de Balliol, a landowner from Barnard Castle in County Durham, who provided the f ...
. He completed his PhD PHD or PhD may refer to:
* Doctor of Philosophy (PhD), an academic qualification
Entertainment
* '' PhD: Phantasy Degree'', a Korean comic series
* ''Piled Higher and Deeper'', a web comic
* Ph.D. (band), a 1980s British group
** Ph.D. (Ph.D. albu ...
at the Sanger Institute, supervised by Richard Durbin while he was a postgraduate student at St John's College, Cambridge
St John's College is a Colleges of the University of Cambridge, constituent college of the University of Cambridge founded by the House of Tudor, Tudor matriarch Lady Margaret Beaufort. In constitutional terms, the college is a charitable corpo ...
. His doctoral research used dynamic programming
Dynamic programming is both a mathematical optimization method and a computer programming method. The method was developed by Richard Bellman in the 1950s and has found applications in numerous fields, from aerospace engineering to economics.
I ...
, finite-state machines and probabilistic automatons for sequence alignment
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Alig ...
.[
While he was a student he completed internships in the office of the ]Mayor of Baltimore
The mayor of Baltimore is the head of the executive branch of the government of the City of Baltimore, Maryland. The Mayor has the duty to enforce city laws, and the power to either approve or veto bills, ordinances, or resolutions passed by the ...
and also in financial services
Financial services are the Service (economics), economic services provided by the finance industry, which encompasses a broad range of businesses that manage money, including credit unions, banks, credit-card companies, insurance companies, acco ...
on valuation of options for the Swiss Bank Corporation.
Research and career
From 2000 to 2003, Birney organised a scientific wager A scientific wager is a wager whose outcome is settled by scientific method. They typically consist of an offer to pay a certain sum of money on the scientific proof or disproof of some currently-uncertain statement. Some wagers have specific date r ...
and sweepstake known as GeneSweep
GeneSweep or Gene Sweepstake was a sweepstake and scientific wager for scientists to bet on the total number of genes in the human genome. The sweepstake was started at a Cold Spring Harbor Laboratory conference in 2000. Initially, bets could be p ...
,[ ] for the genomics community, taking bets on estimates of the total number of genes (and noncoding DNA) in the human genome.
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 computational genomics and inter-individual differences in human and other animal
Animals are multicellular, eukaryotic organisms in the Kingdom (biology), biological kingdom Animalia. With few exceptions, animals Heterotroph, consume organic material, Cellular respiration#Aerobic respiration, breathe oxygen, are Motilit ...
s.
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
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...
and computational biology
Computational biology refers to the use of data analysis, mathematical modeling and computational simulations to understand biological systems and relationships. An intersection of computer science, biology, and big data, the field also has fo ...
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
Velvet is an algorithm package that has been designed to deal with ''de novo'' genome assembly and short read sequencing alignments. This is achieved through the manipulation of de Bruijn graphs for genomic sequence assembly via the removal of er ...
(Daniel Zerbino
) and CRAM (Markus Hsi-Yang Fritz, Rasko Leinonen and Vadim Zalunin). Birney has also contributed to several other projects including the Pfam
Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. The most recent version, Pfam 35.0, was released in November 2021 and contains 19,632 families.
Uses
...
database, InterPro, BioPerl
BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications. It has played an integral role in the Human Genome Project.
Background
BioPerl is an active open source software project sup ...
, and HMMER
HMMER is a free and commonly used software package for sequence analysis written by Sean Eddy. Its general usage is to identify homologous protein or nucleotide sequences, and to perform sequence alignments. It detects homology by comparing ...
and Ensembl genome database project
Ensembl genome database project is a scientific project at the European Bioinformatics Institute, which provides a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other ...
.
, Birney's research group focuses on genomic
Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes. A genome is an organism's complete set of DNA, including all of its genes as well as its hierarchical, three-dim ...
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
Biotechnology and Biological Sciences Research Council (BBSRC), part of UK Research and Innovation, is a non-departmental public body (NDPB), and is the largest UK public funder of non-medical bioscience. It predominantly funds scientific rese ...
(BBSRC), Medical Research Council (MRC) the National Human Genome Research Institute (NHGRI),[ the ]Wellcome Trust
The Wellcome Trust is a charitable foundation focused on health research based in London, in the United Kingdom. It was established in 1936 with legacies from the pharmaceutical magnate Henry Wellcome (founder of one of the predecessors of Glaxo ...
and the European Union
The European Union (EU) is a supranational political and economic union of member states that are located primarily in Europe. The union has a total area of and an estimated total population of about 447million. The EU has often been des ...
.
Birney serves as a consultant to Oxford Nanopore Technologies and on the scientific advisory board of the Earlham Institute
Earlham Institute (EI, formerly The Genome Analysis Centre (TGAC)) is a life science research institute located at the Norwich Research Park (NRP), Norwich, England. EI's research is focused on exploring living systems by applying computationa ...
(formerly TGAC) in Norwich. Since 2022, he has served on the governing board
A board of directors (commonly referred simply as the board) is an executive committee that jointly supervises the activities of an organization, which can be either a for-profit or a nonprofit organization such as a business, nonprofit organiz ...
at Eton College
Eton College () is a public school in Eton, Berkshire, England. It was founded in 1440 by Henry VI under the name ''Kynge's College of Our Ladye of Eton besyde Windesore'',Nevill, p. 3 ff. intended as a sister institution to King's College, C ...
.
Awards and honours
In 2002, Birney was named as one of the MIT Technology Review TR100
The Innovators Under 35 is a peer-reviewed annual award and listicle published by ''MIT Technology Review'' magazine, naming the world's top 35 innovators under the age of 35. at ''Technology Review'' with lists of winners at technologyreview.com
...
top 100 innovators in the world under the age of 35. In 2003, he gave the inaugural Francis Crick Lecture The Francis Crick Medal and Lecture is a prize lecture of the Royal Society established in 2003 with an endowment from Sydney Brenner, the late Francis Crick's close friend and former colleague. It is delivered annually in biology, particularly the ...
at the Royal Society
The Royal Society, formally The Royal Society of London for Improving Natural Knowledge, is a learned society and the United Kingdom's national academy of sciences. The society fulfils a number of roles: promoting science and its benefits, re ...
: In 2005, he was awarded the Overton Prize The ISCB Overton Prize is a Awards in Bioinformatics and Computational Biology, computational biology prize awarded annually for outstanding accomplishment by a scientist in the early to mid stage of his or her career. Laureates have made significan ...
by the International Society for Computational Biology (ISCB) for his advocacy of open source
Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...
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:
Birney was awarded membership of the European Molecular Biology Organization (EMBO) in 2012 and elected a Fellow of the Royal Society (FRS) in 2014.[ One or more of the preceding sentences incorporates text from the royalsociety.org website where: ] His certificate of election and candidature reads:
Birney has been awarded an Honorary Doctor of Science
Doctor of Science ( la, links=no, Scientiae Doctor), usually abbreviated Sc.D., D.Sc., S.D., or D.S., is an academic research degree awarded in a number of countries throughout the world. In some countries, "Doctor of Science" is the degree used f ...
(DSc) degrees: in 2014 from Brunel University London
Brunel University London is a Public university, public Research universities, research university located in the Uxbridge area of London, England. It was founded in 1966 and named after the Victorian era, Victorian engineer and pioneer of the I ...
and in 2021 from University of Tartu, Estonia
Estonia, formally the Republic of Estonia, is a country by the Baltic Sea in Northern Europe. It is bordered to the north by the Gulf of Finland across from Finland, to the west by the sea across from Sweden, to the south by Latvia, a ...
. In 2015, Birney was elected a Fellow of the Academy of Medical Sciences (FMedSci). Birney was appointed Commander of the Order of the British Empire
The Most Excellent Order of the British Empire is a British order of chivalry, rewarding contributions to the arts and sciences, work with charitable and welfare organisations,
and public service outside the civil service. It was established o ...
(CBE) in the 2019 New Year Honours
The 2019 New Year Honours are appointments by some of the 16 Commonwealth realms to various orders and honours to recognise and reward good works by citizens of those countries. The New Year Honours are awarded as part of the New Year celebratio ...
.
Personal life
Birney married in 2003 and has two children.[
]
References
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{{DEFAULTSORT:Birney, Ewan
Living people
Members of the European Molecular Biology Organization
People educated at Eton College
Alumni of Balliol College, Oxford
Alumni of St John's College, Cambridge
British bioinformaticians
Commanders of the Order of the British Empire
Overton Prize winners
Fellows of Churchill College, Cambridge
Wellcome Trust
1972 births
Fellows of the Royal Society
Fellows of the International Society for Computational Biology
Fellows of the Academy of Medical Sciences (United Kingdom)
Human Genome Project scientists