Zerbino Velvet Thesis Statements

John Frederick William Birney (known as Ewan) (born 1972)[5][6]FRSFMedSci[40][41] is joint Director with Rolf Apweiler of the European Bioinformatics Institute (EBI),[42][43][44] part of the European Molecular Biology Laboratory (EMBL) in Hinxton, Cambridgeshire. He is also nonexecutive Director of Genomics England and Chair of the Global Alliance for Genomics and Health[45] and an Associate Faculty member at the Wellcome Trust Sanger Institute[46] and an Honorary Professor of Bioinformatics at the University of Cambridge.[47] Birney has made significant contributions to the analysis of genomes. Through his development of innovative bioinformatics and computational biology tools, researchers around the world are able to predict and annotate regions of interest in DNA with speed and confidence.[14]

Education[edit]

Birney was educated at Eton College as an Oppidan Scholar where he studied GCE Advanced Levels in Maths, Biology, Chemistry and Art.[5][48] Before going to university, Birney completed a gap year internship at Cold Spring Harbor Laboratory supervised by James Watson[6][39] and Adrian Krainer.[39][49][50] He acted as a bookmaker to the genomics community, taking bets on estimates of the total number of genes (and so-called "junk DNA"[51]) in the human genome.[39][52][53]

Birney completed his Bachelor of Arts degree in Biochemistry at Balliol College, Oxford in 1996[5][6][54] followed by a PhD at the Wellcome Trust Sanger Institute, supervised by Richard Durbin[19] as postgraduate student at St John's College, Cambridge.[55] During his university education[when?] he completed an internship in financial services in the City of London for the Swiss Bank Corporation.[39][48]

Research[edit]

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.[53][56] He has played a role in annotating the genome sequences of the human,[57] mouse,[58] chicken[59] and several other organisms. His research group focuses on genomic algorithms and inter-individual differences in human and other animal species.[13][42][44][51][60][61][62][63][64][65]

Birney is known for his role in the ENCODE consortium.[18][53][66][67][68][69][70] 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,[8] GeneWise,[9] GenomeWise,[10]), or in collaboration with students and postdocs, e.g. Exonerate[11] (with Guy Slater), Enredo (Javier Herrero[71]), Pecan (Benedict Paten[29]), the Velvet assembler (Daniel Zerbino[72] ) and CRAM (Markus Hsi-Yang Fritz,[22] Rasko Leinonen[73] and Vadim Zalunin). Birney has also contributed to several other projects including the Pfam[74] database, InterPro,[75]BioPerl,[76][77] and HMMER[78] and Ensembl[79] toolkits.

As of 2015[update] 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.[20][22][23][27][29][30][31][34][80] This research has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC), Medical Research Council (MRC)[81] the Wellcome Trust and the European Union.[82] Birney is also a consultant to Oxford Nanopore Technologies[83] and on the scientific advisory board of The Genome Analysis Centre (TGAC) in Norwich.[84][85]

Awards and honours[edit]

Birney has won several awards: In 2003, he gave the inaugural Francis Crick Lecture at the Royal Society:[14]

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):[15]

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:[86]

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.[2][14] His certificate of election and candidature reads:[40]

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 awareprotein 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:[41]

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.[87] In 2002, Birney was named as one of the MIT Technology ReviewTR100 top 100 innovators in the world under the age of 35:[88] Birney was also awarded EMBO Membership[16] in 2012.[17]

Personal life[edit]

Birney is married to Barley Birney (née Laycock)[13] with two children.[5] He appeared on a special Christmas edition of University Challenge in 2014 representing Balliol College, Oxford with Charlotte Higgins and Alan Beith.[89]

References[edit]

  1. ^Anon (1993-11-04). "John Frederick William Birney". Oxford University Gazette. Oxford University Press. 124 (4305). Archived from the original on 2015-06-16. 
  2. ^ abAnon (2015). "Fellowship of the Royal Society 1660-2015". London: Royal Society. Archived from the original on 15 July 2015. 
  3. ^Ewan Birney's Entry at ORCID
  4. ^Anon (2016). "John Frederick William BIRNEY, Eagle Genomics Limited". London: Companies House. Archived from the original on 2016-04-25. 
  5. ^ abcdefghBIRNEY, Dr Ewan. ukwhoswho.com. Who's Who. 2015 (online Oxford University Press ed.). A & C Black, an imprint of Bloomsbury Publishing plc. (subscription required)
  6. ^ abcdHopkin, Karen (June 2005). "Bring Me Your Genomes: The Ewan Birney Story". The Scientist. 19 (11): 60. Archived from the original on 10 June 2011. Retrieved 2011-06-10. 
  7. ^Hubbard, T.; Barker, D.; Birney, E.; Cameron, G.; Chen, Y.; Clark, L.; Cox, T.; Cuff, J.; Curwen, V.; Down, T.; Durbin, R.; Eyras, E.; Gilbert, J.; Hammond, M.; Huminiecki, L.; Kasprzyk, A.; Lehvaslaiho, H.; Lijnzaad, P.; Melsopp, C.; Mongin, E.; Pettett, R.; Pocock, M.; Potter, S.; Rust, A.; Schmidt, E.; Searle, S.; Slater, G.; Smith, J.; Spooner, W.; Stabenau, A. (2002). "The Ensembl genome database project". Nucleic Acids Research. 30 (1): 38–41. doi:10.1093/nar/30.1.38. PMC 99161. PMID 11752248. 
  8. ^ abBirney, E.; Thompson, J.; Gibson, T. (1996). "PairWise and SearchWise: Finding the optimal alignment in a simultaneous comparison of a protein profile against all DNA translation frames". Nucleic Acids Research. 24 (14): 2730–2739. doi:10.1093/nar/24.14.2730. PMC 145991. PMID 8759004. 
  9. ^ abBirney, E.; Durbin, R. (2000). "Using GeneWise in the Drosophila annotation experiment". Genome Research. 10 (4): 547–548. doi:10.1101/gr.10.4.547. PMC 310858. PMID 10779496. 
  10. ^ abBirney, E.; Clamp, M.; Durbin, R. (2004). "GeneWise and Genomewise". Genome Research. 14 (5): 988–995. doi:10.1101/gr.1865504. PMC 479130. PMID 15123596. 
  11. ^ abSlater, G.; Birney, E. (2005). "Automated generation of heuristics for biological sequence comparison". BMC Bioinformatics. 6: 31. doi:10.1186/1471-2105-6-31. PMC 553969. PMID 15713233. 
  12. ^ENCODE Project Consortium; Birney E; Stamatoyannopoulos JA; Dutta A; Guigó R; Gingeras TR; Margulies EH; Weng Z; Snyder M; Dermitzakis ET; et al. (2007). "Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project". Nature. 447 (7146): 799–816. Bibcode:2007Natur.447..799B. doi:10.1038/nature05874. PMC 2212820. PMID 17571346. 
  13. ^ abcPennisi, Elizabeth (2012). "Profile of Ewan Birney: Genomics' Big Talker". Science. 337 (6099): 1167–1169. doi:10.1126/science.337.6099.1167. PMID 22955814. 
  14. ^ abcdAnon (2014). "Dr Ewan Birney FMedSci FRS". London: Royal Society. Archived from the original on 2015-11-17.  One or more of the preceding sentences incorporates text from the royalsociety.org website where:

    All text published under the heading 'Biography' on Fellow profile pages is available under Creative Commons Attribution 4.0 International License. --"Royal Society Terms, conditions and policies". Archived from the original on 25 September 2015. Retrieved 9 March 2016. 

  15. ^ ab"ISCB Newsletter 8-2 Dr. Ewan Birney Named as the 2005 Overton Prize Winner!". Archived from the original on 28 February 2012. 
  16. ^ ab"The EMBO Pocket Directory"(PDF). European Molecular Biology Organization. Archived from the original on 2015-03-16. 
  17. ^ abAnon (2012). "EMBO MEMBER: Ewan Birney". Heidelberg: European Molecular Biology Organization. 
  18. ^ abEwan Birney publications indexed by Google Scholar
  19. ^ abBirney, Ewan (2000). Sequence alignment in bioinformatics (PhD thesis). University of Cambridge. OCLC 894597337. EThOS uk.bl.ethos.621653. Archived from the original(PDF) on 2017-11-18. 
  20. ^ abEttwiller, Laurence Michele (2004). Computational Investigations into cis-Regulation in Eukaryotes (PhD thesis). University of Cambridge. OCLC 890156758. EThOS uk.bl.ethos.613876. 
  21. ^Ettwiller, L. M.; Rung, J.; Birney, E. (2003). "Discovering Novel cis-Regulatory Motifs Using Functional Networks". Genome Research. 13 (5): 883–895. doi:10.1101/gr.866403. PMC 430934. PMID 12727907. 
  22. ^ abcFritz, Markus (2011). Exploiting high throughput DNA sequencing data for genomic analysis(PDF) (PhD thesis). University of Cambridge. OCLC 890152397. EThOS uk.bl.ethos.610819. 
  23. ^ abHoffman, Michael Milner (2008). Quantifying evolution and natural selection in vertebrate noncoding sequence (PhD thesis). University of Cambridge. OCLC 885435476. EThOS uk.bl.ethos.604139. 
  24. ^Hoffman, M. M.; Birney, E. (2006). "Estimating the Neutral Rate of Nucleotide Substitution Using Introns". Molecular Biology and Evolution. 24 (2): 522–531. doi:10.1093/molbev/msl179. PMID 17122369. 
  25. ^Kölling, Nils (2016). Quantitative genetics of gene expression during fruit fly development (PhD thesis). University of Cambridge. doi:10.17863/CAM.26. EThOS uk.bl.ethos.685469. 
  26. ^"Nils Kölling - Statistical Geneticist & Bioinformatician, Oxford". 
  27. ^ abMeynert, Alison Maria (2009). Function and evolution of regulatory elements in vertebrates (PhD thesis). University of Cambridge. OCLC 890148982. EThOS uk.bl.ethos.608495. 
  28. ^Meynert, A.; Birney, E. (2006). "Picking Pyknons out of the Human Genome". Cell. 125 (5): 836–838. doi:10.1016/j.cell.2006.05.019. PMID 16751093. 
  29. ^ abcPaten, Benedict John (2006). Large-scale multiple alignment and transcriptionally associated pattern discovery in vertebrate genomes (PhD thesis). University of Cambridge. OCLC 890155216. EThOS uk.bl.ethos.612811. 
  30. ^ abRuklisa, Dace (2015). Large Scale Genomic Association Studies in Fruit Fly and Human (PhD thesis). University of Cambridge. OCLC 890151540. EThOS uk.bl.ethos.610178. 
  31. ^ abTimmer, Sander Willem (2015). Understanding the epigenome using system genetics (PhD thesis). University of Cambridge. OCLC 903609296. EThOS uk.bl.ethos.637101. 
  32. ^"Sander Timmer – PhD candidate in Biological Sciences". Archived from the original on 2 July 2013. 
  33. ^Gibson, Greg; Ding, Zhihao; Ni, Yunyun; Timmer, Sander W.; Lee, Bum-Kyu; Battenhouse, Anna; Louzada, Sandra; Yang, Fengtang; Dunham, Ian; Crawford, Gregory E.; Lieb, Jason D.; Durbin, Richard; Iyer, Vishwanath R.; Birney, Ewan (2014). "Quantitative Genetics of CTCF Binding Reveal Local Sequence Effects and Different Modes of X-Chromosome Association". PLoS Genetics. 10 (11): e1004798. doi:10.1371/journal.pgen.1004798. ISSN 1553-7404. 
  34. ^ abZerbino, Daniel Robert (2009). Genome assembly and comparison (PhD thesis). University of Cambridge. OCLC 890153795. EThOS uk.bl.ethos.611752. 
  35. ^Spivakov, M.; Akhtar, J.; Kheradpour, P.; Beal, K.; Girardot, C.; Koscielny, G.; Herrero, J.; Kellis, M.; Furlong, E. E.; Birney, E. (2012). "Analysis of variation at transcription factor binding sites in Drosophila and humans". Genome Biology. 13 (9): R49. doi:10.1186/gb-2012-13-9-r49. PMC 3491393. PMID 22950968. 
  36. ^"Ewan's Blog; bioinformatician at large: ENCODE: My own thoughts". Archived from the original on 12 February 2013. 
  37. ^Junion, G.; Spivakov, M.; Girardot, C.; Braun, M.; Gustafson, E. H.; Birney, E.; Furlong, E. E. M. (2012). "A Transcription Factor Collective Defines Cardiac Cell Fate and Reflects Lineage History". Cell. 148 (3): 473–486. doi:10.1016/j.cell.2012.01.030. PMID 22304916. 
  38. ^ abBirney, Ewan (2014). "Ewan Birney's homepage". European Bioinformatics Institute. Archived from the original on 27 December 2014. 
  39. ^ abcdeAl-Khalili, Jim (2013). "The Life Scientific, Ewan Birney". bbc.co.uk. BBC. 
  40. ^ ab"Certificate of election EC/2014/06: Ewan Birney FRS". London: Royal Society. Archived from the original on 22 December 2015. 
  41. ^ abAnon (2015). "Dr Ewan Birney FRS FMedSci". acmedsci.ac.uk. London: Academy of Medical Sciences. Archived from the original on 2015-07-06. 

Он прикрыл микрофон телефона рукой и гневно посмотрел на своего молодого сотрудника.  - Мистер Чатрукьян, - буквально прорычал он, - дискуссия закончена.

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