Michael Ashburner

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Michael Ashburner

Michael Ashburner
Born 23 May 1942 (1942-05-23) (age 69)[citation needed]
Sussex, England
Nationality United Kingdom
Fields Bioinformatics
Institutions European Bioinformatics Institute (EBI), California Institute of Technology, University of Cambridge, University of California, San Francisco[1]
Alma mater University of Cambridge
Known for Drosophila melanogaster[2]
Gene Ontology[3]
FlyBase[4]
Influences Bruce Alberts[1]
Notable awards Thomas Hunt Morgan Medal 2008,[5] George W. Beadle Award 1999,[6] Benjamin Franklin Award (Bioinformatics) 2006, Accomplishment by a Senior Scientist Award 2011 [1][7]

Michael Ashburner FRS (born 23 May 1942) is a biologist and emeritus Professor in the Department of Genetics at University of Cambridge.[8] He is also the former joint-head of the European Bioinformatics Institute (EBI) of the European Molecular Biology Laboratory (EMBL).

Born in Sussex, England, Ashburner attended High Wycombe Royal Grammar School from 1953 to 1960. He received his Bachelor of Arts in Natural Sciences Tripos (Genetics) in 1964, his PhD from the Department of Genetics in 1968, and was awarded a Doctor of Science in 1978, all from Cambridge.[9]

Ashburner was elected a Foreign Honorary Member of the American Academy of Arts and Sciences in 1993.[10] He received the Gregor Mendel Medal from the Academy of Sciences, Czech Republic in 1998, the first George W. Beadle Award of the Genetics Society of America in 1999, the Genetics Society Medal of the UK Genetics Society in 2005 and the Franklin Award of the Bioinformatics Organization in 2006. Ashburner collaborated widely and mentored numerous PhD students and Post-doctoral researchers during his career.[11]

Contents

[edit] Drosophila research

Most of Ashburner's research has been on the model organism Drosophila melanogaster.[2][12][13][14][15][16] Ashburner's career began in the early period of molecular biology prior to the development of most of the recombinant DNA techniques in use today, such as Northern/Southern/Western blotting. Nevertheless, by observing patterns of "puffing" in polytene chromosomes,[12] he established the existence of a cascade of genetic controls in the post-larval development triggered by ecdysone. The Ashburner model of 1974 became a paradigm for metazoan gene regulation inasmuch as the Jacob-Monod model did for prokaryotes.

Ashburner was also a member of the consortium that eventually sequenced and annotated the D. melanogaster genome. Ashburner's recollections of the sequencing of the D. melanogaster genome forms the basis of a book entitled "Won for All: How the Drosophila Genome Was Sequenced".[17][18][19][20] A prolonged effort by his laboratory to characterise the Adh region[13] became invaluable for validating annotation strategies when large-scale genome information became available. Ashburner and his colleagues have received funding on numerous occasions[21][22] for their studies on Drosophila genomics leveraging the D. melanogaster genome and its annotation.

[edit] Computational biology

Ashburner was also an early pioneer in the application of computers to biology. His contributions include his active participation in setting up FlyBase[4] and the development of Open Biomedical Ontologies[23] to allow machine-searchable annotation of biological information, particularly the Gene Ontology[3][24] and ChEBI.[25] He was instrumental in establishing the EBI,[26] as well as securing its location in the UK,[9][27] and acted as the first head of the EBI jointly with Graham Cameron.[28]

[edit] Open science advocacy

As part of his involvement the sequencing of the D. melanogaster genome, Ashburner played an instrumental role in ensuring that the resulting sequence and annotations would be made publicly available.[17] Additionally, Ashburner made a strong case for the human genome published in Science in 2000 by Celera Genomics to be made freely available,[29][30][31][32] and has spoken out repeatedly against the privitization of genomic resources.[32][33] Ashburner was also one of the signatories of the first open letter to Science in 2001 calling for a centralized, open repository of the scientific literature,[34] and subsequently became a strong advocate of Open Access publishing,[35][36] speaking out for this cause in the scientific literature[9][37] and popular media.[38][39][40] He also provided written evidence to the UK Parliament Select Committee on Science and Technology supporting Open Access publishing[41] and served on the initial advisory board of UK PubMed Central,[42] the first global mirror site of the PubMed Central repository of freely available biological literature.

[edit] References

  1. ^ a b c Michael Ashburner keynote: From sequences to ontologies - adventures in informatics at Intelligent Systems for Molecular Biology July 2011
  2. ^ a b Ashburner, Michael; Golic, Kent G.; Hawley, R. Scott (2005), Drosophila : a laboratory handbook (1st ed.), Plain View, N.Y.: Cold Spring Harbor Laboratory Press, ISBN 0-87969-706-7, http://www.cshlpress.com/default.tpl?action=full&--eqskudatarq=810 
  3. ^ a b Botstein, D.; Cherry, J. M.; Ashburner, M.; Ball, C. A.; Blake, J. A.; Butler, H.; Davis, A. P.; Dolinski, K. et al (2000). "Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium". Nature Genetics 25 (1): 25–29. doi:10.1038/75556. PMC 3037419. PMID 10802651. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3037419.  edit
  4. ^ a b Ashburner, M.; Drysdale, R. (1994). "FlyBase--the Drosophila genetic database". Development (Cambridge, England) 120 (7): 2077–2079. PMID 7925011.  edit
  5. ^ Spradling, A. (2008). "The 2008 Thomas Hunt Morgan Medal". Genetics 178 (3): 1123–1124. doi:10.1534/genetics.104.017832. PMC 2278087. PMID 18385103. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2278087.  edit
  6. ^ Hawley, R.; Kaufman, T. (2000). "The 1999 George W. Beadle Medal. Michael Ashburner". Genetics 154 (1): 5. PMC 1460911. PMID 10681184. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1460911.  edit
  7. ^ Mullins, J.; Morrison Mckay, B. (2011). "International Society for Computational Biology Honors Michael Ashburner and Olga Troyanskaya with Top Bioinformatics/Computational Biology Awards for 2011". PLoS Computational Biology 7 (6): e1002081. doi:10.1371/journal.pcbi.1002081. PMC 3107244. PMID 21673867. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3107244.  edit
  8. ^ "Michael Ashburner, Department of Genetics, University of Cambridge". http://www.gen.cam.ac.uk/research/ashburner.html. Retrieved 2011-07-29. 
  9. ^ a b c Ashburner, M. (2006). "Michael Ashburner". Current Biology 16 (22): R941–R943. doi:10.1016/j.cub.2006.10.010.  edit
  10. ^ "Book of Members, 1780-2010: Chapter A". American Academy of Arts and Sciences. http://www.amacad.org/publications/BookofMembers/ChapterA.pdf. Retrieved 25 April 2011. 
  11. ^ Academic Tree of Michael Ashburner
  12. ^ a b Ashburner, M.; Chihara, C.; Meltzer, P.; Richards, G. (1974). "Temporal control of puffing activity in polytene chromosomes". Cold Spring Harbor symposia on quantitative biology 38: 655–662. PMID 4208797.  edit
  13. ^ a b Ashburner, M.; Misra, S.; Roote, J.; Lewis, S. E.; Blazej, R.; Davis, T.; Doyle, C.; Galle, R. et al (1999). "An exploration of the sequence of a 2.9-Mb region of the genome of Drosophila melanogaster: The Adh region". Genetics 153 (1): 179–219. PMC 1460734. PMID 10471707. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1460734.  edit
  14. ^ Adams, M.; Celniker, S.; Holt, R.; Evans, C.; Gocayne, J.; Amanatides, P.; Scherer, S.; Li, P. et al (2000). "The genome sequence of Drosophila melanogaster". Science 287 (5461): 2185–2195. Bibcode 2000Sci...287.2185.. doi:10.1126/science.287.5461.2185. PMID 10731132.  edit
  15. ^ Ranz, J. M.; Maurin, D.; Chan, Y. S.; Von Grotthuss, M.; Hillier, L. W.; Roote, J.; Ashburner, M.; Bergman, C. M. (2007). "Principles of Genome Evolution in the Drosophila melanogaster Species Group". PLoS Biology 5 (6): e152. doi:10.1371/journal.pbio.0050152. PMC 1885836. PMID 17550304. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=1885836.  edit
  16. ^ Teixeira, L. S.; Ferreira, Á.; Ashburner, M. (2008). Keller, Laurent. ed. "The Bacterial Symbiont Wolbachia Induces Resistance to RNA Viral Infections in Drosophila melanogaster". PLoS Biology 6 (12): e2. doi:10.1371/journal.pbio.1000002. PMC 2605931. PMID 19222304. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2605931.  edit
  17. ^ a b Michael Ashburner (2006). Won for all: how the Drosophila genome was sequenced.. Plainview, N.Y: Cold Spring Harbor Laboratory Press. ISBN 0-87969-802-0. 
  18. ^ Sulston, J. (2006). "All for All". PLoS Biology 4 (6): e198. doi:10.1371/journal.pbio.0040198. http://www.plosbiology.org/article/info%3Adoi%2F10.1371%2Fjournal.pbio.0040198.  edit
  19. ^ Jennifer Rohn (2006). "Sequencing, sushi and sang-froid. Michael Ashburner's account of the fly genome project". http://www.lablit.com/article/96. Retrieved 2011-07-29. 
  20. ^ Venter, J. C. (2006). "GENOMICS: An Ointment for the Fly". Science 313 (5795): 1892. doi:10.1126/science.1134998.  edit
  21. ^ Grants awarded to Michael Ashburner by the UK Biotechnology and Biological Sciences Research Council
  22. ^ Grants awarded to Michael Ashburner by the UK Engineering and Physical Sciences Research Council
  23. ^ Smith, B.; Ashburner, M.; Rosse, C.; Bard, J.; Bug, W.; Ceusters, W.; Goldberg, L. J.; Eilbeck, K. et al (2007). "The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration". Nature Biotechnology 25 (11): 1251–1255. doi:10.1038/nbt1346. PMC 2814061. PMID 17989687. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2814061.  edit
  24. ^ Reference Genome Group of the Gene Ontology Consortium (2009). Bourne, Philip E.. ed. "The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species". PLoS Computational Biology 5 (7): e1000431. doi:10.1371/journal.pcbi.1000431. PMC 2699109. PMID 19578431. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2699109.  edit
  25. ^ Degtyarenko, K.; De Matos, P.; Ennis, M.; Hastings, J.; Zbinden, M.; McNaught, A.; Alcantara, R.; Darsow, M. et al (2007). "ChEBI: A database and ontology for chemical entities of biological interest". Nucleic Acids Research 36 (Database issue): D344–D350. doi:10.1093/nar/gkm791. PMC 2238832. PMID 17932057. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=2238832.  edit
  26. ^ Gavaghan, H. (2001). "Biology moves into the silicon stage". Nature 409 (6822): 964. doi:10.1038/35057452. PMID 11241987.  edit
  27. ^ Attwood T.K., Gisel A., Eriksson N-E. and Bongcam-Rudloff E. (2011). "Concepts, Historical Milestones and the Central Place of Bioinformatics in Modern Biology: A European Perspective". Bioinformatics - Trends and Methodologies. InTech. http://www.intechopen.com/articles/show/title/concepts-historical-milestones-and-the-central-place-of-bioinformatics-in-modern-biology-a-european-. Retrieved 8 Jan 2012. 
  28. ^ "EBI in a nutshell". European Bioinformatics Institute. http://www.ebi.ac.uk/Information/Brochures/pdf/In_a_nutshell_small_file.pdf. Retrieved 8 Jan 2012. 
  29. ^ Marshall, E. (2000). "HUMAN GENOME: Storm Erupts over Terms for Publishing Celera's Sequence". Science 290 (5499): 2042–2043. doi:10.1126/science.290.5499.2042. PMID 11187813.  edit
  30. ^ The Lancet (2001). "Human genome row draws in journals". The Lancet 357 (9250): 81. doi:doi:10.1016/S0140-6736(00)03531-5. 
  31. ^ Moody, Glyn (2004). Digital code of life : how bioinformatics is revolutionizing science, medicine, and business. Hoboken, NJ: Wiley. ISBN 0471327883. 
  32. ^ a b Ashburner, Michael. "Privatising our genes?". http://www.opendemocracy.net/theme_9-genes/article_407.jsp. Retrieved 8 January 2012. 
  33. ^ Vince, Gaia. "Fears over rice genome access". http://www.newscientist.com/article/dn2061. Retrieved 8 January 2012. 
  34. ^ Roberts, R. J.; Varmus, H. E.; Ashburner, M.; Brown, P. O.; Eisen, M. B.; Khosla, C.; Kirschner, M.; Nusse, R. et al (2001). "INFORMATION ACCESS: Building A GenBank of the Published Literature". Science 291 (5512): 2318a. doi:10.1126/science.1060273.  edit
  35. ^ "BioMed Central Author Video - Professor Michael Ashburner Part 2". http://www.youtube.com/watch?v=xPX8VcbcmOo&list=PLEF5AD44D24A208FC&index=3&feature=plpp_video. Retrieved 8 January 2012. 
  36. ^ "BioMed Central Author Video - Professor Michael Ashburner Part 3". http://www.youtube.com/watch?v=FhV6uoROXKc&list=PLEF5AD44D24A208FC&index=4&feature=plpp_video. Retrieved 8 January 2012. 
  37. ^ "BioMed Central Author Video - Professor Michael Ashburner Part 1". http://www.youtube.com/watch?v=4Obpot5ER5o&list=PLEF5AD44D24A208FC&index=2&feature=plpp_video. Retrieved 8 January 2012. 
  38. ^ Ward, Mark. "Scientists threaten journal protest". http://news.bbc.co.uk/1/hi/sci/tech/1296750.stm. Retrieved 4 February 2012. 
  39. ^ Meek, James. "Science world in revolt at power of the journal owners". http://www.guardian.co.uk/uk/2001/may/26/highereducation.physicalsciences. Retrieved 4 February 2012. 
  40. ^ Ward, Mark. "Scientists call for online library". http://news.bbc.co.uk/1/hi/sci/tech/1516824.stm. Retrieved 4 February 2012. 
  41. ^ Ashburner, Michael. "UK Parliament Select Committee on Science and Technology APPENDIX 59". http://www.publications.parliament.uk/pa/cm200304/cmselect/cmsctech/399/399we70.htm. Retrieved 4 February 2012. 
  42. ^ McEntyre, J. R.; Ananiadou, S.; Andrews, S.; Black, W. J.; Boulderstone, R.; Buttery, P.; Chaplin, D.; Chevuru, S. et al (2010). "UKPMC: A full text article resource for the life sciences". Nucleic Acids Research 39 (Database issue): D58–D65. doi:10.1093/nar/gkq1063. PMC 3013671. PMID 21062818. http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pmcentrez&artid=3013671.  edit

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