Michael Ashburner

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Professor Michael Ashburner
Plos ashburner.jpg
Michael Ashburner
Born (1942-05-23) 23 May 1942 (age 72)[1]
Sussex, England
Nationality United Kingdom
Fields Genetics
Bioinformatics
Institutions EBI
UCSF[2]
Caltech
University of Cambridge
Alma mater Churchill College, Cambridge
Thesis Studies on puffing in the salivary gland chromosomes of Drosophila (1968)
Doctoral students Kevin Moses
Voula Velissariou
Mary Boyd
Geoff Richards
Bruce Reed
Christopher Redfern
Virginia Papioannou
Steve McGill
Cathy Martin
Ruth Lovering
Pete Jeffs
Marc Jacobs
Nick Harden
Jan C. Eeken
Mark Bodmer
Ounissa Ait-Ahmed[3]
Other notable students Casey Bergman (postdoc)[4]
Known for Drosophila melanogaster[5]
Gene Ontology[6]
FlyBase[7]
Influences Bruce Alberts[2]
Notable awards Thomas Hunt Morgan Medal (2008)[8]
George W. Beadle Award (1999)[9]
Franklin Award (2006)
Senior Scientist Award (2011)[2][10]
Website
www.gen.cam.ac.uk/research/ashburner.html
library.cshl.edu/oralhistory/speaker/michael-ashburner/

Michael Ashburner FRS (born 23 May 1942) is a biologist and emeritus Professor in the Department of Genetics at University of Cambridge.[11] He is also the former joint-head of the European Bioinformatics Institute (EBI)[12] of the European Molecular Biology Laboratory (EMBL).[13][14]

Education[edit]

Born in Sussex, England, Ashburner attended High Wycombe Royal Grammar School from 1953 to 1960.[1] He received his Bachelor of Arts in Natural Sciences Tripos (Genetics) in 1964, his PhD[15] from the Department of Genetics in 1968, and was awarded a Doctor of Science in 1978, all from Cambridge.[16]

Research[edit]

Most of Ashburner's research has been on the model organism Drosophila melanogaster.[5][17][18][19][20][21] 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,[17] he established the existence of a cascade of genetic controls in the post-larval development triggered by ecdysone.[22] The Ashburner model of 1974 became a paradigm for metazoan gene regulation inasmuch as the Jacob-Monod model did for prokaryotes. Ashburner collaborated widely and mentored numerous PhD students and Postdoctoral research students during his career.[3]

Ashburner was also a member of the consortium that eventually sequenced and annotated the Drosophila 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".[23][24][25][26] A prolonged effort by his laboratory to characterise the Adh region[18] became invaluable for validating annotation strategies when large-scale genome information became available. Ashburner and his colleagues have received funding on numerous occasions[27][28] for their studies on Drosophila genomics leveraging the D. melanogaster genome and its annotation.

Computational biology[edit]

Ashburner was also an early pioneer in the application of computers to biology. His contributions include his active participation in setting up FlyBase[7] and the development of Open Biomedical Ontologies[29] to allow machine-searchable annotation of biological information, particularly the Gene Ontology[6][30] and ChEBI.[31] He was instrumental in establishing the EBI,[32] as well as securing its location in the UK,[16][33] and acted as the first head of the EBI jointly with Graham Cameron.[34]

Open science advocacy[edit]

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.[23] Additionally, Ashburner made a strong case for the human genome published in Science in 2000 by Celera Genomics to be made freely available,[35][36][37][38] and has spoken out repeatedly against the privatization of genomic resources.[38][39] 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,[40] and subsequently became a strong advocate of Open Access publishing,[41][42] speaking out for this cause in the scientific literature[16][43] and popular media.[44][45][46] He also provided written evidence to the UK Parliament Select Committee on Science and Technology supporting Open Access publishing[47] and served on the initial advisory board of UK PubMed Central,[48] the first global mirror site of the PubMed Central repository of freely available biological literature.

Awards[edit]

Ashburner was elected a Foreign Honorary Member of the American Academy of Arts and Sciences in 1993.[49] He received the Gregor Mendel Medal from the Academy of Sciences, Czech Republic in 1998, the first George W. Beadle Award[9] 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's candidacy for the Royal Society reads:

"Distinguished for his wide-ranging researches on the cytology, genetics and evolution of Drosophila melanogaster. He was the first to make a comprehensive map of puffs in the salivary gland polytene chromosomes and to define the stage at which each was expressed. He went on to demonstrate the effects of various stimuli, especially heat-shock and ecdysone, on puffing at specific loci, and correlated particular puffs with particular gene products. Combining genetic, cytological and molecular methodology, he has investigated in fine detail particular chromosome regions, especially that surrounding the Adh (alcohol dehydrogenase) gene, revealing many novel features of structure and function. He has also made important contributions to the understanding of evolution and speciation within the D.melanogaster group of species. Ashburner has unique standing as a scholar and authority in the whole area of Drosophila research."[50]


References[edit]

  1. ^ a b "ASHBURNER, Prof. Michael". Who's Who 2013, A & C Black, an imprint of Bloomsbury Publishing plc, 2013; online edn, Oxford University Press. (subscription required)
  2. ^ a b c Michael Ashburner keynote: From sequences to ontologies - adventures in informatics at Intelligent Systems for Molecular Biology July 2011
  3. ^ a b "FlyTree - Michael Ashburner Details". Archived from the original on 2013-01-04. 
  4. ^ Bergman, CM; Quesneville, H; Anxolabéhère, D; Ashburner, M (2006). "Recurrent insertion and duplication generate networks of transposable element sequences in the Drosophila melanogaster genome". Genome biology 7 (11): R112. doi:10.1186/gb-2006-7-11-r112. PMC 1794594. PMID 17134480.  edit
  5. ^ 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 
  6. ^ a b Botstein, D.; Cherry, J. M.; Ashburner, M.; Ball, C. A.; Blake, J. A.; Butler, H.; Davis, A. P.; Dolinski, K.; Dwight, S. S.; Eppig, J. T.; Harris, M. A.; Hill, D. P.; Issel-Tarver, L.; Kasarskis, A.; Lewis, S.; Matese, J. C.; Richardson, J. E.; Ringwald, M.; Rubin, G. M.; Sherlock, G.; Sherlock, G. (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.  edit
  7. ^ a b Ashburner, M.; Drysdale, R. (1994). "FlyBase--the Drosophila genetic database". Development (Cambridge, England) 120 (7): 2077–2079. PMID 7925011.  edit
  8. ^ Spradling, A. (2008). "The 2008 Thomas Hunt Morgan Medal". Genetics 178 (3): 1123–1124. doi:10.1534/genetics.104.017832. PMC 2278087. PMID 18385103.  edit
  9. ^ a b Hawley, R.; Kaufman, T. (2000). "The 1999 George W. Beadle Medal. Michael Ashburner". Genetics 154 (1): 5. PMC 1460911. PMID 10681184.  edit
  10. ^ 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.  edit
  11. ^ "Michael Ashburner, Department of Genetics, University of Cambridge". Archived from the original on 2011-07-29. 
  12. ^ "Cold Spring Harbor Laboratoty (CSHL) Oral History | Michael Ashburner". Archived from the original on 2013-06-07. 
  13. ^ Michael Ashburner publications in PubMed
  14. ^ Michael Ashburner profile on BiomedExperts
  15. ^ Ashburner, Michael (1968). Studies on puffing in the salivary gland chromosomes of Drosophila (DPhil thesis). University of Cambridge. 
  16. ^ a b c Ashburner, M. (2006). "Michael Ashburner". Current Biology 16 (22): R941–R943. doi:10.1016/j.cub.2006.10.010.  edit
  17. ^ 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. doi:10.1101/sqb.1974.038.01.070. PMID 4208797.  edit
  18. ^ a b Ashburner, M.; Misra, S.; Roote, J.; Lewis, S. E.; Blazej, R.; Davis, T.; Doyle, C.; Galle, R.; George, R.; Harris, N.; Hartzell, G.; Harvey, D.; Hong, L.; Houston, K.; Hoskins, R.; Johnson, G.; Martin, C.; Moshrefi, A.; Palazzolo, M.; Reese, M. G.; Spradling, A.; Tsang, G.; Wan, K.; Whitelaw, K.; Celniker, S. (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.  edit
  19. ^ Adams, M.; Celniker, S.; Holt, R.; Evans, C.; Gocayne, J.; Amanatides, P.; Scherer, S.; Li, P.; Hoskins, R.; Galle, R. F.; George, R. A.; Lewis, S. E.; Richards, S.; Ashburner, M.; Henderson, S. N.; Sutton, G. G.; Wortman, J. R.; Yandell, M. D.; Zhang, Q.; Chen, L. X.; Brandon, R. C.; Rogers, Y. H.; Blazej, R. G.; Champe, M.; Pfeiffer, B. D.; Wan, K. H.; Doyle, C.; Baxter, E. G.; Helt, G.; Nelson, C. R. (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
  20. ^ 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.  edit
  21. ^ Teixeira, L. S.; Ferreira, Á.; Ashburner, M. (2008). "The Bacterial Symbiont Wolbachia Induces Resistance to RNA Viral Infections in Drosophila melanogaster". In Keller, Laurent. PLoS Biology 6 (12): e2. doi:10.1371/journal.pbio.1000002. PMC 2605931. PMID 19222304.  edit
  22. ^ Hill, R. J.; Billas, I. M. L.; Bonneton, F. O.; Graham, L. D.; Lawrence, M. C. (2013). "Ecdysone Receptors: From the Ashburner Model to Structural Biology*". Annual Review of Entomology 58: 251–271. doi:10.1146/annurev-ento-120811-153610. PMID 23072463.  edit
  23. ^ 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. 
  24. ^ Sulston, J. (2006). "All for All". PLoS Biology 4 (6): e198. doi:10.1371/journal.pbio.0040198.  edit
  25. ^ Jennifer Rohn (2006). "Sequencing, sushi and sang-froid. Michael Ashburner's account of the fly genome project". Retrieved 2011-07-29. 
  26. ^ Venter, J. C. (2006). "GENOMICS: An Ointment for the Fly". Science 313 (5795): 1892. doi:10.1126/science.1134998.  edit
  27. ^ Grants awarded to Michael Ashburner by the UK Biotechnology and Biological Sciences Research Council
  28. ^ Grants awarded to Michael Ashburner by the UK Engineering and Physical Sciences Research Council
  29. ^ Smith, B.; Ashburner, M.; Rosse, C.; Bard, J.; Bug, W.; Ceusters, W.; Goldberg, L. J.; Eilbeck, K.; Ireland, A.; Mungall, C. J.; Leontis, N.; Rocca-Serra, P.; Ruttenberg, A.; Sansone, S. A.; Scheuermann, R. H.; Shah, N.; Whetzel, P. L.; Lewis, S.; Lewis, S. (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.  edit
  30. ^ Reference Genome Group of the Gene Ontology Consortium (2009). "The Gene Ontology's Reference Genome Project: A Unified Framework for Functional Annotation across Species". In Bourne, Philip E. PLoS Computational Biology 5 (7): e1000431. doi:10.1371/journal.pcbi.1000431. PMC 2699109. PMID 19578431.  edit
  31. ^ Degtyarenko, K.; De Matos, P.; Ennis, M.; Hastings, J.; Zbinden, M.; McNaught, A.; Alcantara, R.; Darsow, M.; Guedj, M.; Ashburner, M. (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.  edit
  32. ^ Gavaghan, H. (2001). "Biology moves into the silicon stage". Nature 409 (6822): 964. doi:10.1038/35057452. PMID 11241987.  edit
  33. ^ 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. Retrieved 8 Jan 2012. 
  34. ^ "EBI in a nutshell". European Bioinformatics Institute. Retrieved 8 Jan 2012. 
  35. ^ 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
  36. ^ The Lancet (2001). "Human genome row draws in journals". The Lancet 357 (9250): 81. doi:10.1016/S0140-6736(00)03531-5. 
  37. ^ Moody, Glyn (2004). Digital code of life : how bioinformatics is revolutionizing science, medicine, and business. Hoboken, NJ: Wiley. ISBN 0-471-32788-3. 
  38. ^ a b Ashburner, Michael. "Privatising our genes?". Retrieved 8 January 2012. 
  39. ^ Vince, Gaia. "Fears over rice genome access". Retrieved 8 January 2012. 
  40. ^ Roberts, R. J.; Varmus, H. E.; Ashburner, M.; Brown, P. O.; Eisen, M. B.; Khosla, C.; Kirschner, M.; Nusse, R.; Scott, M. (2001). "Information Access: Building A GenBank of the Published Literature". Science 291 (5512): 2318a. doi:10.1126/science.1060273.  edit
  41. ^ "BioMed Central Author Video - Professor Michael Ashburner Part 2/3" on YouTube
  42. ^ "BioMed Central Author Video - Professor Michael Ashburner Part 3/3" on YouTube
  43. ^ "BioMed Central Author Video - Professor Michael Ashburner Part 1/3" on YouTube
  44. ^ Ward, Mark (26 April 2001). "Scientists threaten journal protest". BBC News. Retrieved 4 February 2012. 
  45. ^ Meek, James (29 May 2001). "Science world in revolt at power of the journal owners". The Guardian (London). Retrieved 4 February 2012. 
  46. ^ Ward, Mark (1 September 2001). "Scientists call for online library". BBC News. Retrieved 4 February 2012. 
  47. ^ Ashburner, Michael. "UK Parliament Select Committee on Science and Technology APPENDIX 59". Retrieved 4 February 2012. 
  48. ^ McEntyre, J. R.; Ananiadou, S.; Andrews, S.; Black, W. J.; Boulderstone, R.; Buttery, P.; Chaplin, D.; Chevuru, S.; Cobley, N.; Coleman, L. -A.; Davey, P.; Gupta, B.; Haji-Gholam, L.; Hawkins, C.; Horne, A.; Hubbard, S. J.; Kim, J. -H.; Lewin, I.; Lyte, V.; MacIntyre, R.; Mansoor, S.; Mason, L.; McNaught, J.; Newbold, E.; Nobata, C.; Ong, E.; Pillai, S.; Rebholz-Schuhmann, D.; Rosie, H.; Rowbotham, R. (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.  edit
  49. ^ "Book of Members, 1780-2010: Chapter A". American Academy of Arts and Sciences. Retrieved 25 April 2011. 
  50. ^ "Library and Archive Catalogue". London: The Royal Society. Retrieved 2013-11-11. 

External links[edit]