Michael Ashburner

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Michael Ashburner
Plos ashburner.jpg
Michael Ashburner
Born (1942-05-23) 23 May 1942 (age 74)[1]
Sussex, England
Nationality United Kingdom
Fields
Institutions
Alma mater University of Cambridge (BA, PhD)
Thesis Studies on puffing in the salivary gland chromosomes of Drosophila (1968)
Doctoral students
  • Kevin Moses[3][4]
  • Voula Velissariou[5][6]
  • Mary Boyd
  • Geoff Richards
  • Bruce Reed
  • Christopher Redfern
  • Virginia Papioannou
  • Steve McGill[7]
  • Cathy Martin
  • Ruth Lovering[8]
  • Pete Jeffs[9][10]
  • Marc Jacobs
  • Nick Harden[11]
  • Jan C. Eeken
  • Mark Bodmer[12]
  • Ounissa Ait-Ahmed[13]
Other notable students Casey Bergman (postdoc)[14][15]
Known for
Influences Bruce Alberts[2]
Notable awards
Website
www.gen.cam.ac.uk/research-groups/ashburner

Michael Ashburner FRS (born 23 May 1942) is a biologist and emeritus Professor in the Department of Genetics at University of Cambridge.[23] He is also the former joint-head and co-founder of the European Bioinformatics Institute (EBI)[24] of the European Molecular Biology Laboratory (EMBL)[25][26] and a Fellow of Churchill College, Cambridge.

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[27] from the Department of Genetics in 1968, and was awarded a Doctor of Science in 1978, all from Cambridge.[28]

Research[edit]

Most of Ashburner's research has been on the model organism Drosophila melanogaster.[16][29][30][31][32][33][34] 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,[29] he established the existence of a cascade of genetic controls in the post-larval development triggered by ecdysone.[35] 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.[13]

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".[36][37][38][39] A prolonged effort by his laboratory to characterise the Adh region[30] became invaluable for validating annotation strategies when large-scale genome information became available. Ashburner and his colleagues have received funding from the Biotechnology and Biological Sciences Research Council (BBSRC), the Medical Research Council (MRC)[40] and Engineering and Physical Sciences Research Council (EPSRC)[41] 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[18] and the development of Open Biomedical Ontologies[42] to allow machine-searchable annotation of biological information, particularly the Gene Ontology[17][43][44] and ChEBI.[45] He was instrumental in establishing the EBI,[46] as well as securing its location in the UK,[28][47] and acted as the first head of the EBI jointly with Graham Cameron.[48]

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.[36] Additionally, Ashburner made a strong case for the human genome published in Science in 2000 by Celera Genomics to be made freely available,[49][50][51][52] and has spoken out repeatedly against the privatization of genomic resources.[52][53] 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,[54] and subsequently became a strong advocate of Open Access publishing,[55][56] speaking out for this cause in the scientific literature[28][57] and popular media.[58][59][60] He also provided written evidence to the UK Parliament Select Committee on Science and Technology supporting Open Access publishing[61] and served on the initial advisory board of UK PubMed Central,[62] the first global mirror site of the PubMed Central repository of freely available biological literature.

Awards and honours[edit]

Ashburner was elected a Foreign Honorary Member of the American Academy of Arts and Sciences in 1993.[63] He received the Gregor Mendel Medal from the Academy of Sciences, Czech Republic in 1998, the first George W. Beadle Award[21] of the Genetics Society of America in 1999, an honorary Doctorate from the University of Crete in 2002, the Genetics Society Medal of the UK Genetics Society in 2005 and the Franklin Award of the Bioinformatics Organization in 2006. Ashburner was elected a Fellow of the Royal Society (FRS) in 1990, his certificate of election 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."[19]

References[edit]

  1. ^ a b ASHBURNER, Prof. Michael. Who's Who. 2014 (online Oxford University Press ed.). A & C Black, an imprint of Bloomsbury Publishing plc.  (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. ^ Moses, K; Heberlein, U; Ashburner, M (1990). "The Adh gene promoters of Drosophila melanogaster and Drosophila orena are functionally conserved and share features of sequence structure and nuclease-protected sites". Molecular and Cellular Biology. 10 (2): 539–48. doi:10.1128/mcb.10.2.539. PMC 360832free to read. PMID 2105454. 
  4. ^ Moses, K; Ashburner, M (1985). "Circadian rhythms. Period piece for Drosophila". Nature. 315 (6015): 98. doi:10.1038/315098a0. PMID 3921854. 
  5. ^ Velissariou, V; Ashburner, M (1981). "Cytogenetic and genetic mapping of a salivary gland secretion protein in Drosophila melanogaster". Chromosoma. 84 (2): 173–85. doi:10.1007/bf00399129. PMID 6799259. 
  6. ^ Velissariou, V; Ashburner, M (1980). "The secretory proteins of the larval salivary gland of Drosophila melanogaster: Cytogenetic correlation of a protein and a puff". Chromosoma. 77 (1): 13–27. doi:10.1007/bf00292038. PMID 6768531. 
  7. ^ McGill, S; Chia, W; Karp, R; Ashburner, M (1988). "The molecular analyses of an antimorphic mutation of Drosophila melanogaster, Scutoid". Genetics. 119 (3): 647–61. PMC 1203450free to read. PMID 16052738. 
  8. ^ Lovering, R; Harden, N; Ashburner, M (1991). "The molecular structure of TE146 and its derivatives in Drosophila melanogaster". Genetics. 128 (2): 357–72. PMC 1204473free to read. PMID 1649070. 
  9. ^ Jeffs, P. S.; Holmes, E. C.; Ashburner, M (1994). "The molecular evolution of the alcohol dehydrogenase and alcohol dehydrogenase-related genes in the Drosophila melanogaster species subgroup". Molecular Biology and Evolution. 11 (2): 287–304. PMID 8170369. 
  10. ^ Jeffs, P; Ashburner, M (1991). "Processed pseudogenes in Drosophila". Proceedings of the Royal Society B: Biological Sciences. 244 (1310): 151–9. doi:10.1098/rspb.1991.0064. PMID 1679549. 
  11. ^ Harden, N; Ashburner, M (1990). "Characterization of the FB-NOF transposable element of Drosophila melanogaster". Genetics. 126 (2): 387–400. PMC 1204193free to read. PMID 2174013. 
  12. ^ Bodmer, M; Ashburner, M (1984). "Conservation and change in the DNA sequences coding for alcohol dehydrogenase in sibling species of Drosophila". Nature. 309 (5967): 425–30. doi:10.1038/309425a0. PMID 6427630. 
  13. ^ a b "FlyTree - Michael Ashburner Details". Archived from the original on 2013-01-04. 
  14. ^ 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 1794594free to read. PMID 17134480. 
  15. ^ "The Roberts/Ashburner Response". caseybergman.wordpress.com. Archived from the original on 2013-10-13. 
  16. ^ 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 
  17. ^ 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. (2000). "Gene ontology: Tool for the unification of biology. The Gene Ontology Consortium". Nature Genetics. 25 (1): 25–29. doi:10.1038/75556. PMC 3037419free to read. PMID 10802651.  open access publication - free to read
  18. ^ a b Ashburner, M.; Drysdale, R. (1994). "FlyBase--the Drosophila genetic database". Development (Cambridge, England). 120 (7): 2077–2079. PMID 7925011. 
  19. ^ a b "Certificate of election: Michael Ahsburner. EC/1990/02". London: The Royal Society. Archived from the original on 2015-04-16. 
  20. ^ Spradling, A. (2008). "The 2008 Thomas Hunt Morgan Medal". Genetics. 178 (3): 1123–1124. doi:10.1534/genetics.104.017832. PMC 2278087free to read. PMID 18385103. 
  21. ^ a b Hawley, R.; Kaufman, T. (2000). "The 1999 George W. Beadle Medal. Michael Ashburner". Genetics. 154 (1): 5. PMC 1460911free to read. PMID 10681184. 
  22. ^ 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 3107244free to read. 
  23. ^ "Michael Ashburner, Department of Genetics, University of Cambridge". Archived from the original on 2011-07-29. 
  24. ^ "Cold Spring Harbor Laboratoty (CSHL) Oral History | Michael Ashburner". Archived from the original on 2013-06-07. 
  25. ^ Michael Ashburner archive collection - Wellcome Library finding aid
  26. ^ Michael Ashburner's publications indexed by the Scopus bibliographic database, a service provided by Elsevier. (subscription required)
  27. ^ Ashburner, Michael (1968). Studies on puffing in the salivary gland chromosomes of Drosophila (DPhil thesis). University of Cambridge. 
  28. ^ a b c Ashburner, M. (2006). "Michael Ashburner". Current Biology. 16 (22): R941–R943. doi:10.1016/j.cub.2006.10.010. 
  29. ^ 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. 
  30. ^ 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 1460734free to read. PMID 10471707.  open access publication - free to read
  31. ^ 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. 
  32. ^ Rubin, G.; Yandell, M.; Wortman, J.; Gabor Miklos, G.; Nelson, C.; Hariharan, I.; Fortini, M.; Li, P.; Apweiler, R.; Fleischmann, W.; Cherry, J. M.; Henikoff, S.; Skupski, M. P.; Misra, S.; Ashburner, M.; Birney, E.; Boguski, M. S.; Brody, T.; Brokstein, P.; Celniker, S. E.; Chervitz, S. A.; Coates, D.; Cravchik, A.; Gabrielian, A.; Galle, R. F.; Gelbart, W. M.; George, R. A.; Goldstein, L. S.; Gong, F.; Guan, P. (2000). "Comparative genomics of the eukaryotes". Science. 287 (5461): 2204–2215. Bibcode:2000Sci...287.2204.. doi:10.1126/science.287.5461.2204. PMC 2754258free to read. PMID 10731134. 
  33. ^ 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 1885836free to read. PMID 17550304.  open access publication - free to read
  34. ^ Teixeira, L. S.; Ferreira, Á.; Ashburner, M. (2008). "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 2605931free to read. PMID 19222304.  open access publication - free to read
  35. ^ 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. 
  36. ^ 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. 
  37. ^ Sulston, J. (2006). "All for All". PLoS Biology. 4 (6): e198. doi:10.1371/journal.pbio.0040198. 
  38. ^ Jennifer Rohn (2006). "Sequencing, sushi and sang-froid. Michael Ashburner's account of the fly genome project". Retrieved 2011-07-29. 
  39. ^ Venter, J. C. (2006). "GENOMICS: An Ointment for the Fly". Science. 313 (5795): 1892. doi:10.1126/science.1134998. 
  40. ^ "UK Government Grants awarded to Michael Asburner". Research Councils UK. Archived from the original on 2015-04-15. 
  41. ^ "EPSRC grants awarded to Michael Ashburner". EPSRC. Archived from the original on 2015-04-15. 
  42. ^ 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. (2007). "The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration". Nature Biotechnology. 25 (11): 1251–1255. doi:10.1038/nbt1346. PMC 2814061free to read. PMID 17989687.  open access publication - free to read
  43. ^ 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 2699109free to read. PMID 19578431. 
  44. ^ Wroe, C. J.; Stevens, R.; Goble, C. A.; Ashburner, M. (2003). "A methodology to migrate the gene ontology to a description logic environment using DAML+OIL". Pacific Symposium on Biocomputing: 624–635. PMID 12603063. 
  45. ^ 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 2238832free to read. PMID 17932057. 
  46. ^ Gavaghan, H. (2001). "Biology moves into the silicon stage". Nature. 409 (6822): 964. doi:10.1038/35057452. PMID 11241987. 
  47. ^ 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. 
  48. ^ "EBI in a nutshell" (PDF). European Bioinformatics Institute. Archived from the original (PDF) on 2011-02-06. 
  49. ^ 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. 
  50. ^ The Lancet (2001). "Human genome row draws in journals". The Lancet. 357 (9250): 81. doi:10.1016/S0140-6736(00)03531-5. 
  51. ^ Moody, Glyn (2004). Digital code of life : how bioinformatics is revolutionizing science, medicine, and business. Hoboken, NJ: Wiley. ISBN 0-471-32788-3. 
  52. ^ a b Ashburner, Michael. "Privatising our genes?". Retrieved 8 January 2012. 
  53. ^ Vince, Gaia. "Fears over rice genome access". Retrieved 8 January 2012. 
  54. ^ 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. 
  55. ^ "BioMed Central Author Video - Professor Michael Ashburner Part 2/3" on YouTube
  56. ^ "BioMed Central Author Video - Professor Michael Ashburner Part 3/3" on YouTube
  57. ^ "BioMed Central Author Video - Professor Michael Ashburner Part 1/3" on YouTube
  58. ^ Ward, Mark (26 April 2001). "Scientists threaten journal protest". BBC News. Retrieved 4 February 2012. 
  59. ^ Meek, James (29 May 2001). "Science world in revolt at power of the journal owners". The Guardian. London. Retrieved 4 February 2012. 
  60. ^ Ward, Mark (1 September 2001). "Scientists call for online library". BBC News. Retrieved 4 February 2012. 
  61. ^ Ashburner, Michael. "UK Parliament Select Committee on Science and Technology APPENDIX 59". Retrieved 4 February 2012. 
  62. ^ 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 3013671free to read. PMID 21062818. 
  63. ^ "Book of Members, 1780-2010: Chapter A" (PDF). American Academy of Arts and Sciences. Retrieved 25 April 2011. 
Academic offices
Preceded by
-
Joint Director of the European Bioinformatics Institute (with Graham Cameron)
1992–2001
Succeeded by
Janet Thornton