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Michael Ashburner

From Wikipedia, the free encyclopedia

Michael Ashburner
FRS MAE
Michael Ashburner
Born(1942-05-23)23 May 1942[6]
Brighton, Sussex, England[7]
Died7 July 2023(2023-07-07) (aged 81)
NationalityBritish
EducationHigh Wycombe Grammar School
Alma materUniversity of Cambridge (BA, PhD)
Known for
Spouse
Francesca Ryan
​
(m. 1963)​
[6]
Awards
Scientific career
Fields
Institutions
ThesisStudies on puffing in the salivary gland chromosomes of Drosophila (1968)
Doctoral advisorAlan Henderson[5]
Websitewww.gen.cam.ac.uk/research-groups/ashburner

Michael Ashburner FRS MAE[11] (23 May 1942 – 7 July 2023) was an English biologist and Professor in the Department of Genetics at University of Cambridge.[12][13] He also served as joint-head and co-founder of the European Bioinformatics Institute (EBI)[14] of the European Molecular Biology Laboratory (EMBL)[15][16] and a Fellow of Churchill College, Cambridge.[17][18]

Education

[edit]

Born in Brighton, Sussex, England,[7] Ashburner was educated at the Royal Grammar School, High Wycombe from 1953 to 1960.[6] He studied the Natural Sciences Tripos at the University of Cambridge as an undergraduate student of Churchill College, Cambridge,[6] receiving his Bachelor of Arts degree in Genetics in 1964. His PhD was supervised by Alan Henderson[19][5] and awarded in 1968, followed by a Doctor of Science in 1978.[20]

Research and career

[edit]

Most of Ashburner's research was on the model organism Drosophila melanogaster.[8][21][22][23][24][25][26] 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,[21] he established the existence of a cascade of genetic controls in the post-larval development triggered by ecdysone.[27] 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.[28][29]

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".[30][31][32][33] A prolonged effort by his laboratory to characterise the Adh region[22] 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)[34] and Engineering and Physical Sciences Research Council (EPSRC)[35] 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[10] and the development of Open Biomedical Ontologies[36] to allow machine-searchable annotation of biological information, particularly the Gene Ontology[9][37]

[38] and ChEBI.[39] He was instrumental in establishing the EBI,[40] as well as securing its location in the UK,[20] and acted as the first head of the EBI jointly with Graham Cameron.[41]

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.[30] Additionally, Ashburner made a strong case for the human genome published in Science in 2000 by Celera Genomics to be made freely available,[42][43][44][45] and spoke out repeatedly against the privatization of genomic resources.[45][46] 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,[47] and subsequently became a strong advocate of Open Access publishing,[48][49] speaking out for this cause in the scientific literature[20][50] and popular media.[51][52][53] He also provided written evidence to the UK Parliament Select Committee on Science and Technology supporting Open Access publishing[54] and served on the initial advisory board of UK PubMed Central,[55] 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.[56] He received the Gregor Mendel Medal from the Academy of Sciences, Czech Republic in 1998, the first George W. Beadle Award[2] of the Genetics Society of America in 1999, an honorary Doctorate from the University of Crete in 2002, an honorary Doctor of Science from the University of Edinburgh in 2003, 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,[11] 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."[57]

Ashburner was awarded Member of the Academia Europaea (MAE) in 1989.[58]

Personal life

[edit]

Ashburner married Francesca Ryan and had one son and two daughters, Rebecca, Geoffrey and Isabel.[5][6] He died on 7 July 2023, at the age of 81.[5][18][59]

References

[edit]
  1. ^ Spradling, A. (2008). "The 2008 Thomas Hunt Morgan Medal". Genetics. 178 (3): 1123–1124. doi:10.1534/genetics.104.017832. PMC 2278087. PMID 18385103.
  2. ^ a b Hawley, R.; Kaufman, T. (2000). "The 1999 George W. Beadle Medal. Michael Ashburner". Genetics. 154 (1): 5. doi:10.1093/genetics/154.1.5. PMC 1460911. PMID 10681184.
  3. ^ a b Michael Ashburner keynote: From sequences to ontologies - adventures in informatics at Intelligent Systems for Molecular Biology July 2011
  4. ^ 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. Bibcode:2011PLSCB...7E2081M. doi:10.1371/journal.pcbi.1002081. PMC 3107244.
  5. ^ a b c d Anon (2023). "Professor Michael Ashburner FRS 1942 - 2023". cam.ac.uk. Archived from the original on 21 July 2023.
  6. ^ a b c d e Anon (2024). "Ashburner, Prof. Michael". Who's Who (176th ed.). Oxford: Oxford University Press. p. 2736. doi:10.1093/ww/9780199540884.013.U5810. ISBN 9781399409452. OCLC 1402257203. (Subscription or UK public library membership required.)
  7. ^ a b Q & A Michael Ashburner Retrieved 28/4/21.
  8. ^ 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 978-0-87969-706-8
  9. ^ 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 3037419. PMID 10802651. Open access icon
  10. ^ a b Ashburner, M.; Drysdale, R. (1994). "FlyBase--the Drosophila genetic database". Development. 120 (7): 2077–2079. doi:10.1242/dev.120.7.2077. PMID 7925011.
  11. ^ a b Anon (1990). "Professor Michael Ashburner FRS". royalsociety.org. London: Royal Society. Archived from the original on 23 November 2015.
  12. ^ Rubin, Gerald (2023). "Michael Ashburner (1942-2023)". Current Biology. 33 (17): R881–R883. doi:10.1016/j.cub.2023.08.029. PMID 37619564.
  13. ^ "Emeritus Professor Michael Ashburner, Department of Genetics". gen.cam.ac.uk. University of Cambridge. Archived from the original on 15 January 2013.
  14. ^ "Cold Spring Harbor Laboratoty (CSHL) Oral History | Michael Ashburner". Archived from the original on 20 March 2015.
  15. ^ "iMichael Ashburner archive collection". wellcomelibrary.org. Archived from the original on 9 September 2015.
  16. ^ Michael Ashburner publications indexed by the Scopus bibliographic database. (subscription required)
  17. ^ The Papers of Michael Ashburner held at Churchill Archives Centre
  18. ^ a b Cherbas, Peter; Kaufman, Thom (2023). "In Memoriam: Michael Ashburner". flybase.org. FlyBase.
  19. ^ Ashburner, Michael (1968). Studies on puffing in the salivary gland chromosomes of Drosophila. cam.ac.uk (PhD thesis). University of Cambridge. OCLC 879391061. EThOS uk.bl.ethos.596176.
  20. ^ a b c Ashburner, M. (2006). "Michael Ashburner". Current Biology. 16 (22): R941–R943. Bibcode:2006CBio...16.R941A. doi:10.1016/j.cub.2006.10.010. S2CID 29654933.
  21. ^ 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.
  22. ^ 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. doi:10.1093/genetics/153.1.179. PMC 1460734. PMID 10471707. Open access icon
  23. ^ 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.; et al. (2000). "The genome sequence of Drosophila melanogaster". Science. 287 (5461): 2185–2195. Bibcode:2000Sci...287.2185.. CiteSeerX 10.1.1.549.8639. doi:10.1126/science.287.5461.2185. PMID 10731132.
  24. ^ 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 2754258. PMID 10731134.
  25. ^ 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. Open access icon
  26. ^ 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 2605931. PMID 19222304. Open access icon
  27. ^ 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.
  28. ^ "FlyTree - Michael Ashburner Details". Archived from the original on 11 November 2013.
  29. ^ Pearson, Helen (2001). "Biology's name game: The confused nomenclature of genetics is blighting the field". Nature. 411 (6838): 631–632. doi:10.1038/35079694. PMID 11395736. S2CID 13625682. "Biologists would rather share their toothbrush than share a gene name"
  30. ^ a b Michael Ashburner (2006). Won for all: how the Drosophila genome was sequenced. Plainview, N.Y: Cold Spring Harbor Laboratory Press. ISBN 978-0-87969-802-7.
  31. ^ Sulston, John (2006). "All for All". PLOS Biology. 4 (6): e198. doi:10.1371/journal.pbio.0040198. PMC 1475689.
  32. ^ Rohn, Jennifer (2006). "Sequencing, sushi and sang-froid. Michael Ashburner's account of the fly genome project". Retrieved 29 July 2011.
  33. ^ Venter, J. C. (2006). "GENOMICS: An Ointment for the Fly". Science. 313 (5795): 1892. doi:10.1126/science.1134998. S2CID 82572658.
  34. ^ "UK Government Grants awarded to Michael Asburner". Research Councils UK. Archived from the original on 16 April 2015.
  35. ^ "EPSRC grants awarded to Michael Ashburner". EPSRC. Archived from the original on 16 April 2015.
  36. ^ 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 2814061. PMID 17989687. Open access icon
  37. ^ 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. Bibcode:2009PLSCB...5E0431.. doi:10.1371/journal.pcbi.1000431. PMC 2699109. PMID 19578431.
  38. ^ Wroe, C. J.; Stevens, R.; Goble, C. A.; Ashburner, M. (2002). "A Methodology to Migrate the Gene Ontology to a Description Logic Environment Using Daml+Oil". Biocomputing 2003. Pacific Symposium on Biocomputing 2003. Kauai, Hawaii. pp. 624–635. doi:10.1142/9789812776303_0058. ISBN 978-981-238-217-7. PMID 12603063.
  39. ^ 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.
  40. ^ Gavaghan, H. (2001). "Biology moves into the silicon stage". Nature. 409 (6822): 964. doi:10.1038/35057452. PMID 11241987. S2CID 130676.
  41. ^ "EBI in a nutshell" (PDF). European Bioinformatics Institute. Archived from the original (PDF) on 6 February 2011.
  42. ^ 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. S2CID 37724876.
  43. ^ Anon (2001). "Human genome row draws in journals". The Lancet. 357 (9250): 81. doi:10.1016/S0140-6736(00)03531-5. S2CID 5113446.
  44. ^ Moody, Glyn (2004). Digital code of life : how bioinformatics is revolutionizing science, medicine, and business. Hoboken, NJ: Wiley. ISBN 978-0-471-32788-2.
  45. ^ a b Ashburner, Michael. "Privatising our genes?". Archived from the original on 14 January 2012. Retrieved 8 January 2012.
  46. ^ Vince, Gaia. "Fears over rice genome access". New Scientist. Archived from the original on 10 January 2014. Retrieved 8 January 2012.
  47. ^ 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): 2318–9. doi:10.1126/science.1060273. PMID 11269300. S2CID 34395787.
  48. ^ "BioMed Central Author Video - Professor Michael Ashburner Part 2/3" on YouTube
  49. ^ "BioMed Central Author Video - Professor Michael Ashburner Part 3/3" on YouTube
  50. ^ "BioMed Central Author Video - Professor Michael Ashburner Part 1/3" on YouTube
  51. ^ Ward, Mark (26 April 2001). "Scientists threaten journal protest". BBC News. Archived from the original on 7 August 2007. Retrieved 4 February 2012.
  52. ^ Meek, James (29 May 2001). "Science world in revolt at power of the journal owners". The Guardian. London. Retrieved 4 February 2012.
  53. ^ Ward, Mark (1 September 2001). "Scientists call for online library". BBC News. Archived from the original on 1 July 2004. Retrieved 4 February 2012.
  54. ^ Ashburner, Michael. "UK Parliament Select Committee on Science and Technology APPENDIX 59". Archived from the original on 15 July 2012. Retrieved 4 February 2012.
  55. ^ 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.
  56. ^ "Book of Members, 1780-2010: Chapter A" (PDF). American Academy of Arts and Sciences. Archived from the original (PDF) on 10 May 2011. Retrieved 25 April 2011.
  57. ^ "Certificate of election: Michael Ashburner. EC/1990/02". London: The Royal Society. Archived from the original on 8 July 2019.
  58. ^ Anon (1989). "Michael Ashburner MAE". ae-info.org. Academia Europaea.
  59. ^ Birney, Ewan; Apweiler, Rolf (2023). "We are deeply saddened to hear about the passing of our co-founder and former Head of Research, Michael Ashburner". linkedin.com. European Bioinformatics Institute.

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Academic offices
Preceded by
-
 Joint Director of the European Bioinformatics Institute (with Graham Cameron)
1992–2001 		Succeeded by
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