Biography:Michael Ashburner

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Short description: English biologist (1942–2023)
Michael Ashburner

FRS MAE
Plos ashburner.jpg
Michael Ashburner
Born(1942-05-23)23 May 1942[1]
Brighton, Sussex, England[2]
Died7 July 2023(2023-07-07) (aged 81)
NationalityBritish
EducationHigh Wycombe Grammar School
Alma materUniversity of Cambridge (BA, PhD)
Known for
Spouse(s)
Francesca Ryan (m. 1963)
[1]
Awards
Scientific career
Fields
Institutions
ThesisStudies on puffing in the salivary gland chromosomes of Drosophila (1968)
Doctoral advisorAlan Henderson[11]
Websitewww.gen.cam.ac.uk/research-groups/ashburner

Michael Ashburner FRS MAE[12] (23 May 1942 – 7 July 2023) was an English biologist and Professor in the Department of Genetics at University of Cambridge.[13] He was also the former 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

Born in Brighton, Sussex, England,[2] Ashburner attended High Wycombe Royal Grammar School from 1953 to 1960.[1] He studied at Churchill College, Cambridge,[1] and received his Bachelor of Arts in Natural Sciences Tripos (Genetics) in 1964, his PhD supervised by Alan Henderson[19][11] from the Department of Genetics in 1968, and was awarded a Doctor of Science in 1978.[20]

Research and career

Most of Ashburner's research was on the model organism Drosophila melanogaster.[3][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

Ashburner was also an early pioneer in the application of computers to biology. His contributions include his active participation in setting up FlyBase[5] and the development of Open Biomedical Ontologies[36] to allow machine-searchable annotation of biological information, particularly the Gene Ontology[4][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

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

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[8] 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,[12] 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

Ashburner married Francesca Ryan and had one son and two daughters, Rebecca, Geoffrey and Isabel.[11][1] He died on 7 July 2023, at the age of 81.[11][18][59]

References

  1. ↑ 1.0 1.1 1.2 1.3 1.4 Anon (2014). ",". Who's Who (online Oxford University Press ed.). A & C Black, an imprint of Bloomsbury Publishing plc. doi:10.1093/ww/9780199540884.013.U5810. https://www.ukwhoswho.com/view/article/oupww/whoswho/U5810.  (subscription or UK public library membership required)
  2. ↑ 2.0 2.1 Q & A Michael Ashburner Retrieved 28/4/21.
  3. ↑ 3.0 3.1 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, http://www.cshlpress.com/default.tpl?action=full&--eqskudatarq=810 
  4. ↑ 4.0 4.1 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. PMID 10802651.  open access
  5. ↑ 5.0 5.1 Ashburner, M.; Drysdale, R. (1994). "FlyBase--the Drosophila genetic database". Development 120 (7): 2077–2079. doi:10.1242/dev.120.7.2077. PMID 7925011. 
  6. ↑ "Michael Ashburner, University of Cambridge". European Molecular Biology Organization. https://people.embo.org/profile/michael-ashburner. 
  7. ↑ "The 2008 Thomas Hunt Morgan Medal". Genetics 178 (3): 1123–1124. 2008. doi:10.1534/genetics.104.017832. PMID 18385103. 
  8. ↑ 8.0 8.1 Hawley, R.; Kaufman, T. (2000). "The 1999 George W. Beadle Medal. Michael Ashburner". Genetics 154 (1): 5. doi:10.1093/genetics/154.1.5. PMID 10681184. 
  9. ↑ 9.0 9.1 Michael Ashburner keynote: From sequences to ontologies - adventures in informatics at Intelligent Systems for Molecular Biology July 2011
  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. Bibcode: 2011PLSCB...7E2081M. 
  11. ↑ 11.0 11.1 11.2 11.3 Anon (2023). "Professor Michael Ashburner FRS 1942 - 2023". Archived from the original on 2023-07-21. https://web.archive.org/web/20230721085713/https://www.gen.cam.ac.uk/department/history-of-the-department/michael-ashburner. 
  12. ↑ 12.0 12.1 Anon (1990). "Professor Michael Ashburner FRS". London: Royal Society. https://royalsociety.org/people/michael-ashburner-11006/. 
  13. ↑ "Emeritus Professor Michael Ashburner, Department of Genetics". University of Cambridge. http://www.gen.cam.ac.uk/research/ashburner.html. 
  14. ↑ "Cold Spring Harbor Laboratoty (CSHL) Oral History | Michael Ashburner". http://library.cshl.edu/oralhistory/speaker/michael-ashburner/. 
  15. ↑ "iMichael Ashburner archive collection". http://archives.wellcomelibrary.org/DServe/dserve.exe?dsqIni=Dserve.ini&dsqApp=Archive&dsqCmd=Show.tcl&dsqDb=Catalog&dsqPos=0&dsqSearch=%28AltRefNo%3D%27pp%2Fmia%27%29. 
  16. ↑ Michael Ashburner publications indexed by the Scopus bibliographic database. (Subscription content?)
  17. ↑ The Papers of Michael Ashburner held at Churchill Archives Centre
  18. ↑ 18.0 18.1 Cherbas, Peter; Kaufman, Thom (2023). "In Memoriam: Michael Ashburner". FlyBase. http://flybase.org/commentaries/2023_07/ashburner.html. 
  19. ↑ Ashburner, Michael (1968). Studies on puffing in the salivary gland chromosomes of Drosophila. lib.cam.ac.uk (PhD thesis). University of Cambridge. OCLC 879391061. EThOS uk.bl.ethos.596176.
  20. ↑ 20.0 20.1 20.2 Ashburner, M. (2006). "Michael Ashburner". Current Biology 16 (22): R941–R943. doi:10.1016/j.cub.2006.10.010. 
  21. ↑ 21.0 21.1 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. ↑ 22.0 22.1 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. doi:10.1093/genetics/153.1.179. PMID 10471707.  open access
  23. ↑ 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. doi:10.1126/science.287.5461.2185. PMID 10731132. Bibcode: 2000Sci...287.2185.. 
  24. ↑ Rubin, G.; Yandell, M.; Wortman, J.; Gabor Miklos, G.; Nelson, C.; Hariharan, I.; Fortini, M.; Li, P. et al. (2000). "Comparative genomics of the eukaryotes". Science 287 (5461): 2204–2215. doi:10.1126/science.287.5461.2204. PMID 10731134. Bibcode: 2000Sci...287.2204.. 
  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. PMID 17550304.  open access
  26. ↑ Teixeira, L. S.; Ferreira, Á. (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. PMID 19222304.  open access
  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". http://academictree.org/flytree/peopleinfo.php?pid=13863. 
  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. "“Biologists would rather share their toothbrush than share a gene name”". 
  30. ↑ 30.0 30.1 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. https://archive.org/details/isbn_9780879698027. 
  31. ↑ Sulston, John (2006). "All for All". PLOS Biology 4 (6): e198. doi:10.1371/journal.pbio.0040198. 
  32. ↑ Rohn, Jennifer (2006). "Sequencing, sushi and sang-froid. Michael Ashburner's account of the fly genome project". http://www.lablit.com/article/96. 
  33. ↑ Venter, J. C. (2006). "GENOMICS: An Ointment for the Fly". Science 313 (5795): 1892. doi:10.1126/science.1134998. 
  34. ↑ "UK Government Grants awarded to Michael Asburner". Research Councils UK. http://gtr.rcuk.ac.uk/person/079A6C72-3F4B-43E4-919B-E01E3E69529. 
  35. ↑ "EPSRC grants awarded to Michael Ashburner". EPSRC. http://gow.epsrc.ac.uk/NGBOViewPerson.aspx?PersonId=50745. 
  36. ↑ 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. PMID 17989687.  open access
  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. doi:10.1371/journal.pcbi.1000431. PMID 19578431. Bibcode: 2009PLSCB...5E0431.. 
  38. ↑ Wroe, C. J.; Stevens, R.; Goble, C. A.; Ashburner, M. (2002). "Biocomputing 2003". Pacific Symposium on Biocomputing 2003. Kauai, Hawaii. pp. 624–635. doi:10.1142/9789812776303_0058. ISBN 978-981-238-217-7. 
  39. ↑ 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. PMID 17932057. 
  40. ↑ Gavaghan, H. (2001). "Biology moves into the silicon stage". Nature 409 (6822): 964. doi:10.1038/35057452. PMID 11241987. 
  41. ↑ "EBI in a nutshell". European Bioinformatics Institute. http://www.ebi.ac.uk/Information/Brochures/pdf/In_a_nutshell_small_file.pdf. 
  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. 
  43. ↑ Anon (2001). "Human genome row draws in journals". The Lancet 357 (9250): 81. doi:10.1016/S0140-6736(00)03531-5. 
  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. https://archive.org/details/digitalcodeoflif0000mood. 
  45. ↑ 45.0 45.1 Ashburner, Michael. "Privatising our genes?". http://www.opendemocracy.net/theme_9-genes/article_407.jsp. 
  46. ↑ Vince, Gaia. "Fears over rice genome access". New Scientist. https://www.newscientist.com/article/dn2061. 
  47. ↑ 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): 2318–9. doi:10.1126/science.1060273. PMID 11269300. 
  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. http://news.bbc.co.uk/1/hi/sci/tech/1296750.stm. 
  52. ↑ Meek, James (29 May 2001). "Science world in revolt at power of the journal owners". The Guardian (London). https://www.theguardian.com/uk/2001/may/26/highereducation.physicalsciences. 
  53. ↑ Ward, Mark (1 September 2001). "Scientists call for online library". BBC News. http://news.bbc.co.uk/1/hi/sci/tech/1516824.stm. 
  54. ↑ Ashburner, Michael. "UK Parliament Select Committee on Science and Technology APPENDIX 59". https://publications.parliament.uk/pa/cm200304/cmselect/cmsctech/399/399we70.htm. 
  55. ↑ 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. PMID 21062818. 
  56. ↑ "Book of Members, 1780-2010: Chapter A". American Academy of Arts and Sciences. http://www.amacad.org/publications/BookofMembers/ChapterA.pdf. 
  57. ↑ "Certificate of election: Michael Ashburner. EC/1990/02". London: The Royal Society. http://royalsociety.org. 
  58. ↑ Anon (1989). "Michael Ashburner MAE". Academia Europaea. https://www.ae-info.org/ae/Member/Ashburner_Michael. 
  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.". European Bioinformatics Institute. https://www.linkedin.com/posts/ebi_we-are-deeply-saddened-to-hear-about-the-activity-7083081386139471872-jIAH. 
Academic offices
Preceded by
- 		Joint Director of the European Bioinformatics Institute (with Graham Cameron)
1992–2001 		Succeeded by
Janet Thornton



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