Julian Gough (scientist) explained

Julian Gough
Birth Name:Julian John Thurstan Gough[1]
Birth Date:[2]
Education:The Perse School
Known For:Superfamily database
Thesis Title:Hidden Markov models and their application to the genome analysis in the context of protein structure
Thesis Url:http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.599547
Thesis Year:2001
Doctoral Advisor:Cyrus Chothia

Julian John Thurstan Gough (born 1974)[2] was a Group Leader in the Laboratory of Molecular Biology (LMB) of the Medical Research Council (MRC). He was previously a professor of bioinformatics at the University of Bristol.

Education

Gough was educated at The Perse School[3] in Cambridge and the University of Bristol where he was awarded a joint honours degree in Mathematics and Physics in 1998.[3] He went on to complete his PhD in the Laboratory of Molecular Biology (LMB) supervised by Cyrus Chothia on genome analysis and protein structure as a postgraduate student of Sidney Sussex College, Cambridge, graduating in 2001.[4]

Career and research

Following his PhD, Gough completed postdoctoral research at the LMB and Stanford University, with Michael Levitt. Subsequently, he was a scientist at RIKEN in Tokyo before being appointed a member of faculty at the University of Bristol, where he has worked since 2007.[3] He has also been a visiting scientist at the Pasteur Institute in Paris and an associate professor at Tokyo Medical and Dental University.

Gough's research interests are in bioinformatics, computational biology, molecular biology, genomics which has led to the creation of the Superfamily database[5] [6] of Hidden Markov models (HMMs) representing all proteins of known structure. His research has been published in leading peer reviewed scientific journals including Nature,[7] [8] Science,[9] [10] Cell,[11] Nucleic Acids Research,[12] [13] [14] [15] [16] PNAS,[17] [18] the Biochemical Journal,[19] the Journal of Molecular Biology,[20] [21] [22] Genome Research,[23] Bioinformatics,[24] PLOS Genetics,[25] Nature Genetics[26] and the Journal of Bacteriology.[27]

Gough's research has been funded by the Biotechnology and Biological Sciences Research Council (BBSRC), the Engineering and Physical Sciences Research Council (EPSRC), the Natural Environment Research Council (NERC),[28] the European Union (EU) Seventh Research Framework Programme (FP7), the Japan Society for the Promotion of Science (JSPS) and the Royal Society of London.[29]

Notes and References

  1. Web site: University Library thesis catalog: Julian John Thurstan Gough . https://archive.today/20150415204057/http://ulmss-newton.lib.cam.ac.uk/vwebv/holdingsInfo?bibId=23813 . 15 April 2015 . University of Cambridge . dead .
  2. Web site: https://web.archive.org/web/20160718113254/https://beta.companieshouse.gov.uk/officers/YIBLJ46w1xWVfA-36_J7WMjphfc/appointments. 18 July 2016. Julian GOUGH. London. Companies House, Government of the United Kingdom.
  3. Web site: Julian Gough profile. LinkedIn. dead. https://archive.today/20150415204103/https://uk.linkedin.com/pub/julian-gough/b/25b/3b3. 15 April 2015.
  4. PhD . Julian. Gough . Hidden Markov models and their application to genome analysis in the context of protein structure . 2001. University of Cambridge . https://web.archive.org/web/20150311092300/http://bioinformatics.bris.ac.uk/people/julian_gough/publications/thesis.pdf. 11 March 2015. 879396947. .
  5. Gough . J. . Julian Gough (scientist). Chothia . C. . Cyrus Chothia. SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments . Nucleic Acids Research . 30 . 1 . 268–272 . 2002 . 11752312 . 99153 . 10.1093/nar/30.1.268.
  6. De Lima Morais . D. A. . Fang . H. . Rackham . O. J. L. . Wilson . D. . Pethica . R. . Chothia . C. . Cyrus Chothia. Gough . J. . 10.1093/nar/gkq1130 . SUPERFAMILY 1.75 including a domain-centric gene ontology method . Nucleic Acids Research . 39 . Database issue . D427–D434 . 2010 . 21062816 . 3013712 .
  7. 24670764. 2014. FANTOM Consortium and the RIKEN PMI and CLST (DGT). A promoter-level mammalian expression atlas. Nature. 507. 7493. 462–70. Forrest. A. R.. Kawaji. H. Rehli. M. Baillie. J. K.. De Hoon. M. J.. Haberle. V. Lassmann. T. Kulakovskiy. I. V.. Lizio. M. Itoh. M. Andersson. R. Mungall. C. J.. Meehan. T. F.. Schmeier. S. Bertin. N. Jørgensen. M. Dimont. E. Arner. E. Schmidl. C. Schaefer. U. Medvedeva. Y. A.. Plessy. C. Vitezic. M. Severin. J. Semple. C. Ishizu. Y. Young. R. S.. Francescatto. M. Alam. I. 29. 10.1038/nature13182 . 4529748. 2014Natur.507..462T.
  8. Okazaki . Y. . Furuno . M. . Kasukawa . T. . Adachi . J. . Bono . H. . Kondo . S. . Nikaido . I. . Osato . N. . Saito . R. . Suzuki . 10.1038/nature01266 . H. . Yamanaka . I. . Kiyosawa . H. . Yagi . K. . Tomaru . Y. . Hasegawa . Y. . Nogami . A. . Schönbach . C. . Gojobori . T. . Takashi Gojobori. Baldarelli . R. . Hill . D. P. . Bult . C. . Hume . D. A. . Quackenbush . J. . John Quackenbush. Schriml . L. M. . Kanapin . A. . Matsuda . H. . Batalov . S. . Beisel . K. W. . Blake . J. A. . Bradt . D. . Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs . Nature . 420 . 6915 . 563–573 . 2002 . 12466851 . 2002Natur.420..563O . 29 . free . 10161/11223 . free .
  9. 12805536. 2003. Chothia. C. Cyrus Chothia. Evolution of the protein repertoire. Science. 300. 5626. 1701–3. Gough. J. Julian Gough (scientist). Vogel. C. Teichmann. S. A.. Sarah Teichmann. 10.1126/science.1085371. 2003Sci...300.1701C. 27681885.
  10. 16141072. 2005. Carninci. P. The transcriptional landscape of the mammalian genome. Science. 309. 5740. 1559–63. Kasukawa. T. Katayama. S. Gough. J. Julian Gough (scientist). Frith. M. C.. Maeda. N. Oyama. R. Ravasi. T. Lenhard. B. Wells. C. Kodzius. R. Shimokawa. K. Bajic. V. B.. Brenner . S. E. . Steven E. Brenner. Batalov. S. Forrest. A. R.. Zavolan. M. Davis. M. J.. Wilming. L. G.. Aidinis. V. Allen. J. E.. Ambesi-Impiombato. A. Apweiler. R. Rolf Apweiler. Aturaliya. R. N.. Bailey. T. L.. Bansal. M. Baxter. L. Beisel. K. W.. Bersano. T. Bono. H. 29. 10.1126/science.1112014. 2005Sci...309.1559F. 8712839.
  11. 20211142. 2836267. 2010. Ravasi. T. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 140. 5. 744–52. Suzuki. H. Cannistraci. C. V.. Katayama. S. Bajic. V. B.. Tan. K. Akalin. A. Schmeier. S. Kanamori-Katayama. M. Bertin. N. Carninci. P. Daub. C. O.. Forrest. A. R.. Gough. J. Grimmond. S. Han. J. H.. Hashimoto. T. Hide. W. Hofmann. O. Kamburov. A. Kaur. M. Kawaji. H. Kubosaki. A. Lassmann. T. Van Nimwegen. E. MacPherson. C. R.. Ogawa. C. Radovanovic. A. Schwartz. A. Teasdale. R. D.. Tegnér. J. Lenhard. B. Teichmann . SA . Sarah Teichmann. Arakawa. T. Ninomiya. N. Murakami. K. Tagami. M. Fukuda. S. Imamura. K. Kai. C. Ishihara. R. Kitazume. Y. Kawai. J. Hume. DA. Ideker . T . Trey Ideker. Hayashizaki. Y. 10.1016/j.cell.2010.01.044.
  12. 25348407. 2015. Lewis. T. E.. Genome3D: Exploiting structure to help users understand their sequences. Nucleic Acids Research. 43. Database issue. D382–6. Sillitoe. I. Andreeva. A. Blundell. T. L.. Buchan. D. W.. Chothia. C. Cyrus Chothia. Cozzetto. D. Dana. J. M.. Filippis. I. Gough. J. Julian Gough (scientist). Jones. D. T.. Kelley. L. A.. Kleywegt. G. J.. Gerard Kleywegt. Minneci. F. Mistry. J. Murzin. A. G.. Ochoa-Montaño. B. Oates. M. E.. Punta. M. Rackham. O. J.. Stahlhacke. J. Sternberg. M. J.. Michael Sternberg. Velankar. S. Orengo. C. 10.1093/nar/gku973. 4384030.
  13. 25428371. 2015. Mitchell. A. The InterPro protein families database: The classification resource after 15 years. Nucleic Acids Research. 43. Database issue. D213–21. Chang. H. Y.. Daugherty. L. Fraser. M. Hunter. S. Lopez. R. McAnulla. C. McMenamin. C. Nuka. G. Pesseat. S. Sangrador-Vegas. A. Scheremetjew. M. Rato. C. Yong. S. Y.. Bateman. A . Alex Bateman. Punta. M. Attwood . T. K. . Terri Attwood. Sigrist. C. J.. Redaschi. N. Rivoire. C. Xenarios. I. Kahn. D. Guyot. D. Bork . P . Peer Bork. Letunic. I. Gough . J . Julian Gough (scientist). Oates. M. Haft. D. Huang. H. Natale. D. A.. 4383996. 10.1093/nar/gku1243.
  14. Hunter . S. . Jones . P. . Mitchell . A. . Apweiler . R. . Attwood . T. K. . Bateman . A. . Bernard . T. . Binns . D. . Bork . P. . Burge . 10.1093/nar/gkr948 . S. . De Castro . E. . Coggill . P. . Corbett . M. . Das . U. . Daugherty . L. . Duquenne . L. . Finn . R. D. . Fraser . M. . Gough . J. . Haft . D. . Hulo . N. . Kahn . D. . Kelly . E. . Letunic . I. . Lonsdale . D. . Lopez . R. . Madera . M. . Maslen . J. . McAnulla . C. . McDowall . J. . InterPro in 2011: New developments in the family and domain prediction database . Nucleic Acids Research . 40 . Database issue . D306–D312 . 2011 . 22096229 . 3245097 .
  15. Hunter . S.. Apweiler . R. . Rolf Apweiler . T. . Attwood . Terri Attwood. Bairoch . A. . Amos Bairoch. A. . Bateman . Alex Bateman. D.. Binns . P.. Bork . Peer Bork. U. . Das. Daugherty . L.. Duquenne . L.. Finn . R. D.. Gough . J. . Julian Gough (scientist). Haft . D.. Hulo . N.. Kahn . D.. Kelly . E.. Laugraud . A.. Letunic . I.. Lonsdale . D.. Lopez . R.. Madera . M.. Maslen . J.. McAnulla . C.. McDowall . J.. Mistry . J.. Mitchell . A.. Mulder . N.. Natale . D.. Orengo . C.. Quinn . A. F.. InterPro: the integrative protein signature database. Nucleic Acids Research. 37. Database issue. D211–D215. January 2009 . 0305-1048. 18940856. 2686546. 10.1093/nar/gkn785.
  16. 15608177. 540060. 2005. Mulder. N. J.. InterPro, progress and status in 2005. Nucleic Acids Research. 33. Database issue. D201–5. Apweiler . R . Rolf Apweiler. Attwood . T. K. . Terri Attwood. Bairoch . A . Amos Bairoch. Bateman . A . Alex Bateman. Binns. D. Bradley. P. Bork . P . Peer Bork. Bucher. P. Cerutti. L. Copley. R. Courcelle. E. Das. U. Durbin . R . Richard M. Durbin. Fleischmann. W. Gough . J . Julian Gough (scientist). Haft. D. Harte. N. Hulo. N. Kahn. D. Kanapin. A. Krestyaninova. M. Lonsdale. D. Lopez. R. Letunic. I. Madera. M. Maslen. J. McDowall. J. Mitchell. A. Nikolskaya. A. N.. 29. 10.1093/nar/gki106.
  17. 16061809. 1183549. 2005. Vinogradov. S. N.. Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life. Proceedings of the National Academy of Sciences. 102. 32. 11385–9. Hoogewijs. D. Bailly. X. Arredondo-Peter. R. Guertin. M. Gough. J. Dewilde. S. Moens. L. Vanfleteren. J. R.. 10.1073/pnas.0502103102. 2005PNAS..10211385V. free.
  18. 14528000. 218709. 2003. Gherardi. E. Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor. Proceedings of the National Academy of Sciences. 100. 21. 12039–44. Youles. M. E.. Miguel. R. N.. Blundell. T. L.. Iamele. L. Gough. J. Bandyopadhyay. A. Hartmann. G. Butler. P. J.. 10.1073/pnas.2034936100. 2003PNAS..10012039G. free.
  19. 19272021. 2009. Chothia. C. Genomic and structural aspects of protein evolution. Biochemical Journal. 419. 1. 15–28. Gough. J. 10.1042/BJ20090122.
  20. 11428892. 2001. Apic. G. Domain combinations in archaeal, eubacterial and eukaryotic proteomes. Journal of Molecular Biology. 310. 2. 311–25. Gough . J . Julian Gough (scientist). Teichmann . S. A. . Sarah Teichmann. 10.1006/jmbi.2001.4776.
  21. Gough . J. . Karplus . K. . Hughey . R. . Chothia . C. . Cyrus Chothia. Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure1 . 10.1006/jmbi.2001.5080 . Journal of Molecular Biology . 313 . 4 . 903–919 . 2001 . 11697912 . 10.1.1.144.6577 .
  22. 11518524. 2001. Teichmann. S. A.. Sarah Teichmann. The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli. Journal of Molecular Biology. 311. 4. 693–708. Rison. S. C.. Thornton. J. M.. Janet Thornton. Riley. M. Gough. J. Julian Gough (scientist). Chothia. C. Cyrus Chothia. 10.1006/jmbi.2001.4912. 10.1.1.121.1628.
  23. 12819153. 403710. 2003. Kasukawa. T. Development and evaluation of an automated annotation pipeline and cDNA annotation system. Genome Research. 13. 6B. 1542–51. Furuno. M. Nikaido. I. Bono. H. Hume. D. A.. Bult. C. Hill. D. P.. Baldarelli. R. Gough . J . Julian Gough (scientist). Kanapin. A. Matsuda. H. Schriml. L. M.. Hayashizaki. Y. Okazaki. Y. Quackenbush. J . John Quackenbush. 10.1101/gr.992803.
  24. 23620363. 3673218. 2013. Shihab. H. A.. Predicting the functional consequences of cancer-associated amino acid substitutions. Bioinformatics. 29. 12. 1504–10. Gough. J. Cooper. D. N.. Day. I. N.. Gaunt. T. R.. 10.1093/bioinformatics/btt182.
  25. Liu . J. . Gough . J. . Julian Gough (scientist). Rost . B. . Burkhard Rost. 10.1371/journal.pgen.0020029 . Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines . PLOS Genetics . 2 . 4 . e29 . 2006 . 16683024 . 1449884 . free .
  26. 19377474. 2009. Fantom. Consortium. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics. 41. 5. 553–62. Suzuki. H. Forrest. A. R.. Van Nimwegen. E. Daub. C. O.. Balwierz. P. J.. Irvine. K. M.. Lassmann. T. Ravasi. T. Hasegawa. Y. De Hoon. M. J.. Katayama. S. Schroder. K. Carninci. P. Tomaru. Y. Kanamori-Katayama. M. Kubosaki. A. Akalin. A. Ando. Y. Arner. E. Asada. M. Asahara. H. Bailey. T. Bajic. V. B.. Bauer. D. Beckhouse. A. G.. Bertin. N. Björkegren. J. Brombacher. F. Bulger. E. 29. 10.1038/ng.375. 6711855.
  27. 16585737. 1446993. 2006. Babu. M. M.. A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. Journal of Bacteriology. 188. 8. 2761–73. Priya. M. L.. Selvan. A. T.. Madera. M. Gough. J. Aravind. L. Sankaran. K. 10.1128/JB.188.8.2761-2773.2006.
  28. Web site: https://web.archive.org/web/20150315124310/http://gtr.rcuk.ac.uk/person/458D8209-A829-4661-82E7-EEDF95783CE2. UK Government Grants awarded Julian Gough. Research Councils UK. 15 March 2015.
  29. Web site: https://web.archive.org/web/20150311112906/http://bioinformatics.bris.ac.uk/people/julian_gough.html. Computational Genomics Group: Professor Julian Gough. University of Bristol. 11 March 2015.

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