Julian Gough (scientist)

Julian John Thurstan Gough (born 1974)[2] is a Group Leader in the Laboratory of Molecular Biology (LMB) of the Medical Research Council (MRC).[3][7][8] He was previously a professor of Bioinformatics at the University of Bristol.[9]

For the irish novelist, see Julian Gough.
Julian Gough
Born
Julian John Thurstan Gough[1]

September 1974 (age 45)[2]
EducationThe Perse School
Alma mater
Known forSuperfamily database
Scientific career
Fields
Institutions
ThesisHidden Markov models and their application to the genome analysis in the context of protein structure (2001)
Doctoral advisorCyrus Chothia[5][6]
Websitewww2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/julian-gough/

Education

Gough was educated at The Perse School[10] in Cambridge and the University of Bristol where he was awarded a joint honours degree in Mathematics and Physics in 1998.[9][10] 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.[6]

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.[10] He has also been a visiting scientist at the Pasteur Institute in Paris and an Associate Professor at Tokyo Medical and Dental University.[9]

Gough's research interests are in bioinformatics, computational biology, molecular biology, genomics[3] which has led to the creation of the Superfamily database[11][12] of Hidden Markov models (HMMs) representing all proteins of known structure. His research has been published in leading peer reviewed scientific journals including Nature,[13][14] Science,[15][16] Cell,[17] Nucleic Acids Research,[18][19][20][21][22] PNAS,[23][24] the Biochemical Journal,[25] the Journal of Molecular Biology,[26][27][28] Genome Research,[29] Bioinformatics,[30] PLOS Genetics,[31]Nature Genetics[32] and the Journal of Bacteriology.[33]

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),[34] the European Union (EU) Seventh Research Framework Programme (FP7), the Japan Society for the Promotion of Science (JSPS) and the Royal Society of London.[9]

His former doctoral students and postdocs include Ralph Pethica,[5][35][36] Owen Rackham,[5][37] Hashem Shihab,[38][39][40][41] Matt Oates,[42][43] and Dimitrios Vavoulis.[41][42]

gollark: Oh, minoteaur actually has that (not the threading bit) in its Markdown parsing code.
gollark: Thus, praise ~~Rust~~ ~~Ferris~~ Nim?
gollark: It compiles in reasonable time *and* makes a 600KB binary in debug mode which is much nicer than equivalent Rust.
gollark: I only need something like two routes so a full web framework is overkill.
gollark: ```nimimport optionsimport asyncdispatchimport httpximport tiny_sqliteimport macrosimport karax/[karaxdsl, vdom]import ./dbmacro includeFile(x: string): string = newStrLitNode(readFile(x.strVal))const css = includeFile("./src/style.css")let database = openDatabase("./monitoring.sqlite3")migrate(database)var threadDB {.threadvar.}: Option[DbConn]proc openDB(): DbConn = if isNone threadDB: threadDB = some openDatabase("./monitoring.sqlite3") get threadDBproc mainPage(): string = let vnode = buildHtml(html()): head: style: text css text "Bee deployed" $vnodeproc onRequest(req: Request) {.async.} = if req.httpMethod == some(HttpGet): case req.path.get() of "/": req.send(body=mainPage(), code=Http200, headers="Content-Type: text/html") else: req.send(Http404) else: req.send(Http404)echo "Starting up"run(onRequest, initSettings(Port(7800), "", 0))```This is what I have so far.

References
  1. "University Library thesis catalog: Julian John Thurstan Gough". University of Cambridge. Archived from the original on 16 March 2015.
  2. "Julian GOUGH". London: Companies House, Government of the United Kingdom. Archived from the original on 18 July 2016.
  3. Julian Gough publications indexed by Google Scholar
  4. "Genetrainer (genetically guided fitness) in the running for major technology award". University of Bristol. 3 June 2013. Archived from the original on 11 November 2014.
  5. Julian Gough at the Mathematics Genealogy Project
  6. Gough, Julian (2001). Hidden Markov models and their application to genome analysis in the context of protein structure (PDF) (PhD thesis). University of Cambridge. OCLC 879396947. EThOS 599547. Archived from the original (PDF) on 11 March 2015.
  7. Julian Gough at DBLP Bibliography Server
  8. Julian Gough's publications indexed by the Scopus bibliographic database. (subscription required)
  9. "Computational Genomics Group: Professor Julian Gough". University of Bristol. Archived from the original on 11 March 2015.
  10. "Julian Gough profile". LinkedIn. Archived from the original on 15 April 2015.
  11. Gough, J.; Chothia, C. (2002). "SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments". Nucleic Acids Research. 30 (1): 268–272. doi:10.1093/nar/30.1.268. PMC 99153. PMID 11752312.
  12. De Lima Morais, D. A.; Fang, H.; Rackham, O. J. L.; Wilson, D.; Pethica, R.; Chothia, C.; Gough, J. (2010). "SUPERFAMILY 1.75 including a domain-centric gene ontology method". Nucleic Acids Research. 39 (Database issue): D427–D434. doi:10.1093/nar/gkq1130. PMC 3013712. PMID 21062816.
  13. FANTOM Consortium and the RIKEN PMI and CLST (DGT); 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; et al. (2014). "A promoter-level mammalian expression atlas". Nature. 507 (7493): 462–70. doi:10.1038/nature13182. PMC 4529748. PMID 24670764.
  14. Okazaki, Y.; Furuno, M.; Kasukawa, T.; Adachi, J.; Bono, H.; Kondo, S.; Nikaido, I.; Osato, N.; Saito, R.; Suzuki, H.; Yamanaka, I.; Kiyosawa, H.; Yagi, K.; Tomaru, Y.; Hasegawa, Y.; Nogami, A.; Schönbach, C.; Gojobori, T.; Baldarelli, R.; Hill, D. P.; Bult, C.; Hume, D. A.; Quackenbush, J.; Schriml, L. M.; Kanapin, A.; Matsuda, H.; Batalov, S.; Beisel, K. W.; Blake, J. A.; et al. (2002). "Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs". Nature. 420 (6915): 563–573. doi:10.1038/nature01266. PMID 12466851.
  15. Chothia, C; Gough, J; Vogel, C; Teichmann, S. A. (2003). "Evolution of the protein repertoire". Science. 300 (5626): 1701–3. doi:10.1126/science.1085371. PMID 12805536.
  16. Carninci, P; Kasukawa, T; Katayama, S; Gough, J; Frith, M. C.; Maeda, N; Oyama, R; Ravasi, T; Lenhard, B; Wells, C; Kodzius, R; Shimokawa, K; Bajic, V. B.; Brenner, S. E.; Batalov, S; Forrest, A. R.; Zavolan, M; Davis, M. J.; Wilming, L. G.; Aidinis, V; Allen, J. E.; Ambesi-Impiombato, A; Apweiler, R; Aturaliya, R. N.; Bailey, T. L.; Bansal, M; Baxter, L; Beisel, K. W.; Bersano, T; et al. (2005). "The transcriptional landscape of the mammalian genome". Science. 309 (5740): 1559–63. doi:10.1126/science.1112014. PMID 16141072.
  17. Ravasi, T; 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; Arakawa, T; Ninomiya, N; Murakami, K; Tagami, M; Fukuda, S; Imamura, K; Kai, C; Ishihara, R; Kitazume, Y; Kawai, J; Hume, DA; Ideker, T; Hayashizaki, Y (2010). "An atlas of combinatorial transcriptional regulation in mouse and man". Cell. 140 (5): 744–52. doi:10.1016/j.cell.2010.01.044. PMC 2836267. PMID 20211142.
  18. Lewis, T. E.; Sillitoe, I; Andreeva, A; Blundell, T. L.; Buchan, D. W.; Chothia, C; Cozzetto, D; Dana, J. M.; Filippis, I; Gough, J; Jones, D. T.; Kelley, L. A.; Kleywegt, G. J.; Minneci, F; Mistry, J; Murzin, A. G.; Ochoa-Montaño, B; Oates, M. E.; Punta, M; Rackham, O. J.; Stahlhacke, J; Sternberg, M. J.; Velankar, S; Orengo, C (2015). "Genome3D: Exploiting structure to help users understand their sequences". Nucleic Acids Research. 43 (Database issue): D382–6. doi:10.1093/nar/gku973. PMC 4384030. PMID 25348407.
  19. Mitchell, A; 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; Punta, M; Attwood, T. K.; Sigrist, C. J.; Redaschi, N; Rivoire, C; Xenarios, I; Kahn, D; Guyot, D; Bork, P; Letunic, I; Gough, J; Oates, M; Haft, D; Huang, H; Natale, D. A. (2015). "The InterPro protein families database: The classification resource after 15 years". Nucleic Acids Research. 43 (Database issue): D213–21. doi:10.1093/nar/gku1243. PMC 4383996. PMID 25428371.
  20. Hunter, S.; Jones, P.; Mitchell, A.; Apweiler, R.; Attwood, T. K.; Bateman, A.; Bernard, T.; Binns, D.; Bork, P.; Burge, 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. (2011). "InterPro in 2011: New developments in the family and domain prediction database". Nucleic Acids Research. 40 (Database issue): D306–D312. doi:10.1093/nar/gkr948. PMC 3245097. PMID 22096229.
  21. Hunter, S.; Apweiler, R.; Attwood, T.; Bairoch, A.; Bateman, A.; Binns, D.; Bork, P.; Das, U.; Daugherty, L.; Duquenne, L.; Finn, R. D.; Gough, J.; 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. (January 2009). "InterPro: the integrative protein signature database". Nucleic Acids Research. 37 (Database issue): D211–D215. doi:10.1093/nar/gkn785. ISSN 0305-1048. PMC 2686546. PMID 18940856.
  22. Mulder, N. J.; Apweiler, R; Attwood, T. K.; Bairoch, A; Bateman, A; Binns, D; Bradley, P; Bork, P; Bucher, P; Cerutti, L; Copley, R; Courcelle, E; Das, U; Durbin, R; Fleischmann, W; Gough, J; 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; et al. (2005). "InterPro, progress and status in 2005". Nucleic Acids Research. 33 (Database issue): D201–5. doi:10.1093/nar/gki106. PMC 540060. PMID 15608177.
  23. Vinogradov, S. N.; Hoogewijs, D; Bailly, X; Arredondo-Peter, R; Guertin, M; Gough, J; Dewilde, S; Moens, L; Vanfleteren, J. R. (2005). "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. doi:10.1073/pnas.0502103102. PMC 1183549. PMID 16061809.
  24. Gherardi, E; Youles, M. E.; Miguel, R. N.; Blundell, T. L.; Iamele, L; Gough, J; Bandyopadhyay, A; Hartmann, G; Butler, P. J. (2003). "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. doi:10.1073/pnas.2034936100. PMC 218709. PMID 14528000.
  25. Chothia, C; Gough, J (2009). "Genomic and structural aspects of protein evolution". Biochemical Journal. 419 (1): 15–28. doi:10.1042/BJ20090122. PMID 19272021.
  26. Apic, G; Gough, J; Teichmann, S. A. (2001). "Domain combinations in archaeal, eubacterial and eukaryotic proteomes". Journal of Molecular Biology. 310 (2): 311–25. doi:10.1006/jmbi.2001.4776. PMID 11428892.
  27. Gough, J.; Karplus, K.; Hughey, R.; Chothia, C. (2001). "Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure1". Journal of Molecular Biology. 313 (4): 903–919. CiteSeerX 10.1.1.144.6577. doi:10.1006/jmbi.2001.5080. PMID 11697912.
  28. Teichmann, S. A.; Rison, S. C.; Thornton, J. M.; Riley, M; Gough, J; Chothia, C (2001). "The evolution and structural anatomy of the small molecule metabolic pathways in Escherichia coli". Journal of Molecular Biology. 311 (4): 693–708. CiteSeerX 10.1.1.121.1628. doi:10.1006/jmbi.2001.4912. PMID 11518524.
  29. Kasukawa, T; Furuno, M; Nikaido, I; Bono, H; Hume, D. A.; Bult, C; Hill, D. P.; Baldarelli, R; Gough, J; Kanapin, A; Matsuda, H; Schriml, L. M.; Hayashizaki, Y; Okazaki, Y; Quackenbush, J (2003). "Development and evaluation of an automated annotation pipeline and cDNA annotation system". Genome Research. 13 (6B): 1542–51. doi:10.1101/gr.992803. PMC 403710. PMID 12819153.
  30. Shihab, H. A.; Gough, J; Cooper, D. N.; Day, I. N.; Gaunt, T. R. (2013). "Predicting the functional consequences of cancer-associated amino acid substitutions". Bioinformatics. 29 (12): 1504–10. doi:10.1093/bioinformatics/btt182. PMC 3673218. PMID 23620363.
  31. Liu, J.; Gough, J.; Rost, B. (2006). "Distinguishing Protein-Coding from Non-Coding RNAs through Support Vector Machines". PLoS Genetics. 2 (4): e29. doi:10.1371/journal.pgen.0020029. PMC 1449884. PMID 16683024.
  32. Fantom, Consortium; 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; et al. (2009). "The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line". Nature Genetics. 41 (5): 553–62. doi:10.1038/ng.375. PMC 6711855. PMID 19377474.
  33. Babu, M. M.; Priya, M. L.; Selvan, A. T.; Madera, M; Gough, J; Aravind, L; Sankaran, K (2006). "A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins". Journal of Bacteriology. 188 (8): 2761–73. doi:10.1128/JB.188.8.2761-2773.2006. PMC 1446993. PMID 16585737.
  34. "UK Government Grants awarded Julian Gough". Research Councils UK. Archived from the original on 15 March 2015.
  35. Pethica, Ralph Brian (2011). Sequences, structures and biological functions of molecular evolution (PhD thesis). University of Bristol. OCLC 784569999.
  36. Pethica, R. B.; Levitt, M.; Gough, J. (2012). "Evolutionarily consistent families in SCOP: Sequence, structure and function". BMC Structural Biology. 12: 27. doi:10.1186/1472-6807-12-27. PMC 3495643. PMID 23078280.
  37. Rackham, Owen John Llewellyn (2012). Understanding and controlling the multi-scale complexity of the cell (PhD thesis). University of Bristol. Archived from the original on 16 March 2015.
  38. Ali Shihab, Hashem (2013). Predicting the functional effects of genetic variation (PhD thesis). University of Bristol. Archived from the original on 19 March 2015.
  39. Shihab, H. A.; Gough, J; Mort, M; Cooper, D. N.; Day, I. N.; Gaunt, T. R. (2014). "Ranking non-synonymous single nucleotide polymorphisms based on disease concepts". Human Genomics. 8: 11. doi:10.1186/1479-7364-8-11. PMC 4083756. PMID 24980617.
  40. Shihab, H. A.; Gough, J; Cooper, D. N.; Day, I. N.; Gaunt, T. R. (2013). "Predicting the functional consequences of cancer-associated amino acid substitutions". Bioinformatics. 29 (12): 1504–10. doi:10.1093/bioinformatics/btt182. PMC 3673218. PMID 23620363.
  41. "People in the Computational Genomics group at Bristol". University of Bristol. Archived from the original on 19 March 2015.
  42. Oates, M. E.; Stahlhacke, J; Vavoulis, D. V.; Smithers, B; Rackham, O. J.; Sardar, A. J.; Zaucha, J; Thurlby, N; Fang, H; Gough, J (2015). "The SUPERFAMILY 1.75 database in 2014: A doubling of data". Nucleic Acids Research. 43 (Database issue): D227–33. doi:10.1093/nar/gku1041. PMC 4383889. PMID 25414345.
  43. Oates, M. E.; Romero, P; Ishida, T; Ghalwash, M; Mizianty, M. J.; Xue, B; Dosztányi, Z; Uversky, V. N.; Obradovic, Z; Kurgan, L; Dunker, A. K.; Gough, J (2013). "D²P²: Database of disordered protein predictions". Nucleic Acids Research. 41 (Database issue): D508–16. doi:10.1093/nar/gks1226. PMC 3531159. PMID 23203878.
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