Julian Gough (scientist)

For the irish novelist, see Julian Gough.
Julian Gough
Born Julian John Thurstan Gough[1]
Fields
Institutions
Alma mater
Thesis Hidden Markov models and their application to the genome analysis in the context of protein structure (2001)
Doctoral advisor Cyrus Chothia[4][5]
Doctoral students
Other notable students
Known for SUPERFAMILY[15]
Website
bioinformatics.bris.ac.uk/people/julian_gough.html

Julian John Thurstan Gough is a Professor of Bioinformatics in the Department of Computer Science at the University of Bristol, UK.[2][16][17][18]

Education

Gough was educated at The Perse School[19] in Cambridge and the University of Bristol where he was awarded a joint honours degree in Mathematics and Physics in 1998.[16][19] He went on to complete his PhD in the Laboratory of Molecular Biology (LMB) at the University of Cambridge supervised by Cyrus Chothia on genome analysis and protein structure as a postgraduate student of Sidney Sussex College, Cambridge, graduating in 2001.[5]

Career

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 was worked since 2007.[19] He has also been a visiting scientist at the Pasteur Institute in Paris and an Associate Professor at Tokyo Medical and Dental University.[16]

Research

Gough's research interests are in bioinformatics, computational biology, molecular biology, genomics[2] which has led to the creation of the SUPERFAMILY databse[15][20] of Hidden Markov models (HMMs) representing all proteins of known structure. His research has been published in leading peer reviewed scientific journals including Nature,[21][22] Science,[23][24] Cell,[25] Nucleic Acids Research,[26][27][28][29][30] PNAS,[31][32] the Biochemical Journal,[33] the Journal of Molecular Biology,[34][35][36] Genome Research,[37] Bioinformatics,[11] PLOS Genetics,[38]Nature Genetics[39] and the Journal of Bacteriology.[40]

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),[41] the European Union (EU) Seventh Research Framework Programme (FP7), the Japan Society for the Promotion of Science (JSPS) and the Royal Society of London.[16]

References

  1. ↑ "University Library thesis catalog: Julian John Thurstan Gough". University of Cambridge. Archived from the original on 2015-03-06.
  2. ↑ 2.0 2.1 2.2 Julian Gough's publications indexed by Google Scholar, a free service provided by Google
  3. ↑ "Genetrainer (genetically guided fitness) in the running for major technology award". University of Bristol. 2013-06-03. Archived from the original on 2014-11-11.
  4. ↑ 4.0 4.1 4.2 Julian Gough at the Mathematics Genealogy Project
  5. ↑ 5.0 5.1 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. Archived from the original (PDF) on 2015-03-11.
  6. ↑ Pethica, Ralph Brian (2011). Sequences, structures and biological functions of molecular evolution (PhD thesis). University of Bristol. OCLC 784569999.
  7. ↑ 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.
  8. ↑ Rackham, Owen (2012). Understanding and controlling the multi-scale complexity of the cell (PhD thesis). University of Bristol. Archived from the original on 2015-03-16.
  9. ↑ Ali Shihab, Hashem (2013). Predicting the functional effects of genetic variation (PhD thesis). University of Bristol. Archived from the original on 2015-03-19.
  10. ↑ 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.
  11. ↑ 11.0 11.1 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.
  12. ↑ 12.0 12.1 "People in the Computational Genomics group at Bristol". University of Bristol. Archived from the original on 2015-03-19.
  13. ↑ 13.0 13.1 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. PMID 25414345.
  14. ↑ 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.
  15. ↑ 15.0 15.1 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.
  16. ↑ 16.0 16.1 16.2 16.3 "Computational Genomics Group: Professor Julian Gough". University of Bristol. Archived from the original on 2015-03-11.
  17. ↑ Julian Gough's publications indexed by the DBLP Bibliography Server at the University of Trier
  18. ↑ Julian Gough's publications indexed by the Scopus bibliographic database, a service provided by Elsevier.
  19. ↑ 19.0 19.1 19.2 "Julian Gough profile". LinkedIn.
  20. ↑ 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.
  21. ↑ 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. PMID 24670764.
  22. ↑ 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.; Bradt, D. (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.
  23. ↑ 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.
  24. ↑ 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.
  25. ↑ 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.
  26. ↑ 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. PMID 25348407.
  27. ↑ 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.
  28. ↑ 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.
  29. ↑ 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. (Jan 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.
  30. ↑ 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.
  31. ↑ 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.
  32. ↑ 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.
  33. ↑ Chothia, C; Gough, J (2009). "Genomic and structural aspects of protein evolution". Biochemical Journal 419 (1): 15–28. doi:10.1042/BJ20090122. PMID 19272021.
  34. ↑ 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.
  35. ↑ 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. doi:10.1006/jmbi.2001.5080. PMID 11697912.
  36. ↑ 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. doi:10.1006/jmbi.2001.4912. PMID 11518524.
  37. ↑ 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.
  38. ↑ 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.
  39. ↑ 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. PMID 19377474.
  40. ↑ 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.
  41. ↑ "UK Government Grants awarded Julian Gough". Research Councils UK. Archived from the original on 2015-03-15.