Julian Gough (scientist)

Last updated

Julian Gough
Born
Julian John Thurstan Gough [1]

September 1974 (age 49) [2]
Education The Perse School
Alma mater
Known for Superfamily database
Scientific career
Fields
Institutions
Thesis Hidden Markov models and their application to the genome analysis in the context of protein structure  (2001)
Doctoral advisor Cyrus Chothia [5] [6]
Website www2.mrc-lmb.cam.ac.uk/group-leaders/a-to-g/julian-gough/

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[ when? ] a professor of bioinformatics at the University of Bristol. [9]

Contents

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]

Related Research Articles

The Protein Information Resource (PIR), located at Georgetown University Medical Center, is an integrated public bioinformatics resource to support genomic and proteomic research, and scientific studies. It contains protein sequences databases

<span class="mw-page-title-main">Pfam</span> Database of protein families

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<span class="mw-page-title-main">Amos Bairoch</span>

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<span class="mw-page-title-main">MicrobesOnline</span>

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<span class="mw-page-title-main">SOX6</span> Protein-coding gene in the species Homo sapiens

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<span class="mw-page-title-main">SPRTN</span> Protein-coding gene in the species Homo sapiens

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SUPERFAMILY is a database and search platform of structural and functional annotation for all proteins and genomes. It classifies amino acid sequences into known structural domains, especially into SCOP superfamilies. Domains are functional, structural, and evolutionary units that form proteins. Domains of common Ancestry are grouped into superfamilies. The domains and domain superfamilies are defined and described in SCOP. Superfamilies are groups of proteins which have structural evidence to support a common evolutionary ancestor but may not have detectable sequence homology.

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<span class="mw-page-title-main">Cyrus Chothia</span> English biochemist (1942–2019)

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<span class="mw-page-title-main">Sarah Teichmann</span> German bioinformatician

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References

  1. ↑ "University Library thesis catalog: Julian John Thurstan Gough". University of Cambridge. Archived from the original on 16 March 2015.
  2. 1 2 3 4 "Julian GOUGH". London: Companies House, Government of the United Kingdom. Archived from the original on 18 July 2016.
  3. 1 2 3 Julian Gough publications indexed by Google Scholar OOjs UI icon edit-ltr-progressive.svg
  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. 1 2 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 OOjs UI icon edit-ltr-progressive.svg
  8. ↑ Julian Gough's publications indexed by the Scopus bibliographic database. (subscription required)
  9. 1 2 3 4 "Computational Genomics Group: Professor Julian Gough". University of Bristol. Archived from the original on 11 March 2015.
  10. 1 2 3 "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. Bibcode:2014Natur.507..462T. 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. Bibcode:2002Natur.420..563O. doi: 10.1038/nature01266 . hdl: 10161/11223 . PMID   12466851.
  15. ↑ Chothia, C; Gough, J; Vogel, C; Teichmann, S. A. (2003). "Evolution of the protein repertoire". Science. 300 (5626): 1701–3. Bibcode:2003Sci...300.1701C. doi:10.1126/science.1085371. PMID   12805536. S2CID   27681885.
  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. Bibcode:2005Sci...309.1559F. doi:10.1126/science.1112014. PMID   16141072. S2CID   8712839.
  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. Open Access logo PLoS transparent.svg
  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. Open Access logo PLoS transparent.svg
  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. Open Access logo PLoS transparent.svg
  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. Open Access logo PLoS transparent.svg
  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. Bibcode:2005PNAS..10211385V. 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. Bibcode:2003PNAS..10012039G. 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. Open Access logo PLoS transparent.svg
  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.
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