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] was 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

<span class="mw-page-title-main">Sequence homology</span> Shared ancestry between DNA, RNA or protein sequences

Sequence homology is the biological homology between DNA, RNA, or protein sequences, defined in terms of shared ancestry in the evolutionary history of life. Two segments of DNA can have shared ancestry because of three phenomena: either a speciation event (orthologs), or a duplication event (paralogs), or else a horizontal gene transfer event (xenologs).

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

Pfam is a database of protein families that includes their annotations and multiple sequence alignments generated using hidden Markov models. Last version of Pfam, 36.0, was released in September 2023 and contains 20,795 families. It is currently provided through InterPro database.

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

Amos Bairoch is a Swiss bioinformatician and Professor of Bioinformatics at the Department of Human Protein Sciences of the University of Geneva where he leads the CALIPHO group at the Swiss Institute of Bioinformatics (SIB) combining bioinformatics, curation, and experimental efforts to functionally characterize human proteins.

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

MicrobesOnline is a publicly and freely accessible website that hosts multiple comparative genomic tools for comparing microbial species at the genomic, transcriptomic and functional levels. MicrobesOnline was developed by the Virtual Institute for Microbial Stress and Survival, which is based at the Lawrence Berkeley National Laboratory in Berkeley, California. The site was launched in 2005, with regular updates until 2011.

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

Transcription factor SOX-6 is a protein that in humans is encoded by the SOX6 gene.

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

Spartan (SPRTN) is a protein that in humans is encoded by the SPRTN gene. It is involved in DNA repair. Ruijs-Aalfs syndrome is an autosomal recessive genetic disorder. Characteristics of this disorder are features of premature aging, chromosome instability and development of hepatocellular carcinoma. Ruijs-Aalfs syndrome arises as a result of mutations in the SPRTN gene that encodes a metalloproteinase employed in the repair of protein-linked DNA breaks.

<span class="mw-page-title-main">MEX3B</span> Protein-coding gene in the species Homo sapiens

RNA-binding protein MEX3B is a protein that in humans is encoded by the MEX3B gene.

<span class="mw-page-title-main">CNOT1</span> Protein-coding gene in the species Homo sapiens

CCR4-NOT transcription complex subunit 1 is a protein that in humans is encoded by the CNOT1 gene.

<span class="mw-page-title-main">ANKRD13C</span> Protein-coding gene in the species Homo sapiens

Ankyrin repeat domain-containing protein 13C is a protein that in humans is encoded by the ANKRD13C gene.

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.

<span class="mw-page-title-main">Richard M. Durbin</span> British computational biologist

Richard Michael Durbin is a British computational biologist and Al-Kindi Professor of Genetics at the University of Cambridge. He also serves as an associate faculty member at the Wellcome Sanger Institute where he was previously a senior group leader.

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

Cyrus Homi Chothia was an English biochemist who was an emeritus scientist at the Medical Research Council (MRC) Laboratory of Molecular Biology (LMB) at the University of Cambridge and emeritus fellow of Wolfson College, Cambridge.

<span class="mw-page-title-main">Rolf Apweiler</span> German bioinformatician

Rolf Apweiler is a director of European Bioinformatics Institute (EBI) part of the European Molecular Biology Laboratory (EMBL) with Ewan Birney.

Gerard Jacob Kleywegt is a Dutch X-ray crystallographer and the former team leader of the Protein Data Bank in Europe at the EBI; a member of the Worldwide Protein Data Bank.

dcGO is a comprehensive ontology database for protein domains. As an ontology resource, dcGO integrates Open Biomedical Ontologies from a variety of contexts, ranging from functional information like Gene Ontology to others on enzymes and pathways, from phenotype information across major model organisms to information about human diseases and drugs. As a protein domain resource, dcGO includes annotations to both the individual domains and supra-domains.

<span class="mw-page-title-main">Tim Hubbard</span> Professor of Bioinformatics at Kings College London

Timothy John Phillip Hubbard is a Professor of Bioinformatics at King's College London, Head of Genome Analysis at Genomics England and Honorary Faculty at the Wellcome Trust Sanger Institute in Cambridge, UK. From 1 March 2024, Hubbard became the director of Europe's Life Science Data Infrastructure ELIXIR.

Michael Joseph Ezra Sternberg is a professor at Imperial College London, where he is director of the Centre for Integrative Systems Biology and Bioinformatics and Head of the Structural bioinformatics Group.

Model organism databases (MODs) are biological databases, or knowledgebases, dedicated to the provision of in-depth biological data for intensively studied model organisms. MODs allow researchers to easily find background information on large sets of genes, plan experiments efficiently, combine their data with existing knowledge, and construct novel hypotheses. They allow users to analyse results and interpret datasets, and the data they generate are increasingly used to describe less well studied species. Where possible, MODs share common approaches to collect and represent biological information. For example, all MODs use the Gene Ontology (GO) to describe functions, processes and cellular locations of specific gene products. Projects also exist to enable software sharing for curation, visualization and querying between different MODs. Organismal diversity and varying user requirements however mean that MODs are often required to customize capture, display, and provision of data.

References

  1. "University Library thesis catalog: Julian John Thurstan Gough". University of Cambridge. Archived from the original on 15 April 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.