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Julian Gough
Born
Julian John Thurstan Gough [6]

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 [4] [5]
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). [1] [7] [8] He was previously[ when?] a professor of bioinformatics at the University of Bristol. [9]

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. [5]

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 [1] 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]

References

  1. ^ a b c Julian Gough publications indexed by Google Scholar Edit this at Wikidata
  2. ^ a b c d "Julian GOUGH". London: Companies House, Government of the United Kingdom. Archived from the original on 18 July 2016.
  3. ^ "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.
  4. ^ Julian Gough at the Mathematics Genealogy Project
  5. ^ a b 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.
  6. ^ "University Library thesis catalog: Julian John Thurstan Gough". University of Cambridge. Archived from the original on 15 April 2015.
  7. ^ Julian Gough at DBLP Bibliography Server Edit this at Wikidata
  8. ^ Julian Gough's publications indexed by the Scopus bibliographic database. (subscription required)
  9. ^ a b c d "Computational Genomics Group: Professor Julian Gough". University of Bristol. Archived from the original on 11 March 2015.
  10. ^ a b c "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 icon
  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 icon
  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 icon
  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 icon
  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 icon
  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.
Retrieved from " https://en.wikipedia.org/?title=Julian_Gough_(scientist)&oldid=1223263194"
From Wikipedia, the free encyclopedia

Julian Gough
Born
Julian John Thurstan Gough [6]

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 [4] [5]
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). [1] [7] [8] He was previously[ when?] a professor of bioinformatics at the University of Bristol. [9]

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. [5]

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 [1] 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]

References

  1. ^ a b c Julian Gough publications indexed by Google Scholar Edit this at Wikidata
  2. ^ a b c d "Julian GOUGH". London: Companies House, Government of the United Kingdom. Archived from the original on 18 July 2016.
  3. ^ "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.
  4. ^ Julian Gough at the Mathematics Genealogy Project
  5. ^ a b 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.
  6. ^ "University Library thesis catalog: Julian John Thurstan Gough". University of Cambridge. Archived from the original on 15 April 2015.
  7. ^ Julian Gough at DBLP Bibliography Server Edit this at Wikidata
  8. ^ Julian Gough's publications indexed by the Scopus bibliographic database. (subscription required)
  9. ^ a b c d "Computational Genomics Group: Professor Julian Gough". University of Bristol. Archived from the original on 11 March 2015.
  10. ^ a b c "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 icon
  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 icon
  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 icon
  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 icon
  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 icon
  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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