Publications

Departmental publications database

Citations for Prof. Julian Gough can also be accessed via the departmental publications database, however some long author lists are incomplete.

Also in Google scholar.

PDF files

Oates, M.E., Romero, P., Takashi, I., Ghalwash, M., Mizianty, M.J., Xue, B., Dosztanyi, Z., Uversky, V.N., Obradovic, Z., Kurgan, L., Dunker, A.K. and Gough, J. (2012) D²P²: Database of Disordered Protein Predictions. Nucl. Acids Res. in press.
Fang, H. and Gough, J. (2012) dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucl. Acids Res. in press.
Pethica, R.B. and Gough, J. (2012) Evolutionarily Consistent Families in SCOP: Sequence, Structure and Function. BMC Struct. Biol. in press.
Shihab, H.A., Gough, J., Cooper, D.N., Barker, G.L.A., Edwards, K.J., Day, I.N.M., Gaunt, T. (2012) Predicting the conseuqences of amino acid substitutions: A Functional Analysis Through Hidden Markov Models (FATHMM). Human mutation in press. PDF
Chavali, S., de Lima Morais, D., Gough, J. and Babu, M. (2011) Evolution of eukaryotic genome architecture: insights from the study of a rapidly evolving metazoan, Oikopleura dioica. Bioessays 33(8), 592-601. PDF
Dunker, A.K., and Gough, J. (2011) Intrinsic disorder in the evolving universe of protein structure. Curr Opin Struct Biol, 21(3), 379-81. PDF
Abroi, A. and Gough, J. (2011) Are viruses a source of new protein folds for organisms? - Virosphere structure space and evolution. Bioessays 33(8), 626-635. PDF
de Lima Morais, D., Fang, H., Rackham, O.J.L., Wilson, D., Pethica, R., Chothia, C. and Gough, J. (2011) SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucl Acids Res. 39, D427-D434. PDF
Hunter et al. (2011) InterPro in 2011: new developments in the family and domain prediction database. Nucl Acids Res. 40, D306-D312. PDF
Fang, H. and Gough, J. (2010) The evolutionary dynamics of protein networks. Genome Biology 11(Suppl 1), 12. PDF
Rackham, O., Madera, M., Armstrong, C.T., Vincent, T.L., Wolfson, D.N. and Gough, J. (2010) The Evolution and Structure Prediction of Coiled Coils across All Genomes. J. mol. biol. 403(3), 480-493. PDF
Ravasi, T. et al. (2010) An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man. Cell 140(5), 744-752. PDF
Madera, M., Calmus, R., Thiltgen, G. Karplus, K. and Gough, J. (2010) Improving protein secondary structure prediction using a simple k-mer model. Bioinformatics 26(5), 596-602. PDF
Pethica, R., Barker, G., Kovacs, T. and Gough, J. (2010) TreeVector: Scalable, Interactive, Phylogenetic Trees for the Web. PLoS ONE 5(1), e8934. PDF
Chothia, C. and Gough, J. (2009) in "BJ Darwin Reviews: Evolution and Biochemistry" Portland press ISBN 9781855781740.
Suzuki, H. et al. (2009) The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat. Genet. doi:10.1038/ng.375. PDF
Chothia, C. and Gough, J. (2009) Genomic and Structural Aspects of Protein Evolution. Biochem. J. 419(1), 15-28. PDF
Wilson, D., Pethica, R., Zhou, Y., Talbot, C., Vogel, C., Madera, M., Chothia, C. and Gough, J. (2009) SUPERFAMILY-sophisticated comparative genomics, data mining, visualization and phylogeny. Nucl. Acids Res. 37, D380-D386. PDF
Hunter, S., Apweiler, R., Attwood, T.K., 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., McDowell, J., Mistry, J., Mitchell, A., Mulder, N., Natale, D., Orengo, C., Quinn, A.F., Selengut, J.D., Sigrist, C.J.A., Thimma, M., Thomas, P.D., Valentin, F., Wilson, D., Wu, C.H. and Yeats, C. (2009). InterPro: the integrative protein signature database. Nucl. Acids Res. 37, D211-D215. PDF
Zeng, L., Park, C.H., Venu, R.C., Gough, J. and Wang, G. (2008). Classification, Expression Pattern, and E3 Ligase Activity Assay of Rice U-Box-Containing Proteins. Mol. Plant 1(5), 800-15. PDF
Garrocho-Villegas, V., Bustos-Rivera, G., Gough, J., Vinogradov, S.N., and Arredondo-Peter, R. (2008) Expression and in silico structural analysis of a rice (Oryza sativa) hemoglobin 5. Plant Physiol. Biochem. xx, 1-5. PDF
Mulder N.J. et al. (2007) New developments in the InterPro database. Nucl. Acids Res. 35, D224-28. PDF
Wilson, D., Madera, M., Vogel, C., Chothia, C., Gough, J. (2007) The SUPERFAMILY database in 2007: families and functions. Nucl. Acids Res. 35, D308-13. PDF
Gough, J. (2006) Genomic scale sub-family assignment of protein domains. Nucl. Acids Res. 34(13) 3625-3633. PDF
Vinogradov, S.N., Hoogewijs, D., Bailly, X., Arredondo-Peter, R., Gough, J., Dewilde, S., Moens, L. and Vanfleteren, J.R. (2006). A phylogenomic profile of globins. BMC Evol Biol. 6,31. PDF
Liu, J., Gough, J., Rost, B. (2006). Distinguishing Protein-Coding from Non_coding RNAs through Support Vector Machines. PLoS Genetics 2(4), e29. PDF
Maeda, N., Kasukawa, T., Oyama, R., Gough, J., et al. (2006). Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs. PLoS Genetics 2(4), e62. PDF
Lee, L.J., Hughes, T.R. and Frey B.J. (2006) How many genes are there? Science 311(5768), author reply 1709-11. PDF
Babu, M. M., Priya, M. L., Selvan, A. T., Madera, M., Gough, J. and Sankaran, K. (2006). A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. J Bacteriol. 188(8), 2761-73. PDF
Carninci, P., Kasukawa, T., Katayama, S., Gough, J., et al. (2005). The Transcriptional Landscape of the Mammalian Genome. Science 309(5740), 1559-63. PDF
Vinogradov, S.N., Hoogewijs, D., Bailly, X., Arrendondo-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. Proc Natl Acad Sci USA 102(32), 11385-9. PDF
Gough, J. (2005). Convergent evolution of domain architectures (is rare). Bioinformatics 21(8), 1464-71. PDF
Mulder, N.J. et al. (2005) InterPro, progress and status in 2005. Nucl. Acids Res. 33, D201-5. PDF
Gough, J. (2004). Hidden Markov models: principles and applications. In Computational Genomics (Grant, R. ed.). Horizon scientific press. PDF
Gough, J. and Chothia, C. (2004). The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins. Structure 12, 917-25. PDF
Vogel, C., Berzuini, C., Bashton, M., Gough, J. and Teichmann, S.A. (2004) Supra-domains: Evolutionary units larger than single protein domains. J. Mol. Biol. 336, 809-823. PDF
Madera, M., Vogel, C., Kummerfeld, S.K., Chothia, C. and Gough, J. The SUPERFAMILY database in 2004: additions and improvements. Nucl. Acids Res. 32(1), D235-9. PDF
Gherardi, E., Youles, M.E., Miguel, R.N., Blundell, T.L., Iamele, L., Gough, J., Bandyopadhyay, A., Hartmann, G. and Butler, P.J. Functional map and domain structure of MET, the product of the c-met protooncogene and receptor for hepatocyte growth factor/scatter factor. Proc. Natl. Acad. Sci. U.S.A. 2003 100(21): 12039. PDF
Kanapin, A., Batalov, S., Davis, M.J., Gough, J., Grimmond, S., Kawaji, H., Magrane, M., Matsuda, H., Schonbach, C., Teasdale, R.D., and Yuan, Z. (2003) Mouse Proteome Analysis. Genome Res. 13, 1335-44. PDF
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., and Quackenbush, J.. Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System. Genome Res. 2003 13: 1542-1551. PDF
Chothia, C., Gough, J., Vogel, C., Teichmann, S.A. (2003) Evolution of the protein repertoire. Science. 300(5626), 1701-1703. PDF
Okazaki, Y. et al. (2002). Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature 420(6915), 563-73. PDF
Gough, J. (2002). The SUPERFAMILY database in structural genomics. Acta Crystalographica D, 2002 Nov; D58:1897-1900. PDF
Madera, M. and Gough, J.(2002). A comparison of hidden Markov model procedures for remote homology detection. Nucl. Acids Res. 30(19), 4321-8. PDF
Hua, S.J., Guo, T., Gough, J. and Sun, Z.R. (2002) Proteins with alpha/beta Fold Class Have High Participation in Fusion Events. J. Mol. Biol. 320(4), 713-9. PDF
Jardine, O., Gough, J., Chothia, C., and Teichmann, T. (2001). Comparison of the Small Molecule Metabolic Pathways of Escherichia coli and Saccharomyces cerevisiae. Genome Res. 12(6), 916-29. PDF
Gough, J., Chothia, C.(2002). SUPERFAMILY:HMMs representing all proteins of known structure. SCOP sequence searches, alignments, and genome assignments. Nucl. Acids Res. 30(1), 268-72. PDF
Gough, J., Hughey ,R., Karplus ,K., and Chothia ,C.(2001). Assignment of genome sequences using a library of hidden Markov models that represent all proteins of known structure. J Mol Biol. 313(4), 903-19. PDF
Teichmann, S.A., Rison, S.C.G., Thornton, J.M., Riley, M., Gough, J. and Chothia, C. (2001) Small Molecule Metabolism: An Enzyme Mosaic. Trends Biotechnol. 19(12), 482-6. PDF
Gough, J. (2001). Hidden Markov models and their application to genome analysis in the context of protein structure. PhD thesis, 2001 Nov; Cambridge University. PDF
Teichmann, S.A., Rison, S.C.G., Thornton, J.M., Riley, M., Gough, J. and Chothia, C. (2001) The Evolution and Structural Anatomy of the Small Molecule Metabolic Pathways in Escherichia coli. J. Mol. Biol. 311(4), 693-708. PDF
Apic, G., Gough, J., and Teichmann, S.A.(2001). Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol. 310(2) 311-25. PDF
Apic, G., Gough, J., and Teichmann, S.A.(2001). An insight into domain combinations. Bioinformatics Suppl 1 83-89. PDF
Gough, J.,Chothia, C.,Karplus, K.,Barrett, C.,and Hughey, R.(2000).Optimal hidden Markov models for all sequences of known structure. In Currents in Computational Molecular Biology(Miyano S.,Shamir R., and Takagi T., eds), Universal Academy Press INC. 124-125. PDF