Publications - Prof Julian Gough
  • Fang, H. and Gough, J. (2014) The 'dnet' approach promotes emerging research on cancer patient survival. Genome Medicine in press. PDF
  • Burton, B., Britton, G., Fang, H., Verhagen, J., Smithers, B., Sabatos-Peyton, C., Carney, L., Gough, J., Strobel, S., Wraith, D. (2014) Sequential transcriptional changes dictate safe and effective antigen-specific immunotherapy. Nature Comm. DOI:10.1038/ncomms5741.
  • Van der Lee et al. (2014) Classification of Intrinsically Disordered Regions and Proteins. Chem. Reviews 114, 6589-6631. PDF
  • Sardar, A.J., Oates, M.E., Fang, H., Forrest, A.R.R., Kawaji, H., The FANTOM consortium, Gough, J. and Rackham, O. (2014) The Evolution of Human Cells in Terms of Protein Innovation. mol. biol. evol. doi:10.1093/molbev/mst139. PDF
  • Forrest, A.R.R. et al. (2014) A promoter-level mammalian expression atlas, Nature 507, 462-470. PDF
  • Vavoulis, V.V. and Gough, J. (2014) Non-parametric Bayesian modelling of digital gene expression data. J. Comput. Sci. Syst. Biol. 7, 1-9. PDF
  • Fang, H. and Gough, J. (2013) supraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map. Biochem. Biophys. Res. Commun. DOI:10.1016/j.bbrc.2013.11.103. PDF
  • Gough, J., Yeats, C. and Orengo, C. (2013) Structural annotations of genomes with superfamily and Gene3D. In Protein Families (Orengo C and Bateman, A. ed.s) Wiley. PDF
  • Fang, H., Oates, M.E., Pethica, R.B., Greenwood, J.M., Sardar, A.J., Rackham, O.J.L., Donoghue, P.C.J., Stamatakis, A., de Lima Morais, D.A. and Gough, J. (2013) A daily-updated tree of (sequenced) life as a reference for genome research. Scientific Reports, doi:10.1038/srep02015. PDF
  • Gough, J. and Dunker, A.K. (2013) Sequences and Topology: disorder, modularity, and post/pre translation modification. Curr Opin Struct Biol, DOI 10.1016/j.sbi.2013.05.001. PDF
  • Shihab. H.A., Gough, J., Cooper, D.N., Day, I.N.M. and Gaunt, T.R. (2013) Predicting the functional consequences of cancer-associated amino acid substitutions. Bioinformatics 29(12), 1504-10. PDF.
  • Fang, H. and Gough, J. (2013) A disease-drug-phenotype matrix inferred by walking on a functional domain network. Mol. Biosyst. DOI: 10.1039/C3MB25495J. PDF
  • Radivojac et al. (2013) A large-scale evaluation of computational protein function prediction. Nature Methods 10,221-227. PDF
  • Vavoulis, D.V. and Gough, J. (2013) Non-parametric Bayesian modelling of digital gene expression data. preprint arXiv:1301.4144v1. PDF
  • Fang, H. and Gough, J. (2013) A domain-centric solution to functional genomics via dcGO Predictor BMC Bioinformatics 14(Suppl 3), S3-S9. PDF
  • Lewis, T.E., Sillitoe, I., Andreeva, A., Blundell, T.L, Buchan, D.W., Chothia, C., Cuff, A., Dana, J.M., Filippis, I., Gough, J., Hunter, S., Jones, D.T., Kelley, L.A., Kleywegt, G.J., Minneci, F., Mitchell, A., Murzin, A.G., Ochoa-Montano, B., Rackham, O.J., Smith, J., Sternberg, M.J., Velankar, S., Yeats, C., Orengo, C. (2013) Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucl. Acids Res. 41, D499-D507. PDF
  • 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. (2013) D2P2: Database of Disordered Protein Predictions. Nucl. Acids Res. 41, D508-D516. PDF
  • Fang, H. and Gough, J. (2013) dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucl. Acids Res. 41, D536-D544. PDF
  • Pethica, R.B., Levitt, M. and Gough, J. (2012) Evolutionarily Consistent Families in SCOP: Sequence, Structure and Function. BMC Struct. Biol. 27(12) PDF
  • Shihab, H.A., Gough, J., Cooper, D.N., Barker, G.L.A., Edwards, K.J., Day, I.N.M., Gaunt, T. (2012) Predicting the Functional, Molecular, and Phenotypic Consequences of Amino Acid Substitutions using Hidden Markov Models. Human mutation 34(1), 57-65. 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