Publications on Bioinformatics

2013

Hai Fang, Julian Gough, A disease-drug-phenotype matrix inferred by walking on a functional domain network. Molecular BIosystems, . ISSN 1742-206X. March 2013. No electronic version available.
Predrag Radivojac, Burkhard Rost, Sean D Mooney, Iddo Friedberg, et al., Wyatt T Clark, Tal Ronnen Oron, Alexandra M Schnoes, Tobias Wittkop, Hai Fang, Julian Gough, Steven E Brenner, Christine Orengo, A large-scale evaluation of computational protein function prediction.. Nature Methods, . ISSN 1548-7091. February 2013. No electronic version available.
Hai Fang, Julian Gough, A domain-centric solution to functional genomics via dcGO Predictor. BMC Bioinformatics, 14(Suppl 3). ISSN 1471-2105, pp. S3–S9. February 2013. No electronic version available.

2012

Matthew Oates, Lukasz Kurgan, A. Keith Dunker, Julian Gough, Pedro Romero, Ishida Takashi, M. Ghalwash, M.J. Mizianty, Bin Xue, B. Dosztanyi, V.N. Uversky, Zoran Obradovic, D2P2: Database of Disordered Protein Predictions. Nucleic Acids Research, . December 2012. No electronic version available.
Lewis, T.E., Julian Gough, Hunter, S., Jones, D.T., Kelley, L.A., Kleywegt, G.J., Minneci, F., Mitchell, A., Murzin, A.G., Ochoa-Montano, B., Owen Rackham, Sillitoe, I., Smith, J., Sternberg, M.J.E., Velankar, S., Yeats, C., Orengo, C., Andreeva, A., Blundell, T.L., Buchan, T.L., Chothia, C., Cuff, A., Dana, J. M., Filippis, I., Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Research, . ISSN 1362-4962. November 2012. No electronic version available.
Hai Fang, Julian Gough, dcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Research, . October 2012. No electronic version available.
Pethica, R.B., Julian Gough, Evolutionarily Consistent Families in SCOP: Sequence, Structure and Function.. BMC Struct. Biol., . October 2012. No electronic version available.
Shihab, H.A., Julian Gough, Cooper, D.N., Cooper, D.N., Edwards, K.J., Day, I.N.M., Gaunt, T., Predicting the conseuqences of amino acid substitutions: A Functional Analysis Through Hidden Markov Models (FATHMM).. Human mutation, . October 2012. No electronic version available.
Daniel Berrar, Peter Flach, Caveats and pitfalls of ROC analysis in clinical microarray research (and how to avoid them). Briefings in Bioinformatics, 13(1). ISSN 1467-5463, pp. 83–97. January 2012. PDF, 419 Kbytes. External information

2011

Chavali, S., de Lima Morais, D., Julian Gough, Babu, M., Evolution of eukaryotic genome architecture: insights from the study of a rapidly evolving metazoan, Oikopleura dioica.. Bioessays, 33(8). ISSN 1521-1878, pp. 592–601. December 2011. No electronic version available.
Oliver Ray, Takehide Soh, Katsumi Inoue, Analysing Pathways using ASP-Based approaches. Proceedings 2010 Conference on Algebraic and Numeric Biology, pp. 167–183. October 2011. PDF, 279 Kbytes.
Ken Whelan, Oliver Ray, Ross King, Representation, Simulation and Hypothesis Generation in Graph and Logical Models of Biological Networks. Chapter in Yeast Systems Biology. Methods and Protocols, Methods in Molecular Biology, pp. 465–482. July 2011. No electronic version available.
Adam J. Schwarz, John McGonigle, Beyond thresholding: fully-weighted graph representations of brain functional connectivity. ISMRM 19th Annual Meeting & Exhibition. May 2011. No electronic version available.
Aare Abroi, Julian Gough, Are viruses a source of new protein folds for organisms? - Virosphere structure space and evolution. Bioessays, . ISSN 1521-1878. April 2011. No electronic version available.
A Keith Dunker, Julian Gough, Intrinsic disorder in the evolving universe of protein structure. Current Opinion in Structural Biology, . ISSN 0959-440X. April 2011. No electronic version available.
Hunter, S., Jones, P., Julian Gough, Yeats, C., Yong, S.W., InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research, 40. ISSN 1362-4962, pp. D306–D312. January 2011. No electronic version available.
David de Lima Morais, Hai Fang, Owen Rackham, Derek Wilson, Ralph Pethica, Cyrus Chothia, Julian Gough, SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Research, . ISSN 1362-4962. January 2011. PDF, 3837 Kbytes.

2010

Hai Fang, Julian Gough, The evolutionary dynamics of protein networks. Genome Biology, 11(Suppl 1). ISSN 1465-6906, pp. 12–12. October 2010. No electronic version available. External information
Owen Rackham, Martin Madera, Craig Armstrong, Tom Vincent, Dek Woolfson, Julian Gough, The Evolution and Structure Prediction of Coiled Coils across All Genomes. J. mol. biol., 403(3). ISSN 0022-2836, pp. 480–493. October 2010. No electronic version available. External information
Oliver Ray, Ken Whelan, Ross King, Automatic Revision of Metabolic Networks through Logical Analysis of Experimental Data. 19th International Conference on Inductive Logic Programming, pp. 194–201. July 2010. PDF, 375 Kbytes.
Tim Ravasi, Julian Gough, FANTOM consortium, An Atlas of Combinatorial Transcriptional Regulation in Mouse and Man.. Cell, 140(5). ISSN 0092-8674, pp. 744–752. March 2010. No electronic version available. External information
Martin Madera, Ryan Calmus, Grant Thiltgen, Kevin Karplus, Julian Gough, Improving protein secondary structure prediction using a simple k-mer model.. Bioinformtaics, 26(5). ISSN 1367-4803, pp. 596–602. February 2010. PDF, 529 Kbytes. External information
Ralph Pethica, Gary Barker, Tim Kovacs, Julian Gough, TreeVector: Scalable, Interactive, Phylogenetic Trees for the Web. PLoS ONE, 5(1). ISBN eISSN-1932-6203, pp. e8934–e8934. January 2010. PDF, 254 Kbytes.

2009

Chothia, C., Julian Gough, Genomic and Structural Aspects of Protein Evolution. Chapter in BJ Darwin Reviews: Evolution and Biochemistry. ISBN 9781855781740. December 2009. No electronic version available.
Oliver Ray, Amanda Clare, Maria Liakata, Larisa Soldatova, Ken Whelan, Ross King, Towards the Automation of Scientific Method. IJCAI09 Workshop on Abductive and Inductive Knowledge Development, pp. 27–33. July 2009. PDF, 302 Kbytes.
Oliver Ray, Towards a Rational Approach for the Logical Modelling of Inhibition in Metabolic Networks. International Conference on Advanced Information Networking and Applications (from 2009 IEEE International Workshop on Bioinformatics and Life Science Modeling and Computing), pp. 918–923. May 2009. PDF, 114 Kbytes.
Harakazu Suzuki, Julian Gough, FANTOM Consortium, The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics, . ISSN 1061-4036. April 2009. PDF, 718 Kbytes. External information
Cyrus Chothia, Julian Gough, Genomic and Structural Aspects of Protein Evolution. Biochemical Journal, 419(1). ISSN 0264-6021, pp. 15–28. April 2009. PDF, 884 Kbytes. External information
Derek Wilson, Ralph Pethica, Yiduo Zhou, Charles Talbot, Christine Vogel, Martin Madera, Cyrus CHothia, Julian Gough, SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Research, 37. ISSN 0305-1048, pp. D380–D386. January 2009. PDF, 1243 Kbytes. External information
Sarah Hunter, Rolf Apweiler, Julian Gough, Derek Wilson, Louise Daugherty, Martin Madera, Nicola Mulder, InterPro: the integrative protein signature database. Nucleic Acids Research, 37. ISSN 0305-1048, pp. D211–D215. January 2009. PDF, 250 Kbytes. External information

2008

Martin Madera, Profile Comparer: a program for scoring and aligning profile hidden Markov models. Bioinformatics, 24(22). ISSN 1367-4803, pp. 2630–2631. October 2008. PDF, 99 Kbytes. External information
Zeng, L., Park, C.H., Venu, R.C., Gough, J., Wang, G., Classification, Expression Pattern, and E3 Ligase Activity Assay of Rice U-Box-Containing Proteins. Mol Plant, 1(5). ISSN 1674-2052, pp. 800–815. September 2008. PDF, 824 Kbytes.
Garrocho-Villegas, V., Bustos-Rivera, G., Gough, J., Vinogradov, S.N., Arredondo-Peter, R., Expression and in silico structural analysis of a rice (Oryza sativa) hemoglobin 5. Plant Physiol. Biochem., xx. ISSN 0981-9428, pp. 1–5. May 2008. PDF, 548 Kbytes.
Oliver Ray, Chris Bryant, Inferring the function of genes from synthetic lethal mutations. 2nd International Conference on Complex, Intelligent and Software Intensive Systems (from 1st International Workshop on Intelligent Informatics in Biology and Medicine), pp. 667–671. February 2008. PDF, 75 Kbytes.

2007

Mulder N.J., Copley R., Courcelle E., Das U., Daugherty L., Dibley M., Finn R., Fleischmann W., Gough J., Haft D., Hulo N., Apweiler R., Hunter S., Kahn D., Kanapin A., Kejariwal A., Labarga A., Langendijk-Genevaux P.S., Lonsdale D., Lopez R., Letunic I., Madera M., Attwood T.K., Maslen J., McAnulla C., McDowell J., Mistry J., Mitchell A., Nikolskaya A.N., Orchard S., Orengo C., Petryszak R., Selengut J.D., Bairoch A., Sigrist C.J., Thomas P.D., Valentin F., Wilson D., Wu C.H., Yeats C., Bateman A., Binns D., Bork P., Buillard V., Cerutti L., New developments in the InterPro database. Nucl. Acids Res., 35, pp. D224–D228. January 2007. No electronic version available.
Wilson, D., Madera, M., Vogel, C., Chothia, C., Gough J., The SUPERFAMILY database in 2007: families and functions. Nucl. Acids Res., 35, pp. 308–313. January 2007. No electronic version available.

2006

Oliver Ray, Athos Antoniades, Antonis Kakas, Ioannis Demetriades, Abductive Logic Programming in the Clinical Management of HIV/AIDS. 17th European Conference on Artificial Intelligence. G. Brewka, S.Coradeschi, A. Perini, P. Traverso, (eds.), pp. 437–441. August 2006. PDF, 77 Kbytes.
Gough, J., Genomic scale sub-family assignment of protein domains. Nucl. Acids Res., 34 (13), pp. 3625–3633. July 2006. No electronic version available.
Maeda, N., Beisel, K. W., Bult, C. J., Fletcher, C. F., Forrest, A. R., Furuno, M., Hill, D., Itoh, M., Kanamori-Katayama, M., Katayama, S., Katoh, M., Kasukawa, T., Kawashima, T., Quackenbush, J., Ravasi, T., Ring, B. Z., Shibata, K., Sugiura, K., Takenaka, Y., Teasdale, R. D., Wells, C. A., Zhu, Y., Oyama, R., Kai, C., Kawai, J., Hume, D. A., Carninci, P., Hayashizaki, Y., Gough, J., Frith, M., Engstrom, P. G., Lenhard, B., Aturaliya, R. N., Batalov, S., Transcript Annotation in FANTOM3: Mouse Gene Catalog Based on Physical cDNAs. PLoS Geneteics, 2 (4), pp. 62–62. April 2006. No electronic version available.
Liu, J., Gough, J., Rost, B., Distinguishing Protein-Coding from Non_coding RNAs through Support Vector Machines. PLoS Genetics, 2 (4), pp. 29–29. April 2006. No electronic version available.
Babu, M. M., Priya, M. L., Selvan, A. T., Madera, M., Gough, J., Sankaran, K., A database of bacterial lipoproteins (DOLOP) with functional assignments to predicted lipoproteins. J Bacteriol., 188 (8), pp. 2761–2773. April 2006. No electronic version available.
Vinogradov, S. N., Hoogewijs, D., Bailly, X., Arredondo-Peter, R., Gough, J., Dewilde, S., Moens, L., Vanfleteren, J. R., A phylogenomic profile of globins. BMC Evol Biol., 6, pp. 31–31. April 2006. No electronic version available.
Piero Carninci, Julian Gough, Takeya Kasukawa, Yoshihide Hayashizaki, How many new genes are there? . Science, 311(5768). ISSN 0036-8075, pp. 1709–1711. March 2006. PDF, 368 Kbytes. External information

2005

Vinogradov, S. N., Hoogewijs, D., Bailly, X., Arrendondo-Peter, R., Guertin, M., Gough, J., Dewilde, S., Moens, L., Vanfleteren, J. R., Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life. Proc Natl Acad Sci USA, 102 (32), pp. 11385–11389. August 2005. No electronic version available.
Carninci, P., Wells, C., Nishikawa, S., Nori, F., Ohara, O., Okazaki, Y., Orlando, V., Pang, K. C., Pavan, W. J., Pavesi, G., Pesole, G., Petrovsky, N., Kodzius, R., Piazza, S., Reed, J., Reid, J. F., Ring, B. Z., Ringwald, M., Rost, B., Ruan, Y., Salzberg, S. L., Sandelin, A., Schneider, C. and, Shimokawa, K., Bajic, V. B., Brenner, S. E., Batalov, S., Forrest, A. R., Zavolan, M., Davis, M. J., Wilming, L. G., Kasukawa, T., 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., Katayama, S., Bono, H., Chalk, A. M., Chiu, K. P., Choudhary, V., Christoffels, A., Clutterbuck, D. R., Crowe, M. L., Dalla, E., Dalrymple, B. P., de, Bono, B., Gough, J., Della, Gatta, G., di, Bernardo, D., Down, T., Engstrom, P., Fagiolini, M., Faulkner, G., Fletcher, C. F., Fukushima, T., Furuno, M., Futaki, S., Frith, M. C., Gariboldi, M., Georgii-Hemming, P., Gingeras, T. R., Gojobori, T., Green, R. E., Gustincich, S., Harbers, M., Hayashi, Y., Hensch, T. K., Hirokawa, N., Maeda, N., Hill, D., Huminiecki, L., Iacono, M., Ikeo, K., Iwama, A., Ishikawa, T., Jakt, M., Kanapin, A., Katoh, M., Kawasawa, Y., Oyama, R., Kelso, J., Kitamura, H., Kitano, H., Kollias, G., Krishnan, S. P., Kruger, A., Kummerfeld, S. K., Kurochkin, I. V., Lareau, L. F., Lazarevic, D., Ravasi, T., Lipovich, L., Liu, J., Liuni, S., McWilliam, S., Madan, Babu, M., Madera, M., Marchionni, L., Matsuda, H., Matsuzawa, S., Miki, H., Lenhard, B., Mignone, F., Miyake, S., Morris, K., Mottagui-Tabar, S., Mulder, N., Nakano, N., Nakauchi, H., Ng, P., Nilsson, R., Nishiguchi, S., The Transcriptional Landscape of the Mammalian Genome. Science, 309 (5740), pp. 1559–1563. April 2005. No electronic version available.
Gough, J., Convergent evolution of domain architectures (is rare). Bioinformatics, 21 (8), pp. 1464–1471. April 2005. No electronic version available.
Mulder, N. J., Cerutti, L., Copley, R., Courcelle, E., Das, U., Durbin, R., Fleischmann, W., Gough, J., Haft, D., Harte, N., Hulo, N., Apweiler, R., Kahn, D., Kanapin, A., Krestyaninova, M., Lonsdale, D., Lopez, R., Letunic, I., Madera, M., Maslen, J., McDowall, J., Mitchell, A., Attwood, T. K., Nikolskaya, A. N., Orchard, S., Pagni, M., Ponting, C. P., Quevillon, E., Selengut, J., Sigrist, C. J., Silventoinen, V., Studholme, D. J., Vaughan, R., Bairoch, A., Wu, C. H., Bateman, A., Binns, D., Bradley, P., Bork, P., Bucher, P., InterPro, progress and status in 2005. Nucl. Acids Res., 33. January 2005. No electronic version available.

2004

Gough, J., Computational Genomics: Theory and Application. Chapter in . Grant, R., (eds.), pp. 105–124. September 2004. No electronic version available.
Gough, J., Chothia, C., The linked conservation of structure and function in a family of high diversity: the monomeric cupredoxins. Structure, 12, pp. 917–925. June 2004. No electronic version available.
Vogel, C., Berzuini, C., Bashton, M., Gough, J., Teichmann, S. A., Supra-domains: Evolutionary units larger than single protein domains. J. Mol. Biol., 336, pp. 809–823. February 2004. No electronic version available.
Madera, M., Vogel, C., Kummerfeld, S.K., Chothia, C., Gough, J., The SUPERFAMILY database in 2004: additions and improvements. Nucleic Acids Res., 32 (10), pp. 235–239. January 2004. No electronic version available.

2003

Gherardi, E., Youles, M. E., Miguel, R. N., Blundell, T. L., Iamele, L., Gough, J., Bandyopadhyay, A., Hartmann, G., 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., 100 (21), pp. 12039–12044. October 2003. No electronic version available.
Kanapin, A., Teasdale, R. D., Yuan, Z., Batalov, S., Davis, M. J., Gough, J., Grimmond, S., Kawaji, H., Magrane, M., Matsuda, H., Schonbach, C., Mouse Proteome Analysis. Genome Res., 13, pp. 1335–1344. June 2003. No electronic version available.
Kasukawa, T., Kanapin, A., Matsuda, H., Schriml, L. M., Hayashizaki, Y., Okazaki, Y., Quackenbush, J., Furuno, M., Nikaido, I., Bono, H., Hume, D. A., Bult, C., Hill, D. P., Baldarelli, R., Gough, J., Development and Evaluation of an Automated Annotation Pipeline and cDNA Annotation System. Genome Res., 13, pp. 1542–1551. June 2003. No electronic version available.
Chothia, C., Gough, J., Vogel, C., Teichmann, S. A., Evolution of the protein repertoire. Science, 300 (5626), pp. 1701–1703. June 2003. No electronic version available.

2002

Okazaki, Y., Suzuki, H., Yanagisawa, M., Yang, I., Yang, L., Yuan, Z., Zavolan, M., Zhu, Y., Zimmer, A., Carninci, P., Hayatsu, N., Hirozane-Kishikawa, T., Yamanaka, I., Konno, H., Nakamura, M., Sakazume, N., Sato, K., Shiraki, T., Waki, K., Kawai, J., Aizawa, K., Arakawa, T., Fukuda, S., Kiyosawa, H., Hara, A., Hashizume, W., Imotani, K., Ishii, Y., Yagi, K., Tomaru, Y., Hasegawa, Y., Nogami, A., Schonbach, C., Gojobori, T., Baldarelli, R., Furuno, M., 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., Kasukawa, T., Bradt, D., Brusic, V., Chothia, C., Corbani, L. E., Cousins, S., Dalla, E., Dragani, T. A., Fletcher, C. F., Forrest, A., Frazer, K. S., Adachi, J., Gaasterland T., Gariboldi, M., Gissi, C., Godzik, A., Gough, J., Grimmond, S., Gustincich, S., Hirokawa, N., Jackson, I. J., Jarvis, E. D., Bono, H., Kanai, A., Kawaji, H., Kawasawa, Y., Kedzierski, R. M., King, B. L., Konagaya, A., Kurochkin, I. V., Lee, Y., Lenhard, B., Lyons, P. A., Kondo, S., Maglott, D. R., Maltais, L., Marchionni, L., McKenzie, L., Miki, H., Nagashima, T., Numata, K., Okido, T., Pavan, W. J., Pertea, G., Nikaido, I., Pesole, G., Petrovsky, N., Pillai, R., Pontius, J. U., Qi, D., Ramachandran, S., Ravasi, T., Reed, J. C., Reed, D. J., Reid, J., Osato, N., Ring, B. Z., Ringwald, M., Sandelin, A., Schneider, C., Semple, C. A., Setou, M., Shimada, K., Sultana, R., Takenaka, Y., Taylor, M. S., Saito, R., Teasdale, R. D., Tomita, M., Verardo, R., Wagner, L., Wahlestedt, C., Wang, Y., Watanabe, Y., Wells, C., Wilming, L. G., Wynshaw-Boris, A., Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Nature, 420 (6915), pp. 563–573. December 2002. No electronic version available.
Gough, J., The SUPERFAMILY database in structural genomics.. Acta Cryst., In press. November 2002. No electronic version available.
Madera, M., Gough, J., A comparison of profile hidden Markov model procedures for remote homology detection . Nucl. Acids. Res., 30 (19), pp. 4321–4328. October 2002. No electronic version available.
Gough, J., Hidden Markov models and their application to genome analysis in the context of protein structure. PhD thesis. University of Cambridge. October 2002. No electronic version available.
Hua, S. J., Guo, T., Gough, J., Sun, Z. R., Proteins with alpha/beta Fold Class Have High Participation in Fusion Events. J. Mol. Biol., 320 (4), pp. 713–719. July 2002. No electronic version available.
Jardine, O., Gough, J., Chothia, C., Teichmann, T., Comparison of the Small Molecule Metabolic Pathways of Escherichia coli and Saccharomyces cerevisiae. Genome Res., 12 (6), pp. 916–929. June 2002. No electronic version available.
Gough, J., Chothia, C., SUPERFAMILY:HMMs representing all proteins of known structure.. Nucl. Acids Res., 30 (1), pp. 268–272. January 2002. No electronic version available.

2001

Teichmann, S.A., Rison, S. C. G., Thornton, J. M., Riley, M., Gough, J., Chothia, C., Small Molecule Metabolism: An Enzyme Mosaic. Trends Biotechnol., 19 (12), pp. 482–486. December 2001. No electronic version available.
Gough, J., Karplus, K., Hughey, R., Chothia, C., Assignment of Homology to Genome Sequences Using a Library of Hidden Markov Models That Represent All Protein of Known Structure. J. Mol. Biol., 313 (4), pp. 903–919. November 2001. No electronic version available.
Teichmann, S. A., Rison, S. C., Thornton, J. M., Riley, M., Gough, J., Chothia, C., The Evolution and Structural Anatomy of the Small Molecule Metabolic Pathways in Escherichia coli. J Mol Biol, 311 (4), pp. 693–708. August 2001. No electronic version available.
Apic, G., Gough, J., Teichmann, S. A., Domain combinations in archaeal, eubacterial and eukaryotic proteomes. J Mol Biol., 310 (2), pp. 311–325. July 2001. No electronic version available.
Apic, G., Gough, J., Teichmann, S. A., An insight into domain combinations. Bioinformatics, 17 Suppl 1, pp. 83–89. April 2001. No electronic version available.

2000

Gough, J., Chothia, C., Karplus, K., Barrett, C., Hughey, R., Currents in Computational Molecular Biology. Chapter in . Miyano, S., Shamir, R., Takagi, T., (eds.), pp. 124–125. December 2000. No electronic version available.