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Assignment of homology to genome sequences using a library of hidden Markov models that represent all proteins of known structure.
Gough J, Karplus K, Hughey R, Chothia C. Gough J, et al. J Mol Biol. 2001 Nov 2;313(4):903-19. doi: 10.1006/jmbi.2001.5080. J Mol Biol. 2001. PMID: 11697912
Structured and disordered facets of the GPCR fold.
Venkatakrishnan AJ, Flock T, Prado DE, Oates ME, Gough J, Madan Babu M. Venkatakrishnan AJ, et al. Among authors: gough j. Curr Opin Struct Biol. 2014 Aug;27:129-37. doi: 10.1016/j.sbi.2014.08.002. Epub 2014 Sep 3. Curr Opin Struct Biol. 2014. PMID: 25198166 Review.
Molecular Interaction Networks to Select Factors for Cell Conversion.
Ouyang JF, Kamaraj US, Polo JM, Gough J, Rackham OJL. Ouyang JF, et al. Among authors: gough j. Methods Mol Biol. 2019;1975:333-361. doi: 10.1007/978-1-4939-9224-9_16. Methods Mol Biol. 2019. PMID: 31062318
Molecular Principles of Gene Fusion Mediated Rewiring of Protein Interaction Networks in Cancer.
Latysheva NS, Oates ME, Maddox L, Flock T, Gough J, Buljan M, Weatheritt RJ, Babu MM. Latysheva NS, et al. Among authors: gough j. Mol Cell. 2016 Aug 18;63(4):579-592. doi: 10.1016/j.molcel.2016.07.008. Mol Cell. 2016. PMID: 27540857 Free PMC article.
Evolution of eukaryotic genome architecture: Insights from the study of a rapidly evolving metazoan, Oikopleura dioica: Non-adaptive forces such as elevated mutation rates may influence the evolution of genome architecture.
Chavali S, Morais DA, Gough J, Babu MM. Chavali S, et al. Among authors: gough j. Bioessays. 2011 Aug;33(8):592-601. doi: 10.1002/bies.201100034. Epub 2011 Jun 17. Bioessays. 2011. PMID: 21681984 Review.
The evolution of human cells in terms of protein innovation.
Sardar AJ, Oates ME, Fang H, Forrest AR, Kawaji H; FANTOM Consortium, Gough J, Rackham OJ. Sardar AJ, et al. Among authors: gough j. Mol Biol Evol. 2014 Jun;31(6):1364-74. doi: 10.1093/molbev/mst139. Epub 2014 Apr 1. Mol Biol Evol. 2014. PMID: 24692656 Free PMC article.
An expanded evaluation of protein function prediction methods shows an improvement in accuracy.
Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P. Jiang Y, et al. Among authors: gough j. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.
Ranking non-synonymous single nucleotide polymorphisms based on disease concepts.
Shihab HA, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR. Shihab HA, et al. Among authors: gough j. Hum Genomics. 2014 Jun 30;8(1):11. doi: 10.1186/1479-7364-8-11. Hum Genomics. 2014. PMID: 24980617 Free PMC article.
A disease-drug-phenotype matrix inferred by walking on a functional domain network.
Fang H, Gough J. Fang H, et al. Among authors: gough j. Mol Biosyst. 2013 Jul;9(7):1686-96. doi: 10.1039/c3mb25495j. Epub 2013 Mar 5. Mol Biosyst. 2013. PMID: 23462907
Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models.
Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN, Gaunt TR. Shihab HA, et al. Among authors: gough j. Hum Mutat. 2013 Jan;34(1):57-65. doi: 10.1002/humu.22225. Epub 2012 Nov 2. Hum Mutat. 2013. PMID: 23033316 Free PMC article.
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