Julian Gough - Publications

Affiliations: 
Structural Studies MRC Laboratory of Molecular Biology, Cambridge, England, United Kingdom 

56 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Sillitoe I, Andreeva A, Blundell TL, Buchan DWA, Finn RD, Gough J, Jones D, Kelley LA, Paysan-Lafosse T, Lam SD, Murzin AG, Pandurangan AP, Salazar GA, Skwark MJ, Sternberg MJE, et al. Genome3D: integrating a collaborative data pipeline to expand the depth and breadth of consensus protein structure annotation. Nucleic Acids Research. PMID 31733063 DOI: 10.1093/Nar/Gkz967  0.36
2016 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, ... ... Gough J, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/S13059-016-1037-6  0.8
2016 Rackham OJ, Firas J, Fang H, Oates ME, Holmes ML, Knaupp AS, Suzuki H, Nefzger CM, Daub CO, Shin JW, Petretto E, Forrest AR, Hayashizaki Y, Polo JM, ... Gough J, et al. A predictive computational framework for direct reprogramming between human cell types. Nature Genetics. PMID 26780608 DOI: 10.1038/ng.3487  0.8
2015 Baumgarten S, Simakov O, Esherick LY, Liew YJ, Lehnert EM, Michell CT, Li Y, Hambleton EA, Guse A, Oates ME, Gough J, Weis VM, Aranda M, Pringle JR, Voolstra CR. The genome of Aiptasia, a sea anemone model for coral symbiosis. Proceedings of the National Academy of Sciences of the United States of America. 112: 11893-8. PMID 26324906 DOI: 10.1073/pnas.1513318112  0.8
2015 Linkeviciute V, Rackham OJ, Gough J, Oates ME, Fang H. Function-selective domain architecture plasticity potentials in eukaryotic genome evolution. Biochimie. PMID 25980317 DOI: 10.1016/j.biochi.2015.05.003  0.8
2015 Smithers B, Oates ME, Gough J. Splice junctions are constrained by protein disorder. Nucleic Acids Research. 43: 4814-22. PMID 25934802 DOI: 10.1093/nar/gkv407  0.8
2015 Vavoulis DV, Francescatto M, Heutink P, Gough J. DGEclust: differential expression analysis of clustered count data. Genome Biology. 16: 39. PMID 25853652 DOI: 10.1186/s13059-015-0604-6  0.8
2015 Shihab HA, Rogers MF, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR, Campbell C. An integrative approach to predicting the functional effects of non-coding and coding sequence variation. Bioinformatics (Oxford, England). 31: 1536-43. PMID 25583119 DOI: 10.1093/Bioinformatics/Btv009  0.8
2015 Mitchell A, Chang HY, Daugherty L, Fraser M, Hunter S, Lopez R, McAnulla C, McMenamin C, Nuka G, Pesseat S, Sangrador-Vegas A, Scheremetjew M, Rato C, Yong SY, Bateman A, ... ... Gough J, et al. The InterPro protein families database: the classification resource after 15 years. Nucleic Acids Research. 43: D213-21. PMID 25428371 DOI: 10.1093/Nar/Gku1243  0.8
2015 Oates ME, Stahlhacke J, Vavoulis DV, Smithers B, Rackham OJ, Sardar AJ, Zaucha J, Thurlby N, Fang H, Gough J. The SUPERFAMILY 1.75 database in 2014: a doubling of data. Nucleic Acids Research. 43: D227-33. PMID 25414345 DOI: 10.1093/nar/gku1041  0.8
2015 Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cozzetto D, Dana JM, Filippis I, Gough J, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, Mistry J, et al. Genome3D: exploiting structure to help users understand their sequences. Nucleic Acids Research. 43: D382-6. PMID 25348407 DOI: 10.1093/Nar/Gku973  0.8
2015 Zaucha J, Stahlhacke J, Oates ME, Thurlby N, Rackham OJ, Fang H, Smithers B, Gough J. A proteome quality index. Environmental Microbiology. 17: 4-9. PMID 25339269 DOI: 10.1111/1462-2920.12622  0.8
2014 Fang H, Gough J. The 'dnet' approach promotes emerging research on cancer patient survival. Genome Medicine. 6: 64. PMID 25246945 DOI: 10.1186/s13073-014-0064-8  0.8
2014 Venkatakrishnan AJ, Flock T, Prado DE, Oates ME, Gough J, Madan Babu M. Structured and disordered facets of the GPCR fold. Current Opinion in Structural Biology. 27: 129-37. PMID 25198166 DOI: 10.1016/j.sbi.2014.08.002  0.8
2014 Burton BR, Britton GJ, Fang H, Verhagen J, Smithers B, Sabatos-Peyton CA, Carney LJ, Gough J, Strobel S, Wraith DC. Sequential transcriptional changes dictate safe and effective antigen-specific immunotherapy. Nature Communications. 5: 4741. PMID 25182274 DOI: 10.1038/ncomms5741  0.8
2014 Shihab HA, Gough J, Mort M, Cooper DN, Day IN, Gaunt TR. Ranking non-synonymous single nucleotide polymorphisms based on disease concepts. Human Genomics. 8: 11. PMID 24980617 DOI: 10.1186/1479-7364-8-11  0.8
2014 van der Lee R, Buljan M, Lang B, Weatheritt RJ, Daughdrill GW, Dunker AK, Fuxreiter M, Gough J, Gsponer J, Jones DT, Kim PM, Kriwacki RW, Oldfield CJ, Pappu RV, Tompa P, et al. Classification of intrinsically disordered regions and proteins. Chemical Reviews. 114: 6589-631. PMID 24773235 DOI: 10.1021/Cr400525M  0.8
2014 Sardar AJ, Oates ME, Fang H, Forrest AR, Kawaji H, Gough J, Rackham OJ. The evolution of human cells in terms of protein innovation. Molecular Biology and Evolution. 31: 1364-74. PMID 24692656 DOI: 10.1093/molbev/mst139  0.8
2014 Fang H, Gough J. supraHex: an R/Bioconductor package for tabular omics data analysis using a supra-hexagonal map. Biochemical and Biophysical Research Communications. 443: 285-9. PMID 24309102 DOI: 10.1016/j.bbrc.2013.11.103  0.8
2013 Fang H, Oates ME, Pethica RB, Greenwood JM, Sardar AJ, Rackham OJ, Donoghue PC, Stamatakis A, de Lima Morais DA, Gough J. A daily-updated tree of (sequenced) life as a reference for genome research. Scientific Reports. 3: 2015. PMID 23778980 DOI: 10.1038/srep02015  0.8
2013 Gough J, Dunker AK. Sequences and topology: disorder, modularity, and post/pre translation modification. Current Opinion in Structural Biology. 23: 417-9. PMID 23721748 DOI: 10.1016/J.Sbi.2013.05.001  0.8
2013 Shihab HA, Gough J, Cooper DN, Day IN, Gaunt TR. Predicting the functional consequences of cancer-associated amino acid substitutions. Bioinformatics (Oxford, England). 29: 1504-10. PMID 23620363 DOI: 10.1093/bioinformatics/btt182  0.8
2013 Fang H, Gough J. A domain-centric solution to functional genomics via dcGO Predictor. Bmc Bioinformatics. 14: S9. PMID 23514627 DOI: 10.1186/1471-2105-14-S3-S9  0.8
2013 Fang H, Gough J. A disease-drug-phenotype matrix inferred by walking on a functional domain network. Molecular Biosystems. 9: 1686-96. PMID 23462907 DOI: 10.1039/c3mb25495j  0.8
2013 Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, ... ... Gough J, et al. A large-scale evaluation of computational protein function prediction. Nature Methods. 10: 221-7. PMID 23353650 DOI: 10.1038/Nmeth.2340  0.8
2013 Lewis TE, Sillitoe I, Andreeva A, Blundell TL, Buchan DW, Chothia C, Cuff A, Dana JM, Filippis I, Gough J, Hunter S, Jones DT, Kelley LA, Kleywegt GJ, Minneci F, et al. Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Research. 41: D499-507. PMID 23203986 DOI: 10.1093/Nar/Gks1266  0.8
2013 Oates ME, Romero P, Ishida T, Ghalwash M, Mizianty MJ, Xue B, Dosztányi Z, Uversky VN, Obradovic Z, Kurgan L, Dunker AK, Gough J. D²P²: database of disordered protein predictions. Nucleic Acids Research. 41: D508-16. PMID 23203878 DOI: 10.1093/Nar/Gks1226  0.8
2013 Fang H, Gough J. DcGO: database of domain-centric ontologies on functions, phenotypes, diseases and more. Nucleic Acids Research. 41: D536-44. PMID 23161684 DOI: 10.1093/nar/gks1080  0.8
2013 Shihab HA, Gough J, Cooper DN, Stenson PD, Barker GL, Edwards KJ, Day IN, Gaunt TR. Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models. Human Mutation. 34: 57-65. PMID 23033316 DOI: 10.1002/humu.22225  0.8
2012 Pethica RB, Levitt M, Gough J. Evolutionarily consistent families in SCOP: sequence, structure and function. Bmc Structural Biology. 12: 27. PMID 23078280 DOI: 10.1186/1472-6807-12-27  0.8
2012 Hunter S, Jones P, Mitchell A, Apweiler R, Attwood TK, Bateman A, Bernard T, Binns D, Bork P, Burge S, de Castro E, Coggill P, Corbett M, Das U, Daugherty L, ... ... Gough J, et al. InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Research. 40: D306-12. PMID 22096229 DOI: 10.1093/Nar/Gkr948  0.8
2011 Chavali S, Morais DA, Gough J, Babu MM. 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. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 33: 592-601. PMID 21681984 DOI: 10.1002/bies.201100034  0.8
2011 Abroi A, Gough J. Are viruses a source of new protein folds for organisms? - Virosphere structure space and evolution. Bioessays : News and Reviews in Molecular, Cellular and Developmental Biology. 33: 626-35. PMID 21633962 DOI: 10.1002/bies.201000126  0.8
2011 Dunker AK, Gough J. Sequences and topology: intrinsic disorder in the evolving universe of protein structure. Current Opinion in Structural Biology. 21: 379-81. PMID 21530236 DOI: 10.1016/J.Sbi.2011.04.002  0.8
2011 de Lima Morais DA, Fang H, Rackham OJ, Wilson D, Pethica R, Chothia C, Gough J. SUPERFAMILY 1.75 including a domain-centric gene ontology method. Nucleic Acids Research. 39: D427-34. PMID 21062816 DOI: 10.1093/Nar/Gkq1130  0.8
2010 Rackham OJ, Madera M, Armstrong CT, Vincent TL, Woolfson DN, Gough J. The evolution and structure prediction of coiled coils across all genomes. Journal of Molecular Biology. 403: 480-93. PMID 20813113 DOI: 10.1016/j.jmb.2010.08.032  0.8
2010 Ravasi T, Suzuki H, Cannistraci CV, Katayama S, Bajic VB, Tan K, Akalin A, Schmeier S, Kanamori-Katayama M, Bertin N, Carninci P, Daub CO, Forrest AR, Gough J, Grimmond S, et al. An atlas of combinatorial transcriptional regulation in mouse and man. Cell. 140: 744-52. PMID 20211142 DOI: 10.1016/J.Cell.2010.01.044  0.8
2010 Madera M, Calmus R, Thiltgen G, Karplus K, Gough J. Improving protein secondary structure prediction using a simple k-mer model. Bioinformatics (Oxford, England). 26: 596-602. PMID 20130034 DOI: 10.1093/bioinformatics/btq020  0.8
2009 Suzuki H, Forrest AR, van Nimwegen E, Daub CO, Balwierz PJ, Irvine KM, Lassmann T, Ravasi T, Hasegawa Y, de Hoon MJ, Katayama S, Schroder K, Carninci P, Tomaru Y, ... ... Gough J, et al. The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nature Genetics. 41: 553-62. PMID 19377474 DOI: 10.1038/Ng.375  0.8
2009 Chothia C, Gough J. Genomic and structural aspects of protein evolution. The Biochemical Journal. 419: 15-28. PMID 19272021 DOI: 10.1042/Bj20090122  0.8
2009 Wilson D, Pethica R, Zhou Y, Talbot C, Vogel C, Madera M, Chothia C, Gough J. SUPERFAMILY--sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Research. 37: D380-6. PMID 19036790 DOI: 10.1093/Nar/Gkn762  0.8
2009 Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, Finn RD, Gough J, Haft D, Hulo N, Kahn D, et al. InterPro: the integrative protein signature database. Nucleic Acids Research. 37: D211-5. PMID 18940856 DOI: 10.1093/Nar/Gkn785  0.8
2007 Mulder NJ, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Buillard V, Cerutti L, Copley R, Courcelle E, Das U, Daugherty L, Dibley M, Finn R, ... ... Gough J, et al. New developments in the InterPro database. Nucleic Acids Research. 35: D224-8. PMID 17202162 DOI: 10.1093/Nar/Gkl841  0.8
2007 Wilson D, Madera M, Vogel C, Chothia C, Gough J. The SUPERFAMILY database in 2007: Families and functions Nucleic Acids Research. 35: D308-D313. PMID 17098927 DOI: 10.1093/Nar/Gkl910  0.8
2006 Maeda N, Kasukawa T, Oyama R, Gough J, Frith M, Engström PG, Lenhard B, Aturaliya RN, Batalov S, Beisel KW, Bult CJ, Fletcher CF, Forrest AR, Furuno M, Hill D, et al. Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. Plos Genetics. 2: e62. PMID 16683036 DOI: 10.1371/Journal.Pgen.0020062  0.8
2005 Vinogradov SN, Hoogewijs D, Bailly X, Arredondo-Peter R, Guertin M, Gough J, Dewilde S, Moens L, Vanfleteren JR. Three globin lineages belonging to two structural classes in genomes from the three kingdoms of life. Proceedings of the National Academy of Sciences of the United States of America. 102: 11385-9. PMID 16061809 DOI: 10.1073/Pnas.0502103102  0.8
2005 Mulder NJ, Apweiler R, Attwood TK, 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, et al. InterPro, progress and status in 2005. Nucleic Acids Research. 33: D201-5. PMID 15608177 DOI: 10.1093/Nar/Gki106  0.8
2004 Gough J, Chothia C. The linked conservation of structure and function in a family of high diversity: The monomeric cupredoxins Structure. 12: 917-925. PMID 15274913 DOI: 10.1016/J.Str.2004.03.029  0.8
2004 Vogel C, Berzuini C, Bashton M, Gough J, Teichmann SA. Supra-domains: evolutionary units larger than single protein domains. Journal of Molecular Biology. 336: 809-23. PMID 15095989 DOI: 10.1016/J.Jmb.2003.12.026  0.8
2004 Madera M, Vogel C, Kummerfeld SK, Chothia C, Gough J. The SUPERFAMILY database in 2004: Additions and improvements Nucleic Acids Research. 32: D235-D239. PMID 14681402 DOI: 10.1093/Nar/Gkh117  0.8
2003 Gherardi E, Youles ME, Miguel RN, Blundell TL, Iamele L, Gough J, Bandyopadhyay A, Hartmann G, Butler PJG. 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 of the United States of America. 100: 12039-12044. PMID 14528000 DOI: 10.1073/pnas.2034936100  0.8
2003 Kasukawa T, Furuno M, Nikaido I, Bono H, Hume DA, Bult C, Hill DP, Baldarelli R, Gough J, Kanapin A, Matsuda H, Schriml LM, Hayashizaki Y, Okazaki Y, Quackenbush J. Development and evaluation of an automated annotation pipeline and cDNA annotation system Genome Research. 13: 1542-1551. PMID 12819153 DOI: 10.1101/gr.992803  0.8
2003 Kanapin A, Batalov S, Davis MJ, Gough J, Grimmond S, Kawaji H, Magrane M, Matsuda H, Schönbach C, Teasdale RD, Yuan Z. Mouse proteome analysis. Genome Research. 13: 1335-44. PMID 12819131 DOI: 10.1101/gr.978703  0.8
2003 Chothia C, Gough J, Vogel C, Teichmann SA. Evolution of the protein repertoire. Science (New York, N.Y.). 300: 1701-3. PMID 12805536 DOI: 10.1126/Science.1085371  0.8
2002 Jardine O, Gough J, Chothia C, Teichmann SA. Comparison of the small molecule metabolic enzymes of Escherichia coli and Saccharomyces cerevisiae. Genome Research. 12: 916-29. PMID 12045145 DOI: 10.1101/Gr.228002  0.8
2002 Gough J, Chothia C. SUPERFAMILY: HMMs representing all proteins of known structure. SCOP sequence searches, alignments and genome assignments Nucleic Acids Research. 30: 268-272. PMID 11752312 DOI: 10.1093/Nar/30.1.268  0.8
Show low-probability matches.