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Hypothesis-free phenotype prediction within a genetics-first framework.
Lu C, Zaucha J, Gam R, Fang H, Ben Smithers, Oates ME, Bernabe-Rubio M, Williams J, Zelenka N, Pandurangan AP, Tandon H, Shihab H, Kalaivani R, Sung M, Sardar AJ, Tzovoras BG, Danovi D, Gough J. Lu C, et al. Among authors: ben smithers. Nat Commun. 2023 Feb 17;14(1):919. doi: 10.1038/s41467-023-36634-6. Nat Commun. 2023. PMID: 36808136 Free PMC article.
'Why genes in pieces?'-revisited.
Smithers B, Oates M, Gough J. Smithers B, et al. Nucleic Acids Res. 2019 Jun 4;47(10):4970-4973. doi: 10.1093/nar/gkz284. Nucleic Acids Res. 2019. PMID: 30997511 Free PMC article.
InterPro in 2017-beyond protein family and domain annotations.
Finn RD, Attwood TK, Babbitt PC, Bateman A, Bork P, Bridge AJ, Chang HY, Dosztányi Z, El-Gebali S, Fraser M, Gough J, Haft D, Holliday GL, Huang H, Huang X, Letunic I, Lopez R, Lu S, Marchler-Bauer A, Mi H, Mistry J, Natale DA, Necci M, Nuka G, Orengo CA, Park Y, Pesseat S, Piovesan D, Potter SC, Rawlings ND, Redaschi N, Richardson L, Rivoire C, Sangrador-Vegas A, Sigrist C, Sillitoe I, Smithers B, Squizzato S, Sutton G, Thanki N, Thomas PD, Tosatto SC, Wu CH, Xenarios I, Yeh LS, Young SY, Mitchell AL. Finn RD, et al. Among authors: smithers b. Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199. doi: 10.1093/nar/gkw1107. Epub 2016 Nov 29. Nucleic Acids Res. 2017. PMID: 27899635 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… See abstract for full author list ➔ Jiang Y, et al. Among authors: smithers b. Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6. Genome Biol. 2016. PMID: 27604469 Free PMC article.
Splice junctions are constrained by protein disorder.
Smithers B, Oates ME, Gough J. Smithers B, et al. Nucleic Acids Res. 2015 May 26;43(10):4814-22. doi: 10.1093/nar/gkv407. Epub 2015 Apr 30. Nucleic Acids Res. 2015. PMID: 25934802 Free PMC article.
The SUPERFAMILY 1.75 database in 2014: a doubling of data.
Oates ME, Stahlhacke J, Vavoulis DV, Smithers B, Rackham OJ, Sardar AJ, Zaucha J, Thurlby N, Fang H, Gough J. Oates ME, et al. Among authors: smithers b. Nucleic Acids Res. 2015 Jan;43(Database issue):D227-33. doi: 10.1093/nar/gku1041. Epub 2014 Nov 20. Nucleic Acids Res. 2015. PMID: 25414345 Free PMC article.
A proteome quality index.
Zaucha J, Stahlhacke J, Oates ME, Thurlby N, Rackham OJ, Fang H, Smithers B, Gough J. Zaucha J, et al. Among authors: smithers b. Environ Microbiol. 2015 Jan;17(1):4-9. doi: 10.1111/1462-2920.12622. Epub 2014 Oct 22. Environ Microbiol. 2015. PMID: 25339269 Free article.