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Items: 1 to 50 of 251

1.

Emerging concepts in pseudoenzyme classification, evolution, and signaling.

Ribeiro AJM, Das S, Dawson N, Zaru R, Orchard S, Thornton JM, Orengo C, Zeqiraj E, Murphy JM, Eyers PA.

Sci Signal. 2019 Aug 13;12(594). pii: eaat9797. doi: 10.1126/scisignal.aat9797. Review.

PMID:
31409758
2.

FunFam protein families improve residue level molecular function prediction.

Scheibenreif L, Littmann M, Orengo C, Rost B.

BMC Bioinformatics. 2019 Jul 18;20(1):400. doi: 10.1186/s12859-019-2988-x.

3.

Comparison of Drosophila melanogaster Embryo and Adult Proteome by SWATH-MS Reveals Differential Regulation of Protein Synthesis, Degradation Machinery, and Metabolism Modules.

Fabre B, Korona D, Lees JG, Lazar I, Livneh I, Brunet M, Orengo CA, Russell S, Lilley KS.

J Proteome Res. 2019 Jun 7;18(6):2525-2534. doi: 10.1021/acs.jproteome.9b00076. Epub 2019 May 22.

PMID:
31083952
4.

A CATH domain functional family based approach to identify putative cancer driver genes and driver mutations.

Ashford P, Pang CSM, Moya-García AA, Adeyelu T, Orengo CA.

Sci Rep. 2019 Jan 22;9(1):263. doi: 10.1038/s41598-018-36401-4.

5.

Transcriptional Profiling of Dendritic Cells in a Mouse Model of Food-Antigen-Induced Anaphylaxis Reveals the Upregulation of Multiple Immune-Related Pathways.

Rodriguez MJ, Palomares F, Bogas G, Torres MJ, Diaz-Perales A, Rojo J, Plaza-Seron MDC, Rodriguez-Nogales A, Orengo C, Mayorga C, Perkins JR.

Mol Nutr Food Res. 2019 Feb;63(3):e1800759. doi: 10.1002/mnfr.201800759. Epub 2018 Dec 17.

PMID:
30458065
6.

CATH: expanding the horizons of structure-based functional annotations for genome sequences.

Sillitoe I, Dawson N, Lewis TE, Das S, Lees JG, Ashford P, Tolulope A, Scholes HM, Senatorov I, Bujan A, Ceballos Rodriguez-Conde F, Dowling B, Thornton J, Orengo CA.

Nucleic Acids Res. 2019 Jan 8;47(D1):D280-D284. doi: 10.1093/nar/gky1097.

7.

InterPro in 2019: improving coverage, classification and access to protein sequence annotations.

Mitchell AL, Attwood TK, Babbitt PC, Blum M, Bork P, Bridge A, Brown SD, Chang HY, El-Gebali S, Fraser MI, Gough J, Haft DR, Huang H, Letunic I, Lopez R, Luciani A, Madeira F, Marchler-Bauer A, Mi H, Natale DA, Necci M, Nuka G, Orengo C, Pandurangan AP, Paysan-Lafosse T, Pesseat S, Potter SC, Qureshi MA, Rawlings ND, Redaschi N, Richardson LJ, Rivoire C, Salazar GA, Sangrador-Vegas A, Sigrist CJA, Sillitoe I, Sutton GG, Thanki N, Thomas PD, Tosatto SCE, Yong SY, Finn RD.

Nucleic Acids Res. 2019 Jan 8;47(D1):D351-D360. doi: 10.1093/nar/gky1100.

8.

Comprehensive analysis of long noncoding RNA expression in dorsal root ganglion reveals cell-type specificity and dysregulation after nerve injury.

Baskozos G, Dawes JM, Austin JS, Antunes-Martins A, McDermott L, Clark AJ, Trendafilova T, Lees JG, McMahon SB, Mogil JS, Orengo C, Bennett DL.

Pain. 2019 Feb;160(2):463-485. doi: 10.1097/j.pain.0000000000001416.

9.

Exploring Enzyme Evolution from Changes in Sequence, Structure, and Function.

Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM.

Methods Mol Biol. 2019;1851:263-275. doi: 10.1007/978-1-4939-8736-8_14.

PMID:
30298402
10.

Reply to Gauthier et al.

Rusie LK, Orengo C, Burrell D, Ramachandran A, Houlberg M, Keglovitz K, Munar D, Schneider JA.

Clin Infect Dis. 2019 Jan 7;68(2):349-350. doi: 10.1093/cid/ciy647. No abstract available.

PMID:
30107481
11.

Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells.

Tsuchiya Y, Zhyvoloup A, Baković J, Thomas N, Yu BYK, Das S, Orengo C, Newell C, Ward J, Saladino G, Comitani F, Gervasio FL, Malanchuk OM, Khoruzhenko AI, Filonenko V, Peak-Chew SY, Skehel M, Gout I.

Biochem J. 2018 Jun 6;475(11):1909-1937. doi: 10.1042/BCJ20180043.

12.

Choosing the Best Enzyme Complex Structure Made Easy.

Das S, Orengo C.

Structure. 2018 Apr 3;26(4):528-530. doi: 10.1016/j.str.2018.03.009.

13.

Preexposure Prophylaxis Initiation and Retention in Care Over 5 Years, 2012-2017: Are Quarterly Visits Too Much?

Rusie LK, Orengo C, Burrell D, Ramachandran A, Houlberg M, Keglovitz K, Munar D, Schneider JA.

Clin Infect Dis. 2018 Jul 2;67(2):283-287. doi: 10.1093/cid/ciy160.

PMID:
29506057
14.

Unique signalling connectivity of FGFR3-TACC3 oncoprotein revealed by quantitative phosphoproteomics and differential network analysis.

Lombardi B, Ashford P, Moya-Garcia AA, Rust A, Crawford M, Williams SV, Knowles MA, Katan M, Orengo C, Godovac-Zimmermann J.

Oncotarget. 2017 Oct 25;8(61):102898-102911. doi: 10.18632/oncotarget.22048. eCollection 2017 Nov 28.

15.

Editorial overview: Catalysis and regulation.

Thornton J, Orengo C.

Curr Opin Struct Biol. 2017 Dec;47:vi-viii. doi: 10.1016/j.sbi.2017.11.005. No abstract available.

PMID:
29221623
16.

Gene3D: Extensive prediction of globular domains in proteins.

Lewis TE, Sillitoe I, Dawson N, Lam SD, Clarke T, Lee D, Orengo C, Lees J.

Nucleic Acids Res. 2018 Jan 4;46(D1):D1282. doi: 10.1093/nar/gkx1187. No abstract available.

17.

Gene3D: Extensive prediction of globular domains in proteins.

Lewis TE, Sillitoe I, Dawson N, Lam SD, Clarke T, Lee D, Orengo C, Lees J.

Nucleic Acids Res. 2018 Jan 4;46(D1):D435-D439. doi: 10.1093/nar/gkx1069. Erratum in: Nucleic Acids Res. 2018 Jan 4;46(D1):D1282.

18.

Analysis of temporal transcription expression profiles reveal links between protein function and developmental stages of Drosophila melanogaster.

Wan C, Lees JG, Minneci F, Orengo CA, Jones DT.

PLoS Comput Biol. 2017 Oct 18;13(10):e1005791. doi: 10.1371/journal.pcbi.1005791. eCollection 2017 Oct.

19.

Understanding enzyme function evolution from a computational perspective.

Tyzack JD, Furnham N, Sillitoe I, Orengo CM, Thornton JM.

Curr Opin Struct Biol. 2017 Dec;47:131-139. doi: 10.1016/j.sbi.2017.08.003. Epub 2017 Sep 8. Review.

20.

Structural and Functional View of Polypharmacology.

Moya-García A, Adeyelu T, Kruger FA, Dawson NL, Lees JG, Overington JP, Orengo C, Ranea JAG.

Sci Rep. 2017 Aug 31;7(1):10102. doi: 10.1038/s41598-017-10012-x.

21.

ELIXIR-UK role in bioinformatics training at the national level and across ELIXIR.

Larcombe L, Hendricusdottir R, Attwood TK, Bacall F, Beard N, Bellis LJ, Dunn WB, Hancock JM, Nenadic A, Orengo C, Overduin B, Sansone SA, Thurston M, Viant MR, Winder CL, Goble CA, Ponting CP, Rustici G.

F1000Res. 2017 Jun 21;6. pii: ELIXIR-952. doi: 10.12688/f1000research.11837.1. eCollection 2017.

22.

An overview of comparative modelling and resources dedicated to large-scale modelling of genome sequences.

Lam SD, Das S, Sillitoe I, Orengo C.

Acta Crystallogr D Struct Biol. 2017 Aug 1;73(Pt 8):628-640. doi: 10.1107/S2059798317008920. Epub 2017 Jul 28. Review.

23.

Genome-wide RNA-Sequencing analysis identifies a distinct fibrosis gene signature in the conjunctiva after glaucoma surgery.

Yu-Wai-Man C, Owen N, Lees J, Tagalakis AD, Hart SL, Webster AR, Orengo CA, Khaw PT.

Sci Rep. 2017 Jul 17;7(1):5644. doi: 10.1038/s41598-017-05780-5.

24.

CATH-Gene3D: Generation of the Resource and Its Use in Obtaining Structural and Functional Annotations for Protein Sequences.

Dawson NL, Sillitoe I, Lees JG, Lam SD, Orengo CA.

Methods Mol Biol. 2017;1558:79-110. doi: 10.1007/978-1-4939-6783-4_4.

PMID:
28150234
25.

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.

Nucleic Acids Res. 2017 Jan 4;45(D1):D190-D199. doi: 10.1093/nar/gkw1107. Epub 2016 Nov 29.

26.

CATH: an expanded resource to predict protein function through structure and sequence.

Dawson NL, Lewis TE, Das S, Lees JG, Lee D, Ashford P, Orengo CA, Sillitoe I.

Nucleic Acids Res. 2017 Jan 4;45(D1):D289-D295. doi: 10.1093/nar/gkw1098. Epub 2016 Nov 28.

27.

The Classification of Protein Domains.

Dawson N, Sillitoe I, Marsden RL, Orengo CA.

Methods Mol Biol. 2017;1525:137-164.

PMID:
27896721
28.

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.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

29.

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.

Das S, Lee D, Sillitoe I, Dawson NL, Lees JG, Orengo CA.

Bioinformatics. 2016 Sep 15;32(18):2889. doi: 10.1093/bioinformatics/btw473. Epub 2016 Jul 31. No abstract available.

30.

Novel Computational Protocols for Functionally Classifying and Characterising Serine Beta-Lactamases.

Lee D, Das S, Dawson NL, Dobrijevic D, Ward J, Orengo C.

PLoS Comput Biol. 2016 Jun 22;12(6):e1004926. doi: 10.1371/journal.pcbi.1004926. eCollection 2016 Jun.

31.

Functional innovation from changes in protein domains and their combinations.

Lees JG, Dawson NL, Sillitoe I, Orengo CA.

Curr Opin Struct Biol. 2016 Jun;38:44-52. doi: 10.1016/j.sbi.2016.05.016. Epub 2016 Jun 13. Review.

PMID:
27309309
32.

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing.

Berger B, Gaasterland T, Lengauer T, Orengo CA, Gaeta B, Markel S, Valencia A.

Bioinformatics. 2017 Sep 15;33(18):2968. doi: 10.1093/bioinformatics/btw090. No abstract available.

33.

The Pain in Neuropathy Study (PiNS): a cross-sectional observational study determining the somatosensory phenotype of painful and painless diabetic neuropathy.

Themistocleous AC, Ramirez JD, Shillo PR, Lees JG, Selvarajah D, Orengo C, Tesfaye S, Rice AS, Bennett DL.

Pain. 2016 May;157(5):1132-45. doi: 10.1097/j.pain.0000000000000491.

34.

ISCB's Initial Reaction to The New England Journal of Medicine Editorial on Data Sharing.

Berger B, Gaasterland T, Lengauer T, Orengo C, Gaeta B, Markel S, Valencia A.

PLoS Comput Biol. 2016 Mar 24;12(3):e1004816. doi: 10.1371/journal.pcbi.1004816. eCollection 2016 Mar. No abstract available.

35.

ISCB's initial reaction to New England Journal of Medicine editorial on data sharing.

Valencia A, Markel S, Gaeta B, Gaasterland T, Lengauer T, Berger B, Orengo C.

F1000Res. 2016 Feb 11;5. pii: ISCB Comm J-157. doi: 10.12688/f1000research.8051.1. eCollection 2016.

36.

Landscape of activating cancer mutations in FGFR kinases and their differential responses to inhibitors in clinical use.

Patani H, Bunney TD, Thiyagarajan N, Norman RA, Ogg D, Breed J, Ashford P, Potterton A, Edwards M, Williams SV, Thomson GS, Pang CS, Knowles MA, Breeze AL, Orengo C, Phillips C, Katan M.

Oncotarget. 2016 Apr 26;7(17):24252-68. doi: 10.18632/oncotarget.8132.

37.

Large-Scale Analysis Exploring Evolution of Catalytic Machineries and Mechanisms in Enzyme Superfamilies.

Furnham N, Dawson NL, Rahman SA, Thornton JM, Orengo CA.

J Mol Biol. 2016 Jan 29;428(2 Pt A):253-267. doi: 10.1016/j.jmb.2015.11.010. Epub 2015 Nov 14.

38.

Gene3D: expanding the utility of domain assignments.

Lam SD, Dawson NL, Das S, Sillitoe I, Ashford P, Lee D, Lehtinen S, Orengo CA, Lees JG.

Nucleic Acids Res. 2016 Jan 4;44(D1):D404-9. doi: 10.1093/nar/gkv1231. Epub 2015 Nov 17.

39.

Co-Expression Network Models Suggest that Stress Increases Tolerance to Mutations.

Lehtinen S, Bähler J, Orengo C.

Sci Rep. 2015 Nov 16;5:16726. doi: 10.1038/srep16726.

40.

Diversity in protein domain superfamilies.

Das S, Dawson NL, Orengo CA.

Curr Opin Genet Dev. 2015 Dec;35:40-9. doi: 10.1016/j.gde.2015.09.005. Epub 2015 Nov 3. Review.

41.

Protein function annotation using protein domain family resources.

Das S, Orengo CA.

Methods. 2016 Jan 15;93:24-34. doi: 10.1016/j.ymeth.2015.09.029. Epub 2015 Oct 3. Review.

PMID:
26434392
42.

Gene Function Prediction from Functional Association Networks Using Kernel Partial Least Squares Regression.

Lehtinen S, Lees J, Bähler J, Shawe-Taylor J, Orengo C.

PLoS One. 2015 Aug 19;10(8):e0134668. doi: 10.1371/journal.pone.0134668. eCollection 2015.

43.

Identifying and characterising key alternative splicing events in Drosophila development.

Lees JG, Ranea JA, Orengo CA.

BMC Genomics. 2015 Aug 16;16:608. doi: 10.1186/s12864-015-1674-2.

44.

The history of the CATH structural classification of protein domains.

Sillitoe I, Dawson N, Thornton J, Orengo C.

Biochimie. 2015 Dec;119:209-17. doi: 10.1016/j.biochi.2015.08.004. Epub 2015 Aug 4. Review.

45.

Functional classification of CATH superfamilies: a domain-based approach for protein function annotation.

Das S, Lee D, Sillitoe I, Dawson NL, Lees JG, Orengo CA.

Bioinformatics. 2015 Nov 1;31(21):3460-7. doi: 10.1093/bioinformatics/btv398. Epub 2015 Jul 2. Erratum in: Bioinformatics. 2016 Sep 15;32(18):2889.

46.

Using CATH-Gene3D to Analyze the Sequence, Structure, and Function of Proteins.

Sillitoe I, Lewis T, Orengo C.

Curr Protoc Bioinformatics. 2015 Jun 19;50:1.28.1-21. doi: 10.1002/0471250953.bi0128s50.

PMID:
26087950
47.

CATH FunFHMMer web server: protein functional annotations using functional family assignments.

Das S, Sillitoe I, Lee D, Lees JG, Dawson NL, Ward J, Orengo CA.

Nucleic Acids Res. 2015 Jul 1;43(W1):W148-53. doi: 10.1093/nar/gkv488. Epub 2015 May 11.

48.

FUN-L: gene prioritization for RNAi screens.

Lees JG, Hériché JK, Morilla I, Fernández JM, Adler P, Krallinger M, Vilo J, Valencia A, Ellenberg J, Ranea JA, Orengo C.

Bioinformatics. 2015 Jun 15;31(12):2052-3. doi: 10.1093/bioinformatics/btv073. Epub 2015 Feb 8.

PMID:
25667547
49.

The InterPro protein families database: the classification resource after 15 years.

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, Punta M, Attwood TK, Sigrist CJ, Redaschi N, Rivoire C, Xenarios I, Kahn D, Guyot D, Bork P, Letunic I, Gough J, Oates M, Haft D, Huang H, Natale DA, Wu CH, Orengo C, Sillitoe I, Mi H, Thomas PD, Finn RD.

Nucleic Acids Res. 2015 Jan;43(Database issue):D213-21. doi: 10.1093/nar/gku1243. Epub 2014 Nov 26.

50.

CATH: comprehensive structural and functional annotations for genome sequences.

Sillitoe I, Lewis TE, Cuff A, Das S, Ashford P, Dawson NL, Furnham N, Laskowski RA, Lee D, Lees JG, Lehtinen S, Studer RA, Thornton J, Orengo CA.

Nucleic Acids Res. 2015 Jan;43(Database issue):D376-81. doi: 10.1093/nar/gku947. Epub 2014 Oct 27.

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