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Items: 40

1.

Public health surveillance of multidrug-resistant clones of Neisseria gonorrhoeae in Europe: a genomic survey.

Harris SR, Cole MJ, Spiteri G, Sánchez-Busó L, Golparian D, Jacobsson S, Goater R, Abudahab K, Yeats CA, Bercot B, Borrego MJ, Crowley B, Stefanelli P, Tripodo F, Abad R, Aanensen DM, Unemo M; Euro-GASP study group.

Lancet Infect Dis. 2018 Jul;18(7):758-768. doi: 10.1016/S1473-3099(18)30225-1. Epub 2018 May 15.

2.

Microreact: visualizing and sharing data for genomic epidemiology and phylogeography.

Argimón S, Abudahab K, Goater RJE, Fedosejev A, Bhai J, Glasner C, Feil EJ, Holden MTG, Yeats CA, Grundmann H, Spratt BG, Aanensen DM.

Microb Genom. 2016 Nov 30;2(11):e000093. doi: 10.1099/mgen.0.000093. eCollection 2016 Nov.

3.

Whole-Genome Sequencing for Routine Pathogen Surveillance in Public Health: a Population Snapshot of Invasive Staphylococcus aureus in Europe.

Aanensen DM, Feil EJ, Holden MT, Dordel J, Yeats CA, Fedosejev A, Goater R, Castillo-Ramírez S, Corander J, Colijn C, Chlebowicz MA, Schouls L, Heck M, Pluister G, Ruimy R, Kahlmeter G, Åhman J, Matuschek E, Friedrich AW, Parkhill J, Bentley SD, Spratt BG, Grundmann H; European SRL Working Group.

MBio. 2016 May 5;7(3). pii: e00444-16. doi: 10.1128/mBio.00444-16.

4.

Target selection for structural genomics of infectious diseases.

Yeats C, Dessailly BH, Glass EM, Fremont DH, Orengo CA.

Methods Mol Biol. 2014;1140:35-51. doi: 10.1007/978-1-4939-0354-2_3.

PMID:
24590707
5.

Crystal structures of the human Dysferlin inner DysF domain.

Sula A, Cole AR, Yeats C, Orengo C, Keep NH.

BMC Struct Biol. 2014 Jan 17;14:3. doi: 10.1186/1472-6807-14-3.

6.

Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis.

Lees JG, Lee D, Studer RA, Dawson NL, Sillitoe I, Das S, Yeats C, Dessailly BH, Rentzsch R, Orengo CA.

Nucleic Acids Res. 2014 Jan;42(Database issue):D240-5. doi: 10.1093/nar/gkt1205. Epub 2013 Nov 21.

7.

Evolutionary history of the TBP-domain superfamily.

Brindefalk B, Dessailly BH, Yeats C, Orengo C, Werner F, Poole AM.

Nucleic Acids Res. 2013 Mar 1;41(5):2832-45. doi: 10.1093/nar/gkt045. Epub 2013 Feb 1.

8.

Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains.

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, Mitchell A, Murzin AG, Ochoa-Montaño B, Rackham OJ, Smith J, Sternberg MJ, Velankar S, Yeats C, Orengo C.

Nucleic Acids Res. 2013 Jan;41(Database issue):D499-507. doi: 10.1093/nar/gks1266. Epub 2012 Nov 30.

9.

New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures.

Sillitoe I, Cuff AL, Dessailly BH, Dawson NL, Furnham N, Lee D, Lees JG, Lewis TE, Studer RA, Rentzsch R, Yeats C, Thornton JM, Orengo CA.

Nucleic Acids Res. 2013 Jan;41(Database issue):D490-8. doi: 10.1093/nar/gks1211. Epub 2012 Nov 29.

10.

Low-density lipoprotein receptor gene familial hypercholesterolemia variant database: update and pathological assessment.

Usifo E, Leigh SE, Whittall RA, Lench N, Taylor A, Yeats C, Orengo CA, Martin AC, Celli J, Humphries SE.

Ann Hum Genet. 2012 Sep;76(5):387-401. doi: 10.1111/j.1469-1809.2012.00724.x.

11.

Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology.

Rojas AM, Santamaria A, Malik R, Jensen TS, Körner R, Morilla I, de Juan D, Krallinger M, Hansen DA, Hoffmann R, Lees J, Reid A, Yeats C, Wehner A, Elowe S, Clegg AB, Brunak S, Nigg EA, Orengo C, Valencia A, Ranea JA.

PLoS One. 2012;7(3):e31813. doi: 10.1371/journal.pone.0031813. Epub 2012 Mar 9.

12.

Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis.

Lees J, Yeats C, Perkins J, Sillitoe I, Rentzsch R, Dessailly BH, Orengo C.

Nucleic Acids Res. 2012 Jan;40(Database issue):D465-71. doi: 10.1093/nar/gkr1181. Epub 2011 Dec 1. Erratum in: Nucleic Acids Res. 2012 May;40(10):4725.

13.

InterPro in 2011: new developments in the family and domain prediction database.

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, Duquenne L, Finn RD, Fraser M, Gough J, Haft D, Hulo N, Kahn D, Kelly E, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, McMenamin C, Mi H, Mutowo-Muellenet P, Mulder N, Natale D, Orengo C, Pesseat S, Punta M, Quinn AF, Rivoire C, Sangrador-Vegas A, Selengut JD, Sigrist CJ, Scheremetjew M, Tate J, Thimmajanarthanan M, Thomas PD, Wu CH, Yeats C, Yong SY.

Nucleic Acids Res. 2012 Jan;40(Database issue):D306-12. doi: 10.1093/nar/gkr948. Epub 2011 Nov 16.

14.

The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences.

Yeats C, Lees J, Carter P, Sillitoe I, Orengo C.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W546-50. doi: 10.1093/nar/gkr438. Epub 2011 Jun 6.

15.

Finding the "dark matter" in human and yeast protein network prediction and modelling.

Ranea JA, Morilla I, Lees JG, Reid AJ, Yeats C, Clegg AB, Sanchez-Jimenez F, Orengo C.

PLoS Comput Biol. 2010 Sep 23;6(9). pii: e1000945. doi: 10.1371/journal.pcbi.1000945.

16.

A fast and automated solution for accurately resolving protein domain architectures.

Yeats C, Redfern OC, Orengo C.

Bioinformatics. 2010 Mar 15;26(6):745-51. doi: 10.1093/bioinformatics/btq034. Epub 2010 Jan 29.

PMID:
20118117
17.

Gene3D: merging structure and function for a Thousand genomes.

Lees J, Yeats C, Redfern O, Clegg A, Orengo C.

Nucleic Acids Res. 2010 Jan;38(Database issue):D296-300. doi: 10.1093/nar/gkp987. Epub 2009 Nov 11.

18.

An integrated approach to the interpretation of single amino acid polymorphisms within the framework of CATH and Gene3D.

Izarzugaza JM, Baresic A, McMillan LE, Yeats C, Clegg AB, Orengo CA, Martin AC, Valencia A.

BMC Bioinformatics. 2009 Aug 27;10 Suppl 8:S5. doi: 10.1186/1471-2105-10-S8-S5.

19.

The evolution of protein functions and networks: a family-centric approach.

Dessailly BH, Reid AJ, Yeats C, Lees JG, Cuff A, Orengo CA.

Biochem Soc Trans. 2009 Aug;37(Pt 4):745-50. doi: 10.1042/BST0370745.

PMID:
19614587
20.

InterPro: the integrative protein signature database.

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, Kelly E, Laugraud A, Letunic I, Lonsdale D, Lopez R, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Mulder N, Natale D, Orengo C, Quinn AF, Selengut JD, Sigrist CJ, Thimma M, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.

Nucleic Acids Res. 2009 Jan;37(Database issue):D211-5. doi: 10.1093/nar/gkn785. Epub 2008 Oct 21.

21.

Predicting protein function with hierarchical phylogenetic profiles: the Gene3D Phylo-Tuner method applied to eukaryotic genomes.

Ranea JA, Yeats C, Grant A, Orengo CA.

PLoS Comput Biol. 2007 Nov;3(11):e237. Epub 2007 Oct 18.

22.

Gene3D: comprehensive structural and functional annotation of genomes.

Yeats C, Lees J, Reid A, Kellam P, Martin N, Liu X, Orengo C.

Nucleic Acids Res. 2008 Jan;36(Database issue):D414-8. Epub 2007 Nov 21.

23.

Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone.

Reid AJ, Yeats C, Orengo CA.

Bioinformatics. 2007 Sep 15;23(18):2353-60. Epub 2007 Aug 20.

PMID:
17709341
24.

The implications of alternative splicing in the ENCODE protein complement.

Tress ML, Martelli PL, Frankish A, Reeves GA, Wesselink JJ, Yeats C, Olason PI, Albrecht M, Hegyi H, Giorgetti A, Raimondo D, Lagarde J, Laskowski RA, López G, Sadowski MI, Watson JD, Fariselli P, Rossi I, Nagy A, Kai W, Størling Z, Orsini M, Assenov Y, Blankenburg H, Huthmacher C, Ramírez F, Schlicker A, Denoeud F, Jones P, Kerrien S, Orchard S, Antonarakis SE, Reymond A, Birney E, Brunak S, Casadio R, Guigo R, Harrow J, Hermjakob H, Jones DT, Lengauer T, Orengo CA, Patthy L, Thornton JM, Tramontano A, Valencia A.

Proc Natl Acad Sci U S A. 2007 Mar 27;104(13):5495-500. Epub 2007 Mar 19.

25.

New developments in the InterPro database.

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, Fleischmann W, Gough J, Haft D, Hulo N, Hunter S, Kahn D, Kanapin A, Kejariwal A, Labarga A, Langendijk-Genevaux PS, Lonsdale D, Lopez R, Letunic I, Madera M, Maslen J, McAnulla C, McDowall J, Mistry J, Mitchell A, Nikolskaya AN, Orchard S, Orengo C, Petryszak R, Selengut JD, Sigrist CJ, Thomas PD, Valentin F, Wilson D, Wu CH, Yeats C.

Nucleic Acids Res. 2007 Jan;35(Database issue):D224-8.

26.

The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution.

Greene LH, Lewis TE, Addou S, Cuff A, Dallman T, Dibley M, Redfern O, Pearl F, Nambudiry R, Reid A, Sillitoe I, Yeats C, Thornton JM, Orengo CA.

Nucleic Acids Res. 2007 Jan;35(Database issue):D291-7. Epub 2006 Nov 29.

27.

Exploiting protein structure data to explore the evolution of protein function and biological complexity.

Marsden RL, Ranea JA, Sillero A, Redfern O, Yeats C, Maibaum M, Lee D, Addou S, Reeves GA, Dallman TJ, Orengo CA.

Philos Trans R Soc Lond B Biol Sci. 2006 Mar 29;361(1467):425-40. Review.

28.

Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.

Marsden RL, Lee D, Maibaum M, Yeats C, Orengo CA.

Nucleic Acids Res. 2006 Feb 15;34(3):1066-80. Print 2006.

29.

Gene3D: modelling protein structure, function and evolution.

Yeats C, Maibaum M, Marsden R, Dibley M, Lee D, Addou S, Orengo CA.

Nucleic Acids Res. 2006 Jan 1;34(Database issue):D281-4.

30.

Genome of the host-cell transforming parasite Theileria annulata compared with T. parva.

Pain A, Renauld H, Berriman M, Murphy L, Yeats CA, Weir W, Kerhornou A, Aslett M, Bishop R, Bouchier C, Cochet M, Coulson RM, Cronin A, de Villiers EP, Fraser A, Fosker N, Gardner M, Goble A, Griffiths-Jones S, Harris DE, Katzer F, Larke N, Lord A, Maser P, McKellar S, Mooney P, Morton F, Nene V, O'Neil S, Price C, Quail MA, Rabbinowitsch E, Rawlings ND, Rutter S, Saunders D, Seeger K, Shah T, Squares R, Squares S, Tivey A, Walker AR, Woodward J, Dobbelaere DA, Langsley G, Rajandream MA, McKeever D, Shiels B, Tait A, Barrell B, Hall N.

Science. 2005 Jul 1;309(5731):131-3.

31.

The Chlamydophila abortus genome sequence reveals an array of variable proteins that contribute to interspecies variation.

Thomson NR, Yeats C, Bell K, Holden MT, Bentley SD, Livingstone M, Cerdeño-Tárraga AM, Harris B, Doggett J, Ormond D, Mungall K, Clarke K, Feltwell T, Hance Z, Sanders M, Quail MA, Price C, Barrell BG, Parkhill J, Longbottom D.

Genome Res. 2005 May;15(5):629-40. Epub 2005 Apr 18.

32.

The G5 domain: a potential N-acetylglucosamine recognition domain involved in biofilm formation.

Bateman A, Holden MT, Yeats C.

Bioinformatics. 2005 Apr 15;21(8):1301-3. Epub 2004 Dec 14.

PMID:
15598841
33.

Genomic plasticity of the causative agent of melioidosis, Burkholderia pseudomallei.

Holden MT, Titball RW, Peacock SJ, Cerdeño-Tárraga AM, Atkins T, Crossman LC, Pitt T, Churcher C, Mungall K, Bentley SD, Sebaihia M, Thomson NR, Bason N, Beacham IR, Brooks K, Brown KA, Brown NF, Challis GL, Cherevach I, Chillingworth T, Cronin A, Crossett B, Davis P, DeShazer D, Feltwell T, Fraser A, Hance Z, Hauser H, Holroyd S, Jagels K, Keith KE, Maddison M, Moule S, Price C, Quail MA, Rabbinowitsch E, Rutherford K, Sanders M, Simmonds M, Songsivilai S, Stevens K, Tumapa S, Vesaratchavest M, Whitehead S, Yeats C, Barrell BG, Oyston PC, Parkhill J.

Proc Natl Acad Sci U S A. 2004 Sep 28;101(39):14240-5. Epub 2004 Sep 17.

34.

The PepSY domain: a regulator of peptidase activity in the microbial environment?

Yeats C, Rawlings ND, Bateman A.

Trends Biochem Sci. 2004 Apr;29(4):169-72. No abstract available.

PMID:
15124630
35.

The Pfam protein families database.

Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D138-41.

36.

The BON domain: a putative membrane-binding domain.

Yeats C, Bateman A.

Trends Biochem Sci. 2003 Jul;28(7):352-5. No abstract available.

PMID:
12878000
37.

New knowledge from old: in silico discovery of novel protein domains in Streptomyces coelicolor.

Yeats C, Bentley S, Bateman A.

BMC Microbiol. 2003 Feb 6;3:3. Epub 2003 Feb 6.

38.

Sequencing and analysis of the genome of the Whipple's disease bacterium Tropheryma whipplei.

Bentley SD, Maiwald M, Murphy LD, Pallen MJ, Yeats CA, Dover LG, Norbertczak HT, Besra GS, Quail MA, Harris DE, von Herbay A, Goble A, Rutter S, Squares R, Squares S, Barrell BG, Parkhill J, Relman DA.

Lancet. 2003 Feb 22;361(9358):637-44.

PMID:
12606174
39.

The PASTA domain: a beta-lactam-binding domain.

Yeats C, Finn RD, Bateman A.

Trends Biochem Sci. 2002 Sep;27(9):438. Review.

PMID:
12217513
40.

Intercellular hormones: 8. Release of nucleotides and nucleosides by damaged living cells.

Loofbourow JR, Oppenheim-Errera S, Loofbourow DG, Yeats CA.

Biochem J. 1947;41(1):122-9. No abstract available.

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