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Article

Addou, S; Rentzsch, R; Lee, D; Orengo, CA; (2009) Domain-Based and Family-Specific Sequence Identity Thresholds Increase the Levels of Reliable Protein Function Transfer. J MOL BIOL , 387 (2) 416 - 430. 10.1016/j.jmb.2008.12.045.

Alba, MM; Das, RJ; Orengo, CA; Kellam, P; (2001) Genomewide function conservation and phylogeny in the herpesviridae. GENOME RES , 11 (1) 43 - 54.

Alba, MM; Lee, D; Pearl, FMG; Shepherd, AJ; Martin, N; Orengo, CA; Kellam, P; (2001) VIDA: a virus database system for the organization of animal virus genome open reading frames. Nucleic Acids Research , 29 (1) 133 - 136. 10.1093/nar/29.1.133. Green and gold open access
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Antunes-Martins, A; Perkins, JR; Lees, J; Hildebrandt, T; Orengo, C; Bennett, DL; (2013) Systems biology approaches to finding novel pain mediators. Wiley Interdiscip Rev Syst Biol Med , 5 , Article 1. 10.1002/wsbm.1192%20%5Bdoi%5D.

Antunes-Martins, A; Perkins, JR; Lees, J; Hildebrandt, T; Orengo, C; Bennett, DLH; (2013) Systems biology approaches to finding novel pain mediators. WILEY INTERDISCIPLINARY REVIEWS-SYSTEMS BIOLOGY AND MEDICINE , 5 (1) 11 - 35. 10.1002/wsbm.1192.

Berman, HM; Burley, SK; Chiu, W; Sali, A; Adzhubei, A; Bourne, PE; ... Westbrook, JD; + view all (2006) Outcome of a workshop on archiving structural models of biological macromolecules. STRUCTURE , 14 (8) 1211 - 1217. 10.1016/j.str.2006.06.005.

Berman, HM; Westbrook, JD; Burley, SK; Chiu, W; Sali, A; Adzhubei, A; ... Standley, DM; + view all (2006) Outcome of a Workshop on Archiving Structural Models of Biological Macromolecules. Structure , 14 (8) 1211 - 1217. 10.1016/j.str.2006.06.005.

Bork, P; Orengo, CA; (2004) Sequences and topology - Genes and structures in context - Editorial overview. CURR OPIN STRUC BIOL , 14 (3) 261 - 263. 10.1016/S0959-440X(04)00088-0.

Bork, P; Orengo, CA; (2004) Sequences and topology; Genes and structures in context. Current Opinion in Structural Biology , 14 (3) 261 - 263.

Bray, JE; Marsden, RL; Rison, SCG; Savchenko, A; Edwards, AM; Thornton, JM; Orengo, CA; (2004) A practical and robust sequence search strategy for structural genomics target selection. BIOINFORMATICS , 20 (14) 2288 - 2295. 10.1093/bioinformatics/bth240.

Bray, JE; Todd, AE; Pearl, FMG; Thornton, JM; Orengo, CA; (2000) The CATH Dictionary of Homologous Superfamilies (DHS): a consensus approach for identifying distant structural homologues. PROTEIN ENG , 13 (3) 153 - 165.

Brindefalk, B; Dessailly, BH; Yeats, C; Orengo, C; Werner, F; Poole, AM; (2013) Evolutionary history of the TBP-domain superfamily. Nucleic Acids Res , 41 (5) 2832 - 2845. 10.1093/nar/gkt045.

Brindefalk, B; Dessailly, BH; Yeats, C; Orengo, C; Werner, F; Poole, AM; (2013) Evolutionary history of the TBP-domain superfamily. Nucleic Acids Res , 41 , Article 5. 10.1093/nar/gkt045%20%5Bdoi%5D.

Brown, NP; Orengo, CA; Taylor, WR; (1996) A protein structure comparison methodology. COMPUT CHEM , 20 (3) 359 - 380.

Buchan, DW; Rison, SC; Bray, JE; Lee, D; Pearl, F; Thornton, JM; Orengo, CA; (2003) Gene3D: structural assignments for the biologist and bioinformaticist alike. Nucleic Acids Res , 31 (1) 469 - 473.

Buchan, DW; Shepherd, AJ; Lee, D; Pearl, FM; Rison, SC; Thornton, JM; Orengo, CA; (2002) Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database. Genome Res , 12 (3) 503 - 514. 10.1101/gr.213802.

Buchan, DWA; Rison, SCG; Bray, JE; Lee, D; Pearl, F; Thornton, JM; Orengo, CA; (2003) Gene3D: structural assignments for the biologist and bioinformaticist alike. NUCLEIC ACIDS RES , 31 (1) 469 - 473. 10.1093/nar/gkg051. Gold open access

Buchan, DWA; Shepherd, AJ; Lee, D; Pearl, FMG; Rison, SCG; Thornton, JM; Orengo, CA; (2002) Gene3D: Structural assignment for whole genes and genomes using the CATH domain structure database. GENOME RES , 12 (3) 503 - 514. 10.1101/gr.213802.

Carter, P; Lee, D; Orengo, C; (2008) Chapter 1. Target selection in structural genomics projects to increase knowledge of protein structure and function space. Adv Protein Chem Struct Biol , 75 1 - 52. 10.1016/S0065-3233(07)75001-5.

Carter, P; Lee, D; Orengo, C; (2008) TARGET SELECTION IN STRUCTURAL GENOMICS PROJECTS TO INCREASE KNOWLEDGE OF PROTEIN STRUCTURE AND FUNCTION SPACE. STRUCTURAL GENOMICS, PT A , 75 1 - +. 10.1016/S1876-1623(08)00001-1.

Cuff, A; Redfern, O; Greene, L; Sillitoe, I; Lewis, T; Dibley, M; ... ORENGO, C; + view all (2009) The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space. Structure , 17 (8) 1051 - 1062. 10.1016/j.str.2009.06.015. Gold open access

Cuff, A; Redfern, OC; Greene, L; Sillitoe, I; Lewis, T; Dibley, M; ... Orengo, C; + view all (2009) The CATH Hierarchy Revisited-Structural Divergence in Domain Superfamilies and the Continuity of Fold Space. STRUCTURE , 17 (8) 1051 - 1062. 10.1016/j.str.2009.06.015.

Cuff, AL; Sillitoe, I; Lewis, T; Clegg, AB; Rentzsch, R; Furnham, N; ... Orengo, CA; + view all (2011) Extending CATH: increasing coverage of the protein structure universe and linking structure with function. NUCLEIC ACIDS RES , 39 D420 - D426. 10.1093/nar/gkq1001. Gold open access

Cuff, AL; Sillitoe, I; Lewis, T; Redfern, OC; Garratt, R; Thornton, J; Orengo, CA; (2009) The CATH classification revisited-architectures reviewed and new ways to characterize structural divergence in superfamilies. NUCLEIC ACIDS RES , 37 D310 - D314. 10.1093/nar/gkn877. Gold open access

Dawes, JM; Antunes-Martins, A; Perkins, JR; Paterson, KJ; Sisignano, M; Schmid, R; ... McMahon, SB; + view all (2014) Genome-wide transcriptional profiling of skin and dorsal root Ganglia after ultraviolet-B-induced inflammation. PLoS One , 9 (4) e93338 - ?. 10.1371/journal.pone.0093338.

Dawes, JM; Calvo, M; Perkins, JR; Paterson, KJ; Kiesewetter, H; Hobbs, C; ... McMahon, SB; + view all (2011) CXCL5 mediates UVB irradiation-induced pain. Sci Transl Med , 3 , Article 90. 10.1126/scitranslmed.3002193%20%5Bdoi%5D.

Dawes, JM; Calvo, M; Perkins, JR; Paterson, KJ; Kiesewetter, H; Hobbs, C; ... McMahon, SB; + view all (2011) CXCL5 Mediates UVB Irradiation-Induced Pain. SCIENCE TRANSLATIONAL MEDICINE , 3 (90) , Article ARTN 90ra60. 10.1126/scitranslmed.3002193.

de la Crux, X; Sillitoe, I; Orengo, CA; (2002) Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low-resolution models. Proteins , 46 (1) 72 - 84.

de la Cruz, X; Sillitoe, I; Orengo, C; (2002) Use of structure comparison methods for the refinement of protein structure predictions. I. Identifying the structural family of a protein from low-resolution models. PROTEINS , 46 (1) 72 - 84.

De La Cruz, X; Sillitoe, I; Orengo, C; (2001) Structure Comparisons Beyond the Experimental Realm: Paving the Way for Higher Quality Structure Predictions. Proteins , 46 72 - 84.

Dessailly, BH; Dawson, NL; Mizuguchi, K; Orengo, CA; (2013) Functional site plasticity in domain superfamilies. Biochim Biophys Acta , 1834 , Article 5. 10.1016/j.bbapap.2013.02.042%20%5Bdoi%5D.

Dessailly, BH; Lensink, MF; Orengo, CA; Wodak, SJ; (2008) LigASite - a database of biologically relevant binding sites in proteins with known apo-structures. NUCLEIC ACIDS RES , 36 D667 - D673. 10.1093/nar/gkm839. Gold open access

Dessailly, BH; Nair, R; Jaroszewski, L; Fajardo, JE; Kouranov, A; Lee, D; ... Orengo, C; + view all (2009) PSI-2: structural genomics to cover protein domain family space. Structure , 17 (6) 869 - 881. 10.1016/j.str.2009.03.015.

Dessailly, BH; Redfern, OC; Cuff, A; Orengo, CA; (2009) Exploiting structural classifications for function prediction: towards a domain grammar for protein function. CURR OPIN STRUC BIOL , 19 (3) 349 - 356. 10.1016/j.sbi.2009.03.009.

Dessailly, BH; Redfern, OC; Cuff, AL; Orengo, CA; (2010) Detailed Analysis of Function Divergence in a Large and Diverse Domain Superfamily: Toward a Refined Protocol of Function Classification. STRUCTURE , 18 (11) 1522 - 1535. 10.1016/j.str.2010.08.017.

Dessailly, BH; Redfern, OC; Cuff, AL; Orengo, CA; (2010) Detailed analysis of function divergence in a large and diverse domain superfamily: toward a refined protocol of function classification. Structure , 18 , Article 11. 10.1016/j.str.2010.08.017%20%5Bdoi%5D.

Dessailly, BH; Reid, AJ; Yeats, C; Lees, JG; Cuff, A; Orengo, CA; (2009) The evolution of protein functions and networks: a family-centric approach. BIOCHEMICAL SOCIETY TRANSACTIONS , 37 745 - 750. 10.1042/BST0370745.

Diboun, I; Wernisch, L; Orengo, CA; Koltzenburg, M; (2006) Microarray analysis after RNA amplification can detect pronounced differences in gene expression using limma. BMC GENOMICS , 7 , Article 252. 10.1186/1471-2164-7-252. Green and gold open access
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FLORES, TP; ORENGO, CA; MOSS, DS; THORNTON, JM; (1993) COMPARISON OF CONFORMATIONAL CHARACTERISTICS IN STRUCTURALLY SIMILAR PROTEIN PAIRS. PROTEIN SCI , 2 (11) 1811 - 1826.

Fricker, FR; Antunes-Martins, A; Galino, J; Paramsothy, R; La Russa, F; Perkins, J; ... Bennett, DLH; + view all (2013) Axonal neuregulin 1 is a rate limiting but not essential factor for nerve remyelination. BRAIN , 136 2279 - 2297. 10.1093/brain/awt148.

Furnham, N; Sillitoe, I; Holliday, GL; Cuff, AL; Laskowski, RA; Orengo, CA; Thornton, JM; (2012) Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. PLoS Comput Biol , 8 (3) , Article e1002403 . 10.1371/journal.pcbi.1002403. Green and gold open access
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Furnham, N; Sillitoe, I; Holliday, GL; Cuff, AL; Laskowski, RA; Orengo, CA; Thornton, JM; (2012) Exploring the evolution of novel enzyme functions within structurally defined protein superfamilies. PLoS Comput Biol , 8 , Article 3. 10.1371/journal.pcbi.1002403%20%5Bdoi%5D.

Furnham, N; Sillitoe, I; Holliday, GL; Cuff, AL; Rahman, SA; Laskowski, RA; ... Thornton, JM; + view all (2012) FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic Acids Res , 40 (Database issue) D776 - D782. 10.1093/nar/gkr852.

Furnham, N; Sillitoe, I; Holliday, GL; Cuff, AL; Rahman, SA; Laskowski, RA; ... Thornton, JM; + view all (2012) FunTree: a resource for exploring the functional evolution of structurally defined enzyme superfamilies. Nucleic Acids Res , 40 , Article Database issue. 10.1093/nar/gkr852%20%5Bdoi%5D.

Gaasterland, T; Orengo, CA; (2002) Genomic insights into evolution. Curr Opin Struct Biol , 12 (3) 345 - 347.

Gaasterland, T; Orengo, CA; (2002) Sequences and topology genomic insights into evolution. CURR OPIN STRUC BIOL , 12 (3) 345 - 347.

Grant, A; Lee, D; Orengo, C; (2004) Progress towards mapping the universe of protein folds. Genome Biology , 5 , Article 107.

Greene, LH; Lewis, TE; Addou, S; Cuff, A; Dallman, T; Dibley, M; ... Orengo, CA; + view all (2007) The CATH domain structure database: new protocols and classification levels give a more comprehensive resource for exploring evolution. NUCLEIC ACIDS RES , 35 D291 - D297. 10.1093/nar/gkl959. Gold open access

Harrison, A; Pearl, F; Mott, R; Thornton, J; Orengo, C; (2002) Quantifying the similarities within fold space. J Mol Biol , 323 (5) 909 - 926.

Harrison, A; Pearl, F; Sillitoe, I; Slidel, T; Mott, R; Thornton, J; Orengo, C; (2004) Recognizing the fold of a protein structure. Bioinformatics , 19 (14) 1748 - 1759.

Harrison, A; Pearl, F; Sillitoe, I; Slidel, T; Mott, R; Thornton, J; Orengo, C; (2003) Recognizing the fold of a protein structure. BIOINFORMATICS , 19 (14) 1748 - 1759. 10.1093/bioinformatics/btg240.

Harrison, A; Pearl, F; Sillitoe, I; Slidel, T; Mott, R; Thornton, J; Orengo, C; (2003) Recognizing the fold of a protein structure. Bioinformatics , 19 (14) 1748 - 1759.

Harrison, AP; Johnston, CE; Orengo, CA; (2007) Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips. BMC BIOINFORMATICS , 8 , Article 195. 10.1186/1471-2105-8-195. Green and gold open access
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Hériché, JK; Lees, JG; Morilla, I; Walter, T; Petrova, B; Julia Roberti, M; ... Ellenberg, J; + view all (2014) Integration of biological data by kernels on graph nodes allows prediction of new genes involved in mitotic chromosome condensation. Mol Biol Cell 10.1091/mbc.E13-04-0221.

Hernandez, D; Addou, S; Lee, D; Orengo, C; Shephard, EA; Phillips, IR; (2003) Trimethylaminuria and a human FMO3 mutation database. HUM MUTAT , 22 (3) 209 - 213. 10.1002/humu.10252.

Holzerlandt, R; Orengo, C; Kellam, P; Albà, MM; (2002) Identification of new herpesvirus gene homologs in the human genome. Genome Res , 12 (11) 1739 - 1748. 10.1101/gr.334302.

Hunter, S; Apweiler, R; Attwood, TK; Bairoch, A; Bateman, A; Binns, D; ... Yeats, C; + view all (2009) InterPro: the integrative protein signature database. NUCLEIC ACIDS RES , 37 D211 - D215. 10.1093/nar/gkn785. Gold open access

Hunter, S; Jones, P; Mitchell, A; Apweiler, R; Attwood, TK; Bateman, A; ... Yong, SY; + view all (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res , 40 (Database issue) D306 - D312. 10.1093/nar/gkr948.

Huynen, M; Doerks, T; Eisenhaber, F; Orengo, C; Sunyaev, S; Yuan, YP; Bork, P; (1998) Homology-based fold predictions for Mycoplasma genitalium proteins. JOURNAL OF MOLECULAR BIOLOGY , 280 (3) 323 - 326. 10.1006/jmbi.1998.1884.

Izarzugaza, JM; Hopcroft, LE; Baresic, A; Orengo, CA; Martin, AC; Valencia, A; (2011) Characterization of pathogenic germline mutations in human protein kinases. BMC Bioinformatics , 12 Suppl 4 S1+ - S1+. 10.1186/1471-2105-12-S4-S1%20%5Bdoi%5D.

Izarzugaza, JM; Hopcroft, LE; Baresic, A; Orengo, CA; Martin, AC; Valencia, A; (2011) Characterization of pathogenic germline mutations in human protein kinases. BMC Bioinformatics , 12 Suppl 4 S1 - ?. 10.1186/1471-2105-12-S4-S1.

Izarzugaza, JMG; Baresic, A; McMillan, LEM; Yeats, C; Clegg, AB; Orengo, CA; ... Valencia, A; + view all (2009) An integrated approach to the interpretation of Single Amino Acid Polymorphisms within the framework of CATH and Gene3D. BMC BIOINFORMATICS , 10 , Article S5. 10.1186/1471-2105-10-S8-S5. Green and gold open access
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Izarzugaza, JMG; Redfern, OC; Orengo, CA; Valencia, A; (2009) Cancer-associated mutations are preferentially distributed in protein kinase functional sites. PROTEINS , 77 (4) 892 - 903. 10.1002/prot.22512.

Jones, S; Stewart, M; Michie, A; Swindells, MB; Orengo, C; Thornton, JM; (1998) Domain assignment for protein structures using a consensus approach: characterization and analysis. Protein Sci , 7 (2) 233 - 242. 10.1002/pro.5560070202.

Jones, S; Stewart, M; Michie, M; Swindells, MB; Orengo, CA; Thornton, JM; (1998) Domain Assignment for Protein Structures Using a Consensus Approach: Characterisation and Analysis. Protein Science , 7 233 - 242.

Kahlem, P; Clegg, A; Reisinger, F; Xenarios, I; Hermjakob, H; Orengo, C; Birney, E; (2009) ENFIN - A European network for integrative systems biology. COMPTES RENDUS BIOLOGIES , 332 (11) 1050 - 1058. 10.1016/j.crvi.2009.09.003.

Kellam, P; Liu, X; Martin, N; Orengo, C; Swift, S; Tucker, A; (2001) Comparing, Contrasting and Combining Clusters in Viral Gene Expression. Proceedings of the Sixth Workshop on Intelligent Data Analysis in Medicine and Pharmacology , 6 56 - 62.

Kellam, P; Xiaohui, L; Martin, NJ; Orengo, CA; Swift, S; Tucker, A; (2002) A framework for modelling virus gene expression data. Intelligent Data Analysis , 5 1 - 13.

Lee, D; de Beer, TA; Laskowski, RA; Thornton, JM; Orengo, CA; (2011) 1,000 structures and more from the MCSG. BMC Struct Biol , 11 2+ - 2+. 10.1186/1472-6807-11-2%20%5Bdoi%5D.

Lee, D; de Beer, TAP; Laskowski, RA; Thornton, JM; Orengo, CA; (2011) 1,000 structures and more from the MCSG. BMC STRUCT BIOL , 11 , Article 2. 10.1186/1472-6807-11-2. Green and gold open access
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Lee, D; Grant, A; Buchan, D; Orengo, C; (2003) A structural perspective on genome evolution. Curr Opin Struct Biol , 13 (3) 359 - 369.

Lee, D; Grant, A; Marsden, RL; Orengo, C; (2005) Identification and distribution of protein families in 120 completed genomes using Gene3D. Proteins , 59 (3) 603 - 615. 10.1002/prot.20409.

Lee, D; Redfern, O; Orengo, C; (2007) Predicting protein function from sequence and structure. NAT REV MOL CELL BIO , 8 (12) 995 - 1005. 10.1038/nrm2281.

Lee, D; Redfern, O; Orengo, C; (2007) Predicting protein function from sequence and structure. Nature Reviews Molecular Cell Biology 10.1038/nrm2281.

Lee, D; Rentzsch, R; ORENGO, C; (2010) GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. Nucleic Acids Res , 38 (3) 720 - 737. 10.1093/nar/gkp1049.

Lee, DA; Fefeu, S; Edo-Ukeh, AA; Orengo, CA; Slingsby, C; (2004) EyeSite: a semi-automated database of protein families in the eye. NUCLEIC ACIDS RES , 32 D148 - D152. 10.1093/nar/gkh090. Gold open access

Lee, DA; Rentzsch, R; Orengo, C; (2010) GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. Nucleic Acids Res , 38 (3) 720 - 737. 10.1093/nar/gkp1049.

Lee, DA; Rentzsch, R; Orengo, C; (2010) GeMMA: functional subfamily classification within superfamilies of predicted protein structural domains. Nucleic Acids Res , 38 , Article 3. 10.1093/nar/gkp1049%20%5Bdoi%5D.

Lees, J; Yeats, C; Perkins, J; Sillitoe, I; Rentzsch, R; Dessailly, BH; Orengo, C; (2012) Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. Nucleic Acids Res , 40 (Database issue) D465 - D471. 10.1093/nar/gkr1181.

Lees, J; Yeats, C; Perkins, J; Sillitoe, I; Rentzsch, R; Dessailly, BH; Orengo, C; (2012) Gene3D: a domain-based resource for comparative genomics, functional annotation and protein network analysis. Nucleic Acids Res , 40 , Article Database issue. 10.1093/nar/gkr1181%20%5Bdoi%5D.

Lees, J; Yeats, C; Redfern, O; Clegg, A; Orengo, C; (2010) Gene3D: merging structure and function for a Thousand genomes. NUCLEIC ACIDS RES , 38 D296 - D300. 10.1093/nar/gkp987. Gold open access

Lees, J; Yeats, C; Redfern, O; Clegg, A; Orengo, C; (2010) Gene3D: merging structure and function for a Thousand genomes. Nucleic Acids Res , 38 , Article Database issue. 10.1093/nar/gkp987%20%5Bdoi%5D.

Lees, JG; Heriche, JK; Morilla, I; Ranea, JA; Orengo, CA; (2011) Systematic computational prediction of protein interaction networks. PHYS BIOL , 8 (3) , Article 035008. 10.1088/1478-3975/8/3/035008.

Lees, JG; Lee, D; Studer, RA; Dawson, NL; Sillitoe, I; Das, S; ... Orengo, CA; + view all (2013) Gene3D: Multi-domain annotations for protein sequence and comparative genome analysis. Nucleic Acids Research , 42 (D1) D240-D245. 10.1093/nar/gkt1205. Green and gold open access
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Lehtinen, S; Marsellach, FX; Codlin, S; Schmidt, A; Clément-Ziza, M; Beyer, A; ... Pancaldi, V; + view all (2013) Stress induces remodelling of yeast interaction and co-expression networks. Mol Biosyst , 9 (7) 1697 - 1707. 10.1039/c3mb25548d.

Lewis, TE; Sillitoe, I; Andreeva, A; Blundell, TL; Buchan, DW; Chothia, C; ... Orengo, C; + view all (2013) Genome3D: a UK collaborative project to annotate genomic sequences with predicted 3D structures based on SCOP and CATH domains. Nucleic Acids Research , 41 (Database issue) D499 - D507. 10.1093/nar/gks1266. Green and gold open access
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Lobley, A; Swindells, MB; Orengo, CA; Jones, DT; (2007) Inferring function using patterns of native disorder in proteins. PLOS COMPUT BIOL , 3 (8) , Article e162. 10.1371/journal.pcbi.0030162. Green and gold open access
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Lobley, AE; Nugent, T; Orengo, CA; Jones, DT; (2008) FFPred: an integrated feature-based function prediction server for vertebrate proteomes. NUCLEIC ACIDS RES , 36 W297 - W302. 10.1093/nar/gkn193. Gold open access

Loewenstein, Y; Raimondo, D; Redfern, O; Watson, J; Frishman, D; Linial, M; ... Tramontano, A; + view all (2009) Protein function annotation by homology-based inference. [Review]. Genome Biology , 10 , Article 207. 10.1186/gb-2009-10-2-207.

Maratou, K; Wallace, VCJ; Hasnie, FS; Okuse, K; Hosseini, R; Jina, N; ... Rice, ASC; + view all (2009) Comparison of dorsal root ganglion gene expression in rat models of traumatic and HIV-associated neuropathic pain. EUR J PAIN , 13 (4) 387 - 398. 10.1016/j.ejpain.2008.05.011.

Maréchal, A; Meunier, B; Lee, D; Orengo, C; Rich, PR; (2012) Yeast cytochrome c oxidase: a model system to study mitochondrial forms of the haem-copper oxidase superfamily. Biochimica et Biophysica Acta (BBA) - Bioenergetics , 1817 (4) 620 - 628. 10.1016/j.bbabio.2011.08.011. Green and gold open access
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Marsden, RL; Lee, D; Maibaum, M; Yeats, C; Orengo, CA; (2006) Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space. NUCLEIC ACIDS RES , 34 (3) 1066 - 1080. 10.1093/nar/gkj494. Gold open access

Marsden, RL; Lewis, TA; Orengo, CA; (2007) Towards a comprehensive structural coverage of completed genomes: a structural genomics viewpoint. BMC BIOINFORMATICS , 8 , Article 86. 10.1186/1471-2105-8-86. Green and gold open access
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Marsden, RL; Orengo, CA; (2008) The classification of protein domains. Methods Mol Biol , 453 123 - 146. 10.1007/978-1-60327-429-6_5.

Marsden, RL; Ranea, JAG; Sillero, A; Redfern, O; Yeats, C; Maibaum, M; ... Orengo, CA; + view all (2006) Exploiting protein structure data to explore the evolution of protein function and biological complexity. PHILOS T R SOC B , 361 (1467) 425 - 440. 10.1098/rstb.2005.1801. Gold open access

Martin, AC; Orengo, CA; Hutchinson, EG; Jones, S; Karmirantzou, M; Laskowski, RA; ... Thornton, JM; + view all (1998) Protein folds and functions. STRUCTURE , 6 (7) 875 - 884.

Michie, AD; Orengo, CA; Thornton, JM; (1996) Analysis of domain structural class using an automated class assignment protocol. J MOL BIOL , 262 (2) 168 - 185.

Morilla, I; Lees, JG; Reid, AJ; Orengo, C; Ranea, JAG; (2010) Assessment of protein domain fusions in human protein interaction networks prediction Application to the human kinetochore model. NEW BIOTECHNOL , 27 (6) 755 - 765.

Morilla, I; Ranea, J; Lees, J; ORENGO, C; (2010) Assessment of Protein Domain Fusions in Human Protein Interaction Networks Prediction: application to the human kinetochore model. New Biotechnology (27) 755 - 765. 10.1002/gepi.20486.

Mulder, NJ; Apweiler, R; Attwood, TK; Bairoch, A; Bateman, A; Binns, D; ... Yeats, C; + view all (2007) New developments in the InterPro database. Nucleic Acids Research , 35 (Supplement 1) , Article D224-D228. 10.1093/nar/gkl841. Green and gold open access
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Nagano, N; Orengo, CA; Thornton, JM; (2002) One fold with many functions: The evolutionary relationships between TIM barrel families based on their sequences, structures and functions. J MOL BIOL , 321 (5) 741 - 765. 10.1016/S0022-2836(02)00649-6.

Nair, R; Liu, J; Soong, T; Acton, T; Everett, J; Kouranov, A; ... Rost, B; + view all (2009) Structural genomics is the largest contributor of novel structural leverage. J Struct Funct Genomics 181 - 191. 10.1007/s10969-008-9055-6.

ORENGO, C; (1994) CLASSIFICATION OF PROTEIN FOLDS. CURRENT OPINION IN STRUCTURAL BIOLOGY , 4 (3) 429 - 440. 10.1016/S0959-440X(94)90113-9.

Orengo, C; Whisstock, J; (2012) Structural insights into multi-protein communication systems. CURRENT OPINION IN STRUCTURAL BIOLOGY , 22 (3) 313 - 315. 10.1016/j.sbi.2012.05.007.

Orengo, C; Whisstock, J; (2012) Structural insights into multi-protein communication systems. Curr Opin Struct Biol , 22 , Article 3. 10.1016/j.sbi.2012.05.007%20%5Bdoi%5D.

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Pearl, F; Todd, A; Sillitoe, I; Dibley, M; Redfern, O; Lewis, T; ... Orengo, C; + view all (2005) The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. NUCLEIC ACIDS RES , 33 D247 - D251. Gold open access

Pearl, F; Todd, A; Sillitoe, I; Dibley, M; Redfern, O; Lewis, T; ... Orengo, C; + view all (2005) The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis. Nucleic Acids Research , 33 247 - 251. Gold open access

Pearl, F; Todd, AE; Bray, JE; Martin, ACR; Salamov, AA; Suwa, M; ... Orengo, CA; + view all (2000) Using the CATH domain database to assign structures and functions to the genome sequences. BIOCHEMICAL SOCIETY TRANSACTIONS , 28 269 - 275.

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Pearl, FMG; Martin, N; Bray, JE; Buchan, DWA; Harrison, AP; Lee, D; ... Orengo, CA; + view all (2001) A rapid classification protocol for the CATH Domain Database to support structural genomics. NUCLEIC ACIDS RES , 29 (1) 223 - 227. Gold open access

Perkins, JR; Antunes-Martins, A; Calvo, M; Grist, J; Rust, W; Schmid, R; ... Bennett, DLH; + view all (2014) A comparison of RNA-seq and exon arrays for whole genome transcription profiling of the L5 spinal nerve transection model of neuropathic pain in the rat. MOLECULAR PAIN , 10 , Article ARTN 7. 10.1186/1744-8069-10-7. Green and gold open access
file

Perkins, JR; Dawes, JM; McMahon, SB; Bennett, DL; Orengo, C; Kohl, M; (2012) ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data. BMC Genomics , 13 296+ - 296+. 10.1186/1471-2164-13-296%20%5Bdoi%5D.

Perkins, JR; Dawes, JM; McMahon, SB; Bennett, DL; Orengo, C; Kohl, M; (2012) ReadqPCR and NormqPCR: R packages for the reading, quality checking and normalisation of RT-qPCR quantification cycle (Cq) data. BMC Genomics , 13 296 - ?. 10.1186/1471-2164-13-296.

Perkins, JR; Diboun, I; Dessailly, BH; Lees, JG; Orengo, C; (2010) Transient Protein-Protein Interactions: Structural, Functional, and Network Properties. STRUCTURE , 18 (10) 1233 - 1243. 10.1016/j.str.2010.08.007.

Perkins, JR; Diboun, I; Dessailly, BH; Lees, JG; Orengo, C; (2010) Transient protein-protein interactions: structural, functional, and network properties. Structure , 18 , Article 10. 10.1016/j.str.2010.08.007%20%5Bdoi%5D.

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Perkins, JR; Lees, J; Antunes-Martins, A; Diboun, I; McMahon, SB; Bennett, DL; Orengo, C; (2013) PainNetworks: a web-based resource for the visualisation of pain-related genes in the context of their network associations. Pain , 154 (12) 2586.e1 - 2586.12. 10.1016/j.pain.2013.09.003.

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Ranea, J.A.G.; Buchan, D.W.A.; Thornton, J.M.; Orengo, C.A.; (2004) Evolution of protein superfamilies and bacterial genome size. Journal of Molecular Biology , 336 (4) pp. 871-887. 10.1016/j.jmb.2003.12.044.

Ranea, JAG; Buchan, DWA; Thornton, JM; Orengo, CA; (2004) Evolution of protein superfamilies and bacterial genome size. J MOL BIOL , 336 (4) 871 - 887. 10.1016/j.jmb.2003.12.044.

Ranea, JAG; Grant, A; Thornton, JM; Orengo, CA; (2005) Microeconomic principles explain an optimal genome size in bacteria. TRENDS GENET , 21 (1) 21 - 25. 10.1016/j.tig.2004.11.014.

Ranea, JAG; Morilla, I; Lees, JG; Reid, AJ; Yeats, C; Clegg, AB; ... Orengo, C; + view all (2010) Finding the "Dark Matter'' in Human and Yeast Protein Network Prediction and Modelling. PLOS COMPUT BIOL , 6 (9) , Article e1000945. 10.1371/journal.pcbi.1000945. Green and gold open access
file

Ranea, JAG; Sillero, A; Thornton, JM; Orengo, CA; (2006) Protein superfamily evolution and the last universal common ancestor (LUCA). J MOL EVOL , 63 (4) 513 - 525. 10.1007/s00239-005-0289-7.

Ranea, JAG; Yeats, C; Grant, A; Orengo, CA; (2007) Predicting protein function with hierarchical phylogenetic profiles: The Gene3D phylo-tuner method applied to eukaryotic Genomes. PLoS Computational Biology , 3 (11) , Article e237. 10.1371/journal.pcbi.0030237. Green and gold open access
file

Redfern, OC; Dessailly, B; Orengo, CA; (2008) Exploring the structure and function paradigm. CURR OPIN STRUC BIOL , 18 (3) 394 - 402. 10.1016/j.sbi.2008.05.007. Gold open access

Redfern, OC; Dessailly, BH; Dallman, TJ; Sillitoe, I; Orengo, CA; (2009) FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies. PLOS COMPUT BIOL , 5 (8) , Article e1000485. 10.1371/journal.pcbi.1000485. Green and gold open access
file

Redfern, OC; Harrison, A; Dallman, T; Pearl, FMG; Orengo, CA; (2007) CATHEDRAL: A fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures. PLOS COMPUT BIOL , 3 (11) , Article e232. 10.1371/journal.pcbi.0030232. Green and gold open access
file

Reeves, GA; Dallman, TJ; Redfern, OC; Akpor, A; Orengo, CA; (2006) Structural diversity of domain superfamilies in the CATH database. J MOL BIOL , 360 (3) 725 - 741. 10.1016/j.jmb.2006.05.035.

Reffern, O; Grant, A; Maibaum, M; Orengo, C; (2005) Survey of current protein family databases and their application in comparative, structural and functional genomics. JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES , 815 (1-2) 97 - 107. 10.1016/j.jchromb.2004.11.010.

Reid, AJ; Ranea, JAG; Clegg, AB; Orengo, CA; (2010) CODA: Accurate Detection of Functional Associations between Proteins in Eukaryotic Genomes Using Domain Fusion. PLOS ONE , 5 (6) , Article e10908. 10.1371/journal.pone.0010908. Green and gold open access
file

Reid, AJ; Ranea, JAG; Orengo, CA; (2010) Comparative evolutionary analysis of protein complexes in E. coli and yeast. BMC GENOMICS , 11 , Article 79. 10.1186/1471-2164-11-79. Green and gold open access
file

Reid, AJ; Yeats, C; Orengo, CA; (2007) Methods of remote homology detection can be combined to increase coverage by 10% in the midnight zone. BIOINFORMATICS , 23 (18) 2353 - 2360. 10.1093/bioinformatics/btm355.

Rentzsch, R; Orengo, CA; (2013) Protein function prediction using domain families. BMC Bioinformatics , 14 Suppl 3 S5 - ?. 10.1186/1471-2105-14-S3-S5.

Rentzsch, R; Orengo, CA; (2009) Protein function prediction - the power of multiplicity. TRENDS BIOTECHNOL , 27 (4) 210 - 219. 10.1016/j.tibtech.2009.01.002.

Rojas, AM; Santamaria, A; Malik, R; Jensen, TS; Körner, R; Morilla, I; ... Ranea, JA; + view all (2012) Uncovering the molecular machinery of the human spindle--an integration of wet and dry systems biology. PLoS One , 7 (3) , Article e31813 . 10.1371/journal.pone.0031813. Green and gold open access
file

Salamov, AA; Suwa, M; Orengo, CA; Swindells, MB; (1999) Genome analysis: Assigning protein coding regions to three-dimensional structures. PROTEIN SCI , 8 (4) 771 - 777.

Salamov, AA; Suwa, M; Orengo, CA; Swindells, MB; (1999) Combining sensitive database searches with multiple intermediates to detect distant homologues. PROTEIN ENG , 12 (2) 95 - 100.

Salem, GM; Hutchinson, EG; Orengo, CA; Thornton, JM; (1999) Correlation of observed fold frequency with the occurrence of local structural motifs. J MOL BIOL , 287 (5) 969 - 981.

Shepherd, AJ; Martin, NJ; Johnson, RG; Kellam, P; Orengo, CA; (2002) PFDB: a generic protein family database integrating the CATH domain structure database with sequence based protein family resources. BIOINFORMATICS , 18 (12) 1666 - 1672.

Siepen, JA; Belhajjame, K; Selley, JN; Embury, SM; Paton, NW; Goble, CA; ... Hubbard, SJ; + view all (2008) ISPIDER Central: an integrated database web-server for proteomics. NUCLEIC ACIDS RES , 36 W485 - W490. 10.1093/nar/gkn196. Gold open access

Sillitoe, I; Cuff, AL; Dessailly, BH; Dawson, NL; Furnham, N; Lee, D; ... Orengo, CA; + view all (2013) New functional families (FunFams) in CATH to improve the mapping of conserved functional sites to 3D structures. Nucleic Acids Res , 41 (Database issue) D490 - D498. 10.1093/nar/gks1211. Gold open access

Sillitoe, I; Dibley, M; Bray, J; Addou, S; Orengo, C; (2005) Assessing strategies for improved superfamily recognition. PROTEIN SCI , 14 (7) 1800 - 1810. 10.1110/ps.041056105.

Sillitoe, I; Dibley, M; Bray, J; Addou, S; Orengo, C; (2005) Assessing Strategies For Improved Superfamily Recognition in Genome Annotation. Protein Science , 14 1800 - 1810.

Studer, RA; Christin, PA; Williams, MA; Orengo, CA; (2014) Stability-activity tradeoffs constrain the adaptive evolution of RubisCO. Proc Natl Acad Sci U S A 10.1073/pnas.1310811111.

Studer, RA; Dessailly, BH; Orengo, CA; (2013) Residue mutations and their impact on protein structure and function: detecting beneficial and pathogenic changes. BIOCHEMICAL JOURNAL , 449 581 - 594. 10.1042/8J20121221.

Sula, A; Cole, AR; Yeats, C; Orengo, C; Keep, NH; (2014) Crystal structures of the human Dysferlin inner DysF domain. BMC Struct Biol , 14 (1) 3 - ?. 10.1186/1472-6807-14-3.

Swift, S; Tucker, A; Vinciotti, V; Martin, N; Orengo, C; Liu, XH; Kellam, P; (2004) Consensus clustering and functional interpretation of gene-expression data. GENOME BIOLOGY , 5 , Article R94. 10.1186/gb-2004-5-11-r94. Green and gold open access
file

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Thornton, J; Orengo, CA; Laskowski, RA; Milburn, DR; Porter, C; Todd, A; (2000) Protein folds, functions and evolution. J MED GENET , 37 S31 - S31.

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Todd, AE; Marsden, RL; Thornton, JM; Orengo, CA; (2005) Progress of structural genomics initiatives: An analysis of solved target structures (vol 348, pg 1235, 2005). J MOL BIOL , 353 (3) 760 - 760.

Todd, AE; Marsden, RL; Thornton, JM; Orengo, CA; (2005) Progress of structural genomics initiatives: An analysis of solved target structures. J MOL BIOL , 348 (5) 1235 - 1260. 10.1016/j.jmb.2005.03.037.

Todd, AE; Orengo, CA; Thornton, JM; (2002) Sequence and structural differences between enzyme and nonenzyme homologs. STRUCTURE , 10 (10) 1435 - 1451.

Todd, AE; Orengo, CA; Thornton, JM; (2002) Plasticity of enzyme active sites. TRENDS BIOCHEM SCI , 27 (8) 419 - 426.

Todd, AE; Orengo, CA; Thornton, JM; (2002) Sequence and structural differences between enzyme and non enzyme homologues. Structure , 10 1 - 20.

Todd, AE; Orengo, CA; Thornton, JM; (2001) Evolution of function in protein superfamilies, from a structural perspective. J MOL BIOL , 307 (4) 1113 - 1143. 10.1006/jmbi.2001.4513.

Todd, AE; Orengo, CA; Thornton, JM; (1999) Evolution of protein function, from a structural perspective. CURR OPIN CHEM BIOL , 3 (5) 548 - 556.

Todd, AE; Orengo, CA; Thornton, JM; (1999) DOMPLOT: a program to generate schematic diagrams of the structural domain organization within proteins, annotated by ligand contacts. PROTEIN ENG , 12 (5) 375 - 379.

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Watson, JD; Sanderson, S; EzerskY, A; Savchenk, A; Edwards, A; Orengo, C; ... Thornton, JM; + view all (2007) Towards fully automated structure-based function prediction in structural genomics: A case study. JOURNAL OF MOLECULAR BIOLOGY , 367 (5) 1511 - 1522. 10.1016/j.jmb.2007.01.063.

Watson, JD; Todd, AE; Bray, J; Laskowski, RA; Edwards, A; Joachimiak, A; ... Thornton, JM; + view all (2003) Target selection and determination of function in structural genomics. IUBMB LIFE , 55 (4-5) 249 - 255. 10.1080/1521654031000123385.

Yeats, C; Dessailly, BH; Glass, EM; Fremont, DH; Orengo, CA; (2014) Target selection for structural genomics of infectious diseases. Methods Mol Biol , 1140 35 - 51. 10.1007/978-1-4939-0354-2_3.

Yeats, C; Lees, J; Carter, P; Sillitoe, I; Orengo, C; (2011) The Gene3D Web Services: a platform for identifying, annotating and comparing structural domains in protein sequences. Nucleic Acids Research , 39 W546-W550. 10.1093/nar/gkr438. Green and gold open access
file

Yeats, C; Lees, J; Reid, A; Kellam, P; Liu, X; Orengo, C; Martin, N; (2008) Gene3D: Comprehensive structural and functional annotation of genomes. Nucleic Acids Research , 36 (SUPPL. 1) D414- D418. 10.1093/nar/gkm1019. Green and gold open access
file

Yeats, C; Lees, J; Reid, A; Kellam, P; Martin, N; Liu, X; Orengo, C; (2008) Gene3D: comprehensive structural and functional annotation of genomes. NUCLEIC ACIDS RES , 36 D414 - D418. 10.1093/nar/gkm1019. Gold open access

Yeats, C; Maibaum, M; Marsden, R; Dibley, M; Lee, D; Addou, S; Orengo, CA; (2006) Gene3D: modelling protein structure, function and evolution. NUCLEIC ACIDS RES , 34 D281 - D284. 10.1093/nar/gkj057. Gold open access

Yeats, C; Redfern, O; ORENGO, C; (2010) A fast and automated solution for accurately resolving protein domain architectures. Bioinformatics , 26 (6) 745 - 751. 10.1093/bioinformatics/btq034.

Yeats, C; Redfern, OC; Orengo, C; (2010) A fast and automated solution for accurately resolving protein domain architectures. BIOINFORMATICS , 26 (6) 745 - 751. 10.1093/bioinformatics/btq034.

Yeats, C; Redfern, OC; Orengo, C; (2010) A fast and automated solution for accurately resolving protein domain architectures. Bioinformatics , 26 , Article 6. 10.1093/bioinformatics/btq034%20%5Bdoi%5D.

Yu, C; Sonnen, AFP; George, R; Dessailly, BH; Stagg, LJ; Evans, EJ; ... Davis, SJ; + view all (2011) Rigid-body Ligand Recognition Drives Cytotoxic T-lymphocyte Antigen 4 (CTLA-4) Receptor Triggering. J BIOL CHEM , 286 (8) 6685 - 6696. 10.1074/jbc.M110.182394. Gold open access

Book

Pearl, FMG; Orengo, CA; Thornton, JM; (1999) Protein Structure Classification. Macmillan Reference Ltd

Thornton, JM; Mitchie, AD; Hutchinson, EG; Laskowski, RA; Orengo, CA; (1999) Software Tools for Protein Structure Analysis and Fold Classification. (Vol.7). Open University Press: Oxford.

Book chapter

Dessailly, B; ORENGO, C; (2009) Functional Diversity WIthin Folds and Superfamilies. In: From Protein Structure To Function with Bioinformatics. Springer-London

Marsden, RL; Orengo, CA; (2008) Target selection for structural genomics: an overview. In: UNSPECIFIED (3 - 25).

Martin, ACR; (2002) Comparative Modelling. In: Orengo, CA and Jones, DT and Thornton, JM, (eds.) Bioinformatics: Genes, Proteins and Computers. Bios Scientific Publishers: Oxford.

Martin, ACR; (2002) Internet Technologies for Bioinformatics. In: Orengo, CA and Jones, DT and Thornton, JM, (eds.) UNSPECIFIED Bios Scientific Publishers: Oxford.

Orengo, C; Thornton, JM; (2001) Protein Fold Classification. In: Rossman, MG and Arnold, E, (eds.) Tables of Macromolecular Crystallography. Kluwer Academic Publishers: Dordrecht.

Orengo, CA; (2003) Protein Structure Comparison. In: Orengo, CA and Jones, DT and Thornton, JM and eds,, (eds.) Bioinformatics: Sequence, Structure, Function. BIOS Publishing

Orengo, CA; (2002) Protein Structure Comparison. In: Orengo, CA and Jones, DT and Thornton, JM, (eds.) Bioinformatics: Sequence, Structure, Function. BIOS Publishing

Orengo, CA; (2002) Sequence Comparison Methods. In: Orengo, CA and Jones, DT and Thornton, JM, (eds.) Bioinformatics. BIOS Publishing

Orengo, CA; Pearl, FM; Thornton, JM; (2003) The CATH domain structure database. In: Bourne, PE, (ed.) Structural Bioinformatics. (249 - 271). Wiley Publishing

Orengo, CA; Pearl, FM; Thornton, JM; (2003) The CATH domain structure database. In: UNSPECIFIED (249 - 271).

Redfern, O; Orengo, CA; (2004) Structural Comparison of Proteins. In: Hancock, JM and Zvelebil, MJ, (eds.) Dictionary of Bioinformatics and Computational Biology. Wiley

Proceedings paper

Diboun, I; Harrison, AP; Jones, NG; McMahon, SB; Orengo, CA; Koltzenburg, M; (2004) "Amplification of RNA results in predictable changes in gene representation in microarray studies". In: Society for Neuroscience 34th Annual Meeting (Neuroscience 2004), San Diego, USA.

Hirsch, M; Tucker, A; Swift, S; Martin, N; Orengo, C; Kellam, P; Liu, X; (2006) Improved robustness in time series analysis of gene expression data by polynomial model based clustering. In: COMPUTATIONAL LIFE SCIENCES II, PROCEEDINGS. (pp. 1 - 10).

Kellam, P; Liu, X; Martin, N; Orengo, C; Swift, S; Tucker, A; (2001) UNSPECIFIED In: (Proceedings) A Framework for Modelling Short, High Dimensional Multivirate Time Series: Preliminary Results in Virus Gene Expression Data, LNCS 2189. (pp. 218 - 227). Springer-Verlag: Berlin.

Maibaum, M; Zamboulis, L; Rimon, G; Orengo, C; Martin, N; Poulovassilis, A; (2005) Cluster based integration of heterogeneous biological databases using the AutoMed toolkit. In: DATA INTEGRATION IN THE LIFE SCIENCES, PROCEEDINGS. (pp. 191 - 207).

Orengo, CA; Bray, JE; Buchan, DWA; Harrison, A; Lee, D; Pearl, FMG; ... Thornton, JM; + view all (2002) The CATH protein family database: A resource for structural and functional annotation of genomes. In: PROTEOMICS. (pp. 11 - 21). WILEY-V C H VERLAG GMBH

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