Biological network topology features predict gene dependencies in cancer cell-lines. Benstead-Hume G, Wooller SK, Renaut J, Woodbine L, Dias S, Carr AM, Pearl FMG. https://doi.org/10.1093/bioadv/vbac084

A combined bioinformatics and LC-MS-based approach for the development and benchmarking of a comprehensive database of Lymnaea CNS proteins.

Wooller S, Anagnostopoulou A, Kuropka B, Crossley M, Benjamin PR, Pearl F, Kemenes I, Kemenes G, Eravci M. J Exp Biol. 2022 Apr 1;225(7):jeb243753. doi: 10.1242/jeb.243753. Epub 2022 Apr 12. PMID: 35403696

 

Aneuploidy tolerance caused by BRG1 loss allows chromosome gains and recovery of fitness. Schiavoni F, Zuazua-Villar P, Roumeliotis TI, Benstead-Hume G, Pardo M, Pearl FMG, Choudhary JS, Downs JA. Nat Commun. 2022 Apr 1;13(1):1731. doi: 10.1038/s41467-022-29420-3. PMID: 35365638

 

Uncovering an allosteric mode of action for a selective inhibitor of human Bloom syndrome protein. Chen X, Ali YI, Fisher CE, Arribas-Bosacoma R, Rajasekaran MB, Williams G, Walker S, Booth JR, Hudson JJ, Roe SM, Pearl LH, Ward SE, Pearl FM, Oliver AW. Elife. 2021 Mar 1;10:e65339. doi: 10.7554/eLife.65339. PMID: 33647232 .

 

PIK3Cδ expression by fibroblasts promotes triple-negative breast cancer progression.Gagliano T, Shah K, Gargani S, Lao L, Alsaleem M, Chen J, Ntafis V, Huang P, Ditsiou A, Vella V, Yadav K, Bienkowska K, Bresciani G, Kang K, Li L, Carter P, Benstead-Hume G, O'Hanlon T, Dean M, Pearl FM, Lee SC, Rakha EA, Green AR, Kontoyiannis DL, Song E, Stebbing J, Giamas G. J Clin Invest. 2020 Jun 1;130(6):3188-3204. doi: 10.1172/JCI128313. PMID: 32125284

Defining Signatures of Arm-Wise Copy Number Change and Their Associated Drivers in Kidney Cancers. Benstead-Hume G, Wooller SK, Downs JA, Pearl FMG. Int J Mol Sci. 2019 Nov 16;20(22):5762. doi: 10.3390/ijms20225762. PMID: 31744086

Identifying the Impact of Inframe Insertions and Deletions on Protein Function in Cancer. Baeissa HM, Pearl FMG. J Comput Biol. 2020 May;27(5):786-795. doi: 10.1089/cmb.2018.0192. Epub 2019 Aug 28. PMID: 31460787

 

Cell-derived extracellular vesicles can be used as a biomarker reservoir for glioblastoma tumor subtyping. Lane R, Simon T, Vintu M, Solkin B, Koch B, Stewart N, Benstead-Hume G, Pearl FMG, Critchley G, Stebbing J, Giamas G. Commun Biol. 2019 Aug 19;2:315. doi: 10.1038/s42003-019-0560-x. eCollection 2019. PMID: 31453379 .

 

Predicting synthetic lethal interactions using conserved patterns in protein interaction networks. Benstead-Hume G, Chen X, Hopkins SR, Lane KA, Downs JA, Pearl FMG. PLoS Comput Biol. 2019 Apr 17;15(4):e1006888. doi: 10.1371/journal.pcbi.1006888. eCollection 2019 Apr. PMID: 30995217

Repression of Transcription at DNA Breaks Requires Cohesin throughout Interphase and Prevents Genome Instability.

Meisenberg C, Pinder SI, Hopkins SR, Wooller SK, Benstead-Hume G, Pearl FMG, Jeggo PA, Downs JA. Mol Cell. 2019 Jan 17;73(2):212-223.e7. doi: 10.1016/j.molcel.2018.11.001. Epub 2018 Dec 13. PMID: 30554942

 

Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework.

Glusman G, Rose PW, Prlić A, Dougherty J, Duarte JM, Hoffman AS, Barton GJ, Bendixen E, Bergquist T, Bock C, Brunk E, Buljan M, Burley SK, Cai B, Carter H, Gao J, Godzik A, Heuer M, Hicks M, Hrabe T, Karchin R, Leman JK, Lane L, Masica DL, Mooney SD, Moult J, Omenn GS, Pearl F, Pejaver V, Reynolds SM, Rokem A, Schwede T, Song S, Tilgner H, Valasatava Y, Zhang Y, Deutsch EW. Genome Med. 2017 Dec 18;9(1):113. doi: 10.1186/s13073-017-0509-y. PMID: 29254494

 

Computational Approaches to Identify Genetic Interactions for Cancer Therapeutics.

Benstead-Hume G, Wooller SK, Pearl FMG. J Integr Bioinform. 2017 Sep 23;14(3):20170027. doi: 10.1515/jib-2017-0027. PMID: 28941356 

 

Bioinformatics in translational drug discovery.

Wooller SK, Benstead-Hume G, Chen X, Ali Y, Pearl FMG. Biosci Rep. 2017 Jul 7;37(4):BSR20160180. doi: 10.1042/BSR20160180. Print 2017 Aug 31. PMID: 28487472

'Big data' approaches for novel anti-cancer drug discovery.

Benstead-Hume G, Wooller SK, Pearl FMG. Expert Opin Drug Discov. 2017 Jun;12(6):599-609. doi: 10.1080/17460441.2017.1319356. Epub 2017 May 2. PMID: 28462602

 

Identification and analysis of mutational hotspots in oncogenes and tumour suppressors.

Baeissa H, Benstead-Hume G, Richardson CJ, Pearl FMG. Oncotarget. 2017 Mar 28;8(13):21290-21304. doi: 10.18632/oncotarget.15514. PMID: 28423505

 

A first generation inhibitor of human Greatwall kinase, enabled by structural and functional characterisation of a minimal kinase domain construct.

Ocasio CA, Rajasekaran MB, Walker S, Le Grand D, Spencer J, Pearl FM, Ward SE, Savic V, Pearl LH, Hochegger H, Oliver AW. Oncotarget. 2016 Nov 1;7(44):71182-71197. doi: 10.18632/oncotarget.11511. PMID: 27563826

Mutational patterns in oncogenes and tumour suppressors.

Baeissa HM, Benstead-Hume G, Richardson CJ, Pearl FM. Biochem Soc Trans. 2016 Jun 15;44(3):925-31. doi: 10.1042/BST20160001. PMID: 27284061

 

Mouse and Human Genetic Analyses Associate Kalirin with Ventral Striatal Activation during Impulsivity and with Alcohol Misuse.

Peña-Oliver Y, Carvalho FM, Sanchez-Roige S, Quinlan EB, Jia T, Walker-Tilley T, Rulten SL, Pearl FM, Banaschewski T, Barker GJ, Bokde AL, Büchel C, Conrod PJ, Flor H, Gallinat J, Garavan H, Heinz A, Gowland P, Paillere Martinot ML, Paus T, Rietschel M, Robbins TW, Smolka MN, Schumann G, Stephens DN; IMAGEN Consortium. Front Genet. 2016 Apr 7;7:52. doi: 10.3389/fgene.2016.00052. eCollection 2016. PMID: 27092175 Free PMC article.

 

Therapeutic opportunities within the DNA damage response.

Pearl LH, Schierz AC, Ward SE, Al-Lazikani B, Pearl FM. Nat Rev Cancer. 2015 Mar;15(3):166-80. doi: 10.1038/nrc3891. PMID: 25709118 Free article. Review.

 

Definition of a Family of Tissue-Protective Cytokines Using Functional Cluster Analysis: A Proof-of-Concept Study.

Mengozzi M, Ermilov P, Annenkov A, Ghezzi P, Pearl F. Front Immunol. 2014 Mar 17;5:115. doi: 10.3389/fimmu.2014.00115. eCollection 2014. PMID: 24672526 

 

Deriving a mutation index of carcinogenicity using protein structure and protein interfaces.

Espinosa O, Mitsopoulos K, Hakas J, Pearl F, Zvelebil M. PLoS One. 2014 Jan 15;9(1):e84598. doi: 10.1371/journal.pone.0084598. eCollection 2014. PMID: 24454733 

Conserved regulation of cardiac calcium uptake by peptides encoded in small open reading frames.

Magny EG, Pueyo JI, Pearl FM, Cespedes MA, Niven JE, Bishop SA, Couso JP. Science. 2013 Sep 6;341(6150):1116-20. doi: 10.1126/science.1238802. Epub 2013 Aug 22

MoKCa database--mutations of kinases in cancer.

Richardson CJ, Gao Q, Mitsopoulous C, Zvelebil M, Pearl LH, Pearl FM. Nucleic Acids Res. 2009 Jan;37(Database issue):D824-31. doi: 10.1093/nar/gkn832. Epub 2008 Nov 5. PMID: 18986996

 

The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space.

Cuff A, Redfern OC, Greene L, Sillitoe I, Lewis T, Dibley M, Reid A, Pearl F, Dallman T, Todd A, Garratt R, Thornton J, Orengo C. Structure. 2009 Aug 12;17(8):1051-62. doi: 10.1016/j.str.2009.06.015. PMID: 19679085 Free PMC article.

 

CATHEDRAL: a fast and effective algorithm to predict folds and domain boundaries from multidomain protein structures.

Redfern OC, Harrison A, Dallman T, Pearl FM, Orengo CA. PLoS Comput Biol. 2007 Nov;3(11):e232. doi: 10.1371/journal.pcbi.0030232. PMID: 18052539

Orengo CA, Pearl FM, Thornton JM. The CATH domain structure database. Methods Biochem Anal. 2003 44:249-71.

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. doi: 10.1093/nar/gkl959. Epub 2006 Nov 29. PMID: 17135200

The CATH Domain Structure Database and related resources Gene3D and DHS provide comprehensive domain family information for genome analysis.

Pearl F, Todd A, Sillitoe I, Dibley M, Redfern O, Lewis T, Bennett C, Marsden R, Grant A, Lee D, Akpor A, Maibaum M, Harrison A, Dallman T, Reeves G, Diboun I, Addou S, Lise S, Johnston C, Sillero A, Thornton J, Orengo C. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D247-51. doi: 10.1093/nar/gki024. PMID: 15608188

Pearl FM, Bennett CF, Bray JE, Harrison AP, Martin N, Shepherd A, Sillitoe I, Thornton J, Orengo CA.The CATH database: an extended protein family resource for structural and functional genomics. Nucleic Acids Res. 2003 31:452-5.

Recognizing the fold of a protein structure.

Harrison A, Pearl F, Sillitoe I, Slidel T, Mott R, Thornton J, Orengo C. Bioinformatics. 2003 Sep 22;19(14):1748-59. doi: 10.1093/bioinformatics/btg240. PMID: 14512345

 

Gene3D: structural assignments for the biologist and bioinformaticist alike.

Buchan DW, Rison SC, Bray JE, Lee D, Pearl F, Thornton JM, Orengo CA. Nucleic Acids Res. 2003 Jan 1;31(1):469-73. doi: 10.1093/nar/gkg051. PMID: 12520054 Free PMC article.

Quantifying the similarities within fold space.

Harrison A, Pearl F, Mott R, Thornton J, Orengo C. J Mol Biol. 2002 Nov 8;323(5):909-26. doi: 10.1016/s0022-2836(02)00992-0. PMID: 12417203

Gene3D: structural assignment for whole genes and genomes using the CATH domain structure database.

Buchan DW, Shepherd AJ, Lee D, Pearl FM, Rison SC, Thornton JM, Orengo CA. Genome Res. 2002 Mar;12(3):503-14. doi: 10.1101/gr.213802. PMID: 11875040 Free PMC article.

 

The CATH extended protein-family database: providing structural annotations for genome sequences.

Pearl FM, Lee D, Bray JE, Buchan DW, Shepherd AJ, Orengo CA. Protein Sci. 2002 Feb;11(2):233-44. doi: 10.1110/ps.16802. PMID: 11790833 Free PMC article.

 

The CATH protein family database: a resource for structural and functional annotation of genomes.

Orengo CA, Bray JE, Buchan DW, Harrison A, Lee D, Pearl FM, Sillitoe I, Todd AE, Thornton JM. Proteomics. 2002 Jan;2(1):11-21. PMID: 11788987

CATH Publications

Orengo CA, Sillitoe I, Reeves G, Pearl FM.Review: What Can Structural Classifications Reveal about Protein Evolution? J Struct Biol, 2001 134:145-65.

Pearl FMG, Martin NM, Bray JE, Buchan DWA, Harrison AP, Lee D, Reeves GA, Shepherd AJ, Sillitoe I, Todd AE, Thornton JM, Orengo CA : A rapid classifcation protocol for the CATH domain database to support structural genomics Nuc Acids Res, 2001 29: 223-227.

Alba MM, Lee D, Pearl FMG, Shepherd AJ, Martin NM, Orengo CA, Kellum P : VIDA: a virus database system for the organization of virus genome open reading frames Nuc Acids Res, 2001 29: 133-136.

Pearl FMG, Todd AE, Bray JE, Martin ACR, Salamov AA, Suwa M, Swindells MB, Thornton JM, Orengo CA (2000): Using the CATH domain database to assign structures and function to the genome sequences. Biochem Soc Trans., 2000 28: 269-275.

Pearl FMG, Lee D, Bray JE, Sillitoe I, Todd AE, Harrison AP, Thornton JM, Orengo CA: Assigning genomic sequences to CATH. Nuc Acids Res, 2000, 28: 277-282.

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

Thornton JM, Orengo CA, Todd AE, Pearl FMG : Protein folds, functions and evolution. J Mol Biol, 1999, 293: 333-342.

Orengo CA, Pearl FMG, Bray JE, Todd AE, Martin AC, LoConte L, Thornton JM : The CATH database provides insights into protein structure/function relationships. Nuc Acids Res, 1999 27: 275-279.

 

BOOK CHAPTERS

Pearl FMG, Thornton JM, Orengo CA (2000): Protein structure classification. Encyclopaedia of life sciences, Macmillan Reference Ltd.

Pearl F & Orengo C (2002): Protein structure classifications. In Bioinformatics: Genes, Proteins & Computers (Orengo CA, Jones DT and Thornton JM (Eds).BIOS.

Orengo, C.A.& Pearl, F. (2003). The CATH Database. in Bourne, P. (ed.) . Structural Bioinformatics. Wiley Publishing.

Pearl F, Bennett C Orengo CA (2004) The CATH database. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics (GGPB). Wiley Publishing.

Pearl FMG, Thornton JM, Orengo CA (2007): Protein structure classification. Encyclopaedia of life sciences, Macmillan Reference Ltd.

Orengo, C.A.& Pearl, F. (2009). The CATH Database. in Bourne, P. (ed.) Structural Bioinformatics 2^nd Edition. Wiley Publishing.