Publications

Ogo A Ogo, John Tyson, Simon J Cockell, Alison Howard, Ruth A Valentine and Dianne Ford (2015) The zinc finger protein ZNF658 regulates the transcription of genes involved in zinc homeostasis and affects ribosome biogenesis through the zinc transcriptional regulatory element (ZTRE). Mol Cell Biol Jan 12 2015 doi: 10.1128/MCB.01298-14

Iannetti A, Ledoux AC, Tudhope SJ, Sellier H, Zhao B, Mowla S, Moore A, Hummerich H, Gewurz BE, Cockell SJ, Jat PS, Willmore E and Perkins ND (2014) Regulation of p53 and Rb Links the Alternative NF-κB Pathway to EZH2 Expression and Cell Senescence. PLoS Genet 10(9): e1004642. doi: 10.1371/journal.pgen.1004642

Keith Flanagan, Simon Cockell, Colin Harwood, Jennifer Hallinan, Sirintra Nakjang, Beth Lawry, Anil Wipat (2014)  A distributed computational search strategy for the identification of diagnostics targets: Application to finding aptamer targets for methicillin-resistant staphylococci. Journal of Integrative Bioinformatics – JIB (ISSN 1613-4516), 11(2), 2014. doi: 10.2390/biecoll-jib-2014-242

Simon Cockell, Matthew Bashton, and Colin S. Gillespie Chapter 17. Bioconductor Tools for Microarray Data Analysis in Microarray Image and Data Analysis. CRC Press Mar 2014, 459-479 ISBN: 978-1-4665-8682-6

Andreas Werner, Simon J. Cockell, Jane Falconer, Mark Carlile, Sammer Alnumeir and John Robinson (2014) Contribution of natural antisense transcription to an endogenous siRNA signature in human cells. BMC Genomics 15:19 first published online January 13th 2014 doi:10.1186/1471-2164-15-19

Philip M. E. Probert, Git W. Chung, Simon J. Cockell, Loranne Agius, Pasquale Mosesso, Steven A. White, Fiona Oakley, Colin D. A. Brown, and Matthew C. Wright (2013) Utility of B-13 Progenitor-Derived Hepatocytes in Hepatotoxicity and Genotoxicity Studies. Toxicol. Sci. first published online November 14, 2013 doi:10.1093/toxsci/kft258

V Nesbitt, R Pitceathly, S Cockell, J Poulton, S Rahman, M Hanna, R Taylor, P Chinnery, D Turnbull, R McFarland (2013) The medical research council neuromuscular centre for translational research mitochondrial disease patient cohort study uk: from conceptualisation to utilisation. J. Neurol. Neurosurg. Psychiatry 84(11):e2. doi: 10.1136/jnnp-2013-306573.69

Phillip Lord, Simon Cockell and Robert Stevens (2012) Three Steps to Heaven: Semantic Publishing in a Real-World Workflow. Future Internet 4(4): 1004-1015. doi:10.3390/fi4041004

Ka Cheong Lee, Kay Padget, Hannah Curtis, Ian G. Cowell, Davide Moiani, Zbyslaw Sondka, Nicholas J. Morris, Graham H. Jackson, Simon J. Cockell, John A. Tainer, and Caroline A. Austin (2012) MRE11 facilitates the removal of human topoisomerase II complexes from genomic DNA. Biology Open; Advance Online Publication July 16, 2012. doi: 10.1242/bio.20121834

Jochen Weile, Katherine James, Jennifer Hallinan, Simon J Cockell, Phillip Lord, Anil Wipat and Darren Wilkinson (2012) Bayesian integration of networks without gold standards. Bioinformatics 28(11) 1495-1500. doi: 10.1093/bioinformatics/bts154.

Laurence D Parnell, Pierre Lindenbaum, Khader Shameer, Giovanni Marco Dall’Olio, Daniel C. Swan, Lars Juhl Jensen, Simon J. Cockell, Brent S Pedersen, Mary E. Mangan, Christopher A. Miller, Istvan Albert (2011) BioStar: An Online Question & Answer Resource for the Bioinformatics Community. PLoS Comput. Biol. 7(10): e1002216. doi:10.1371/journal.pcbi.1002216.

Stadler L, Hoffmann T, Tomlinson D, Song Q, Lee T, Busby M, Nyathi Y, Gendra E, Tiede C, Flanagan K, Cockell SJ, Wipat A, Harwood C, Wagner S, Knowles M, Davis J, Ko Ferrigno P (2011) Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and Applications of the SQT variant Protein Engineering Design and Selection 24(9): 751-63 doi: 10.1093/protein/gzr019.

Weile J, Pocock M, Cockell SJ, Lord P, Dewar JM, Holstein E, Wilkinson D, Lydall D, Hallinan J, Wipat A (2011) Customisable views on semantically integrated networks for systems biology Bioinformatics first published online March 16, 2011 doi:10.1093/bioinformatics/btr134 PubMed

Christine Hoogland, Martin O’Gorman, Philippe Bogard, Frank Gibson, Matthias Berth, Simon J Cockell, Andreas Ekefjärd, Ola Forsstrom-Olsson, Anna Kapferer, Mattias Nilsson, Salvador Martínez-Bartolomé, Juan Pablo Albar, Sira Echevarría-Zomeño, Montserrat Martínez-Gomariz, Johann Joets, Pierre-Alain Binz, Chris F Taylor, Andrew Dowsey, Andrew R Jones. (2010) Guidelines for reporting the use of gel image informatics in proteomics. Nature Biotechnology 28:655-6 PubMed

Kaveh Emami, Nicholas J. Morris, Simon J. Cockell, Gabriela Golebiowska, Qing-Yao Shu, Angharad M.R. Gatehouse (2010) Changes in Protein Expression Profiles Between a Low Phytic Acid Rice (Oryza sativa L. ssp. japonica) Line and its Parental Line: A Proteomic and Bioinformatic Approach. Journal of Agricultural and Food Chemistry 58(11):6912-22 PubMed

Simon J Cockell, Jochen Weile, Phillip Lord, Claire Wipat, Dmytro Andriychenko, Matthew Pocock, Darren Wilkinson, Malcolm Young and Anil Wipat (2010) An integrated dataset for in silico drug discovery. Journal of Integrative Bioinformatics 7(3):116. PubMed

S.J. Cockell, B. Oliva, and R. M. Jackson. (2007)  Evaluating in silico predictions of protein-protein interactions using Comparative Docking Bioinformatics 23, 573-581  PubMed

Conference papers:

A CD4+T-Cell Gene Expression Signature Predicts Drug Survival On Methotrexate Monotherapy in Early Rheumatoid Arthritis. (Pratt AG, Brown PM, Cockell SJ, Wilson G, Isaacs JD) – Annual Scientific Meeting of the American College of Rheumatology (ACR) (November 9th-14th 2012)

The Medical Research Council Neuromuscular Centre for Translational Research Mitochondrial Disease Patient Cohort Study UK: from conceptualisation to utilisation (Nesbitt V, Pitceathly R, Cockell S, Poulton J, Rahman S, Hanna M, Turnbull D, McFarland R) – United Kingdom Neuromuscular Translational Research Conference (March 22nd-23rd 2012)

Three Steps to Heaven (Phillip Lord, Simon Cockell and Robert Stevens) – Sepublica Workshop at 9th Extended Semantic Web Conference 2012 (May 27th-31st, 2012) – awarded ‘best paper’.