Simon Cockell

Simon Cockell has been the manager of the Bioinformatics Support Unit since July 2011. During this time, the importance of high-throughput approaches in biology has increased exponentially, and Simon has overseen a BSU that has quadrupled in size in order to meet these increasing demands.

Simon trained as a molecular biologist, studying signal transduction regulation in Drosophila melanogaster development during his Ph.D. at Leicester University. He made the move into Bioinformatics in 2004 by undertaking a Masters by Research (M.Res.) in Bioinformatics and Computational Biology at the University of Leeds, supported by the BBSRC. Graduating top of his class, with distinction, he moved to Newcastle University to join the nascent Bioinformatics Support Unit in September 2005. His main areas of research interest are:

  • Analysis of transcriptomics data
    • Methods for microarray analysis and data mining
    • Analysis of transcript-level RNA Sequencing data
  • High-Throughput Sequencing data analysis
    • RNA-Seq
    • ChIP-Seq
    • and more...
  • Integration of biological data
    • In support of the above
    • Also with a focus on drug repositioning

To contact Simon, email simon.cockell@newcastle.ac.uk.

###Publications

Donadio, Janaina L. S., Marcelo M. Rogero, Simon Cockell, John Hesketh, and Silvia M. F. Cozzolino. 2017. “Influence of Genetic Variations in Selenoprotein Genes on the Pattern of Gene Expression After Supplementation with Brazil Nuts.” Nutrients 9 (7). doi:10.3390/nu9070739.

Elder, A, S Bomken, I Wilson, H J Blair, S Cockell, F Ponthan, K Dormon, D Pal, O Heidenreich, and J Vormoor. 2017. “Abundant and Equipotent Founder Cells Establish and Maintain Acute Lymphoblastic Leukaemia.” Leukemia, May. doi:10.1038/leu.2017.140.

James, Katherine, Simon J. Cockell, and Nikolay Zenkin. 2017. “Deep Sequencing Approaches for the Analysis of Prokaryotic Transcriptional Boundaries and Dynamics.” Methods (San Diego, Calif.), April. doi:10.1016/j.ymeth.2017.04.016.

James, Katherine, Pamela Gamba, Simon J. Cockell, and Nikolay Zenkin. 2016. “Misincorporation by RNA Polymerase Is a Major Source of Transcription Pausing in Vivo.” Nucleic Acids Research, October, gkw969. doi:10.1093/nar/gkw969.

Méplan, Catherine, Ian T. Johnson, Abigael C. J. Polley, Simon Cockell, David M. Bradburn, Daniel M. Commane, Ramesh P. Arasaradnam, Francis Mulholland, Anze Zupanic, John C. Mathers, and John Hesketh. 2016. “Transcriptomics and Proteomics Show That Selenium Affects Inflammation, Cytoskeleton, and Cancer Pathways in Human Rectal Biopsies.” FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology, April. doi:10.1096/fj.201600251R.

Moles, A., J. A. Butterworth, A. Sanchez, J. E. Hunter, J. Leslie, H. Sellier, D. Tiniakos, S. J. Cockell, D. A. Mann, F. Oakley, and N. D. Perkins. 2016. “A RelA(P65) Thr505 Phospho-Site Mutation Reveals an Important Mechanism Regulating NF-ΚB-Dependent Liver Regeneration and Cancer.” Oncogene, February. doi:10.1038/onc.2015.526.

Hardyman, Joy, John Tyson, Kelly Jackson, Christine Aldridge, Simon Cockell, Luisa Wakeling, Ruth A. Valentine, and Dianne Ford. 2016. “Zinc Sensing by Metal-Responsive Transcription Factor 1 (MTF1) Controls Metallothionein and ZnT1 Expression to Buffer the Sensitivity of the Transcriptome Response to Zinc.” Metallomics, January. doi:10.1039/C5MT00305A.

Mullen, Joseph, Simon J. Cockell, Hannah Tipney, Peter M. Woollard, and Anil Wipat. 2016. “Mining Integrated Semantic Networks for Drug Repositioning Opportunities.” PeerJ 4 (January): e1558. doi:10.7717/peerj.1558.

James, Katherine, Shereen Al-Ali, Jessica Tarn, Simon J. Cockell, Colin S. Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin T. Pease, Paul Emery, Peter Lanyon, John A. Hunter, Monica Gupta, Michele Bombardieri, Nurhan Sutcliffe, Costantino Pitzalis, John McLaren, Annie Cooper, Marian Regan, Ian Giles, David Isenberg, Vadivelu Saravanan, David Coady, Bhaskar Dasgupta, Neil McHugh, Steven Young-Min, Robert Moots, Nagui Gendi, Mohammed Akil, Bridget Griffiths, UK Primary Sjögren’s Syndrome registry, Anil Wipat, Julia Newton, David E. Jones, John Isaacs, Jennifer Hallinan, and Wan-Fai Ng. 2015. “A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome.” PloS One 10 (12): e0143970. doi:10.1371/journal.pone.0143970.

Hunter, J. E., J. A. Butterworth, B. Zhao, H. Sellier, K. J. Campbell, H. D. Thomas, C. M. Bacon, S. J. Cockell, B. E. Gewurz, and N. D. Perkins. 2015. “The NF-ΚB Subunit c-Rel Regulates Bach2 Tumour Suppressor Expression in B-Cell Lymphoma.” Oncogene, November. doi:10.1038/onc.2015.399.

Manville, Catriona M., Kayleigh Smith, Zbyslaw Sondka, Holly Rance, Simon Cockell, Ian G. Cowell, Ka Cheong Lee, Nicholas J. Morris, Kay Padget, Graham H. Jackson, and Caroline A. Austin. 2015. “Genome-Wide ChIP-Seq Analysis of Human TOP2B Occupancy in MCF7 Breast Cancer Epithelial Cells.” Biology Open, October, bio.014308. doi:10.1242/bio.014308.

Dubarry, Marion, Conor Lawless, A. Peter Banks, Simon Cockell, and David Lydall. 2015. “Genetic Networks Required to Coordinate Chromosome Replication by DNA Polymerases Α, Δ, and Ε in Saccharomyces Cerevisiae.” G3: GenesGenomesGenetics, August, g3.115.021493. doi:10.1534/g3.115.021493.

Gabriel, Alem S., Fadhel M. Lafta, Edward C. Schwalbe, Sirintra Nakjang, Simon J. Cockell, Alice Iliasova, Amir Enshaei, Claire Schwab, Vikki Rand, Steven C. Clifford, Sally E. Kinsey, Chris D. Mitchell, Ajay Vora, Christine J. Harrison, Anthony V. Moorman, and Gordon Strathdee. 2015. “Epigenetic Landscape Correlates with Genetic Subtype but Does Not Predict Outcome in Childhood Acute Lymphoblastic Leukemia.” Epigenetics 10 (8): 717–26. doi:10.1080/15592294.2015.1061174.

Ogo, Ogo A., 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.” Molecular and Cellular Biology 35 (6): 977–87. doi:10.1128/MCB.01298-14.

Wakeling, Luisa A., Laura J. Ions, Suzanne M. Escolme, Simon J. Cockell, Tianhong Su, Madhurima Dey, Emily V. Hampton, Gail Jenkins, Linda J. Wainwright, Jill A. McKay, and Dianne Ford. 2015. “SIRT1 Affects DNA Methylation of Polycomb Group Protein Target Genes, a Hotspot of the Epigenetic Shift Observed in Ageing.” Human Genomics 9: 14. doi:10.1186/s40246-015-0036-0.

Iannetti, Alessio, Adeline C. Ledoux, Susan J. Tudhope, Hélène Sellier, Bo Zhao, Sophia Mowla, Adam Moore, Holger Hummerich, Benjamin E. Gewurz, Simon J. Cockell, Parmjit S. Jat, Elaine Willmore, and Neil D. Perkins. 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.

Simon Cockell, Matthew Bashton, and ColinS Gillespie. 2014. “Bioconductor Tools for Microarray Data Analysis.” In Microarray Image and Data Analysis, 459–79. Digital Imaging and Computer Vision. CRC Press. http://www.crcnetbase.com/doi/abs/10.1201/b16622-18.

Probert, Philip M. E., Git W. Chung, Simon J. Cockell, Loranne Agius, Pasquale Mosesso, Steven A. White, Fiona Oakley, Colin D. A. Brown, and Matthew C. Wright. 2014. “Utility of B-13 Progenitor-Derived Hepatocytes in Hepatotoxicity and Genotoxicity Studies.” Toxicological Sciences 137 (2): 350–70. doi:10.1093/toxsci/kft258.

Werner, Andreas, Simon 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 (1): 19. doi:10.1186/1471-2164-15-19.

Flanagan, Keith, Simon Cockell, Colin Harwood, Jennifer Hallinan, Sirintra Nakjang, Beth Lawry, and 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 11 (2): 242. doi:10.2390/biecoll-jib-2014-242.

Nesbitt, Victoria, Robert Pitceathly, Simon Cockell, Joanna Poulton, Shamima Rahman, Michael Hanna, Robert Taylor, Patrick Chinnery, Douglass Turnbull, and Robert McFarland. 2013. “The Medical Research Council Neuromuscular Centre for Translational Research Mitochondrial Disease Patient Cohort Study Uk: From Conceptualisation to Utilisation.” Journal of Neurology, Neurosurgery & Psychiatry 84 (11): e2–e2. doi:10.1136/jnnp-2013-306573.69.

Lord, Phillip, Simon Cockell, and Robert Stevens. 2012. “Three Steps to Heaven: Semantic Publishing in a Real World Workflow.” Future Internet 4 (4): 1004–15. doi:10.3390/fi4041004.

Lee, Ka Cheong, 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 1 (9): 863–73. doi:10.1242/bio.20121834.

Weile, Jochen, Katherine James, Jennifer Hallinan, Simon J. Cockell, Phillip Lord, Anil Wipat, and Darren J. Wilkinson. 2012. “Bayesian Integration of Networks Without Gold Standards.” Bioinformatics 28 (11): 1495–1500. doi:10.1093/bioinformatics/bts154.

Parnell, Laurence D., 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, and 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, Lukas Kurt Josef, Toni Hoffmann, Darren Charles Tomlinson, Qifeng Song, Tracy Lee, Michael Busby, Yvonne Nyathi, Elisenda Gendra, Christian Tiede, Keith Flanagan, Simon J. Cockell, Anil Wipat, Colin Harwood, Simon D. Wagner, Margaret A. Knowles, Jason J. Davis, Neil Keegan, and Paul Ko Ferrigno. 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, Jochen, Matthew Pocock, Simon J. Cockell, Phillip Lord, James M. Dewar, Eva-Maria Holstein, Darren Wilkinson, David Lydall, Jennifer Hallinan, and Anil Wipat. 2011. “Customizable Views on Semantically Integrated Networks for Systems Biology.” Bioinformatics (Oxford, England) 27 (9): 1299–1306. doi:10.1093/bioinformatics/btr134.

Hoogland, Christine, 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, and Andrew R. Jones. 2010. “Guidelines for Reporting the Use of Gel Image Informatics in Proteomics.” Nature Biotechnology 28 (7): 655–56. doi:10.1038/nbt0710-655.

Emami, Kaveh, Nicholas J. Morris, Simon J. Cockell, Gabriela Golebiowska, Qing-Yao Shu, and 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. doi:10.1021/jf904082b.

Cockell, Simon J., 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). doi:10.2390/biecoll-jib-2010-116.

Cockell, Simon J., Baldo Oliva, and Richard M. Jackson. 2007. “Structure-Based Evaluation of in Silico Predictions of Protein-Protein Interactions Using Comparative Docking.” Bioinformatics (Oxford, England) 23 (5): 573–81. doi:10.1093/bioinformatics/btl661.

###Conferences

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)

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

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)

Andra Waagmeester, Gareth Palidwor, Pawel Szczesny, Istvan Albert, Mary Mangan, Chris Miller, Simon Cockell, Pierre Lindenbaum, Daniel A. M. M. Silvestre, Giovanni Marco Dall’Olio & Chris Evelo. Acknowledging contributions to online expert assistance. Poster at ACM Web Science Conference 2011 Workshop, 15 June 2011.

Simon J Cockell, Jochen Weile, Phillip Lord, Claire Wipat, Dmytro Andriychenko, Matthew Pocock, Darren Wilkinson, Malcolm Young and Anil Wipat. An Ondex dataset for in silico drug discovery. Poster at 4th Annual BBSRC Systems Biology Grant Holders’ Workshop, Edinburgh, UK.

Catherine Canevet, Keywan Hassani-Pak, Simon J Cockell</ and Matthew Pocock. ONDEX – Data Integration and Visualisation. Workshop at BioSysBio 2009, Cambridge, UK.

Simon J Cockell, Matthew Pocock, Catherine Canevet, James Dewar, Eva Holstein, Steve Addinall, Phillip Lord, David Lydall, Darren Wilkindon and Anil Wipat. Exploring Yeast Telomere Maintenance Using Ondex. Poster at 3rd Annual BBSRC Systems Biology Grant Holders’ Workshop, Nottingham, UK.