Publications

Chan, Chun Ming, Christopher D. MacDonald, Gary J. Litherland, David J. Wilkinson, Andrew Skelton, G. Nicholas Europe-Finner, and Andrew D. Rowan. 2016. “Cytokine-Induced MMP13 Expression in Human Chondrocytes Is Dependent on Activating Transcription Factor 3 (ATF3) Regulation.” The Journal of Biological Chemistry, December. doi:10.1074/jbc.M116.756601.

McClurg, Urszula L., David M. W. Cork, Steven Darby, Claudia A. Ryan-Munden, Sirintra Nakjang, Leticia Mendes Côrtes, Achim Treumann, Luke Gaughan, and Craig N. Robson. 2016. “Identification of a Novel K311 Ubiquitination Site Critical for Androgen Receptor Transcriptional Activity.” Nucleic Acids Research, November. doi:10.1093/nar/gkw1162.

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.

Tomalin, Lewis Elwood, Alison Michelle Day, Zoe Elizabeth Underwood, Graham Robert Smith, Piero Dalle Pezze, Charalampos Rallis, Waseema Patel, Bryan Craig Dickinson, Jürg Bähler, Thomas Francis Brewer, Christopher Joh-Leung Chang, Daryl Pierson Shanley, and Elizabeth Ann Veal. 2016. “Increasing Extracellular H2O2 Produces a Bi-Phasic Response in Intracellular H2O2, with Peroxiredoxin Hyperoxidation Only Triggered Once the Cellular H2O2-Buffering Capacity Is Overwhelmed.” Free Radical Biology and Medicine 95 (June): 333–48. doi:10.1016/j.freeradbiomed.2016.02.035.

Ryan, S. L., E. Matheson, V. Grossmann, P. Sinclair, M. Bashton, C. Schwab, W. Towers, M. Partington, A. Elliott, L. Minto, S. Richardson, T. Rahman, B. Keavney, R. Skinner, N. Bown, T. Haferlach, P. Vandenberghe, C. Haferlach, M. Santibanez-Koref, A. V. Moorman, A. Kohlmann, J. a. E. Irving, and C. J. Harrison. 2016. “The Role of the RAS Pathway in iAMP21-ALL.” Leukemia, May. doi:10.1038/leu.2016.80.

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.

Alhasan, Abd A., Osagie G. Izuogu, Haya H. Al-Balool, Jannetta S. Steyn, Amanda Evans, Maria Colzani, Cedric Ghevaert, Joanne C. Mountford, Lamin Marenah, David J. Elliott, Mauro Santibanez-Koref, and Michael S. Jackson. 2016. “Circular RNA Enrichment in Platelets Is a Signature of Transcriptome Degradation.” Blood 127 (9): e1–e11. doi:10.1182/blood-2015-06-649434.

Meulenbelt, Ingrid M., Nidhi Bhutani, Wouter den Hollander, Steffen Gay, Udo Oppermann, Louise N. Reynard, Andrew J. Skelton, David A. Young, Frank Beier, and John Loughlin. 2016. “The First International Workshop on the Epigenetics of Osteoarthritis.” Connective Tissue Research, March, 1–12. doi:10.3109/03008207.2016.1168409.

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.

Esfandiari, Arman, Thomas A. Hawthorne, Sirintra Nakjang, and John Lunec. 2016. “Chemical Inhibition of Wild-Type P53 Induced Phosphatase 1 (WIP1/PPM1D) by GSK2830371 Potentiates the Sensitivity to MDM2 Inhibitors in a P53-Dependent Manner.” Molecular Cancer Therapeutics, February. doi:10.1158/1535-7163.MCT-15-0651.

Carroll, Bernadette, Dorothea Maetzel, Oliver DK Maddocks, Gisela Otten, Matthew Ratcliff, Graham R. Smith, Elaine A. Dunlop, João F. Passos, Owen R. Davies, Rudolf Jaenisch, Andrew R. Tee, Sovan Sarkar, and Viktor I. Korolchuk. 2016. “Control of TSC2-Rheb Signaling Axis by Arginine Regulates mTORC1 Activity.” ELife, January, e11058. doi:10.7554/eLife.11058.

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.

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, Peter Woollard, and Anil Wipat. 2016. “An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations.” PloS One 11 (5): e0155811. doi:10.1371/journal.pone.0155811.

Khundakar, Ahmad A., Peter S. Hanson, Daniel Erskine, Nichola Z. Lax, Joseph Roscamp, Evangelia Karyka, Eliona Tsefou, Preeti Singh, Simon J. Cockell, Andrew Gribben, Lynne Ramsay, Peter G. Blain, Urs P. Mosimann, Deborah J. Lett, Matthias Elstner, Douglass M. Turnbull, Charles C. Xiang, Michael J. Brownstein, John T. O’Brien, John-Paul Taylor, Johannes Attems, Alan J. Thomas, Ian G. McKeith, and Christopher M. Morris. 2016. “Analysis of Primary Visual Cortex in Dementia with Lewy Bodies Indicates GABAergic Involvement Associated with Recurrent Complex Visual Hallucinations.” Acta Neuropathologica Communications 4 (1): 66. doi:10.1186/s40478-016-0334-3.

Zeybel, Müjdat, Sezgin Vatansever, Timothy Hardy, Ayşegül Akder Sarı, Fulya Cakalağaoğlu, Arzu Avcı, Gemma Louise Zeybel, Serçin Karahüseyinoğlu, Matthew Bashton, John C. Mathers, Belkıs Ünsal, and Jelena Mann. 2016. “DNA Methylation Profiling Identifies Novel Markers of Progression in Hepatitis B-Related Chronic Liver Disease.” Clinical Epigenetics 8: 48. doi:10.1186/s13148-016-0218-1.

Williams, Rachel C., Andrew J. Skelton, Stephen M. Todryk, Andrew D. Rowan, Philip M. Preshaw, and John J. Taylor. 2016. “Leptin and Pro-Inflammatory Stimuli Synergistically Upregulate MMP-1 and MMP-3 Secretion in Human Gingival Fibroblasts.” PloS One 11 (2): e0148024. doi:10.1371/journal.pone.0148024.

Barter, Matt J., Maria Tselepi, Rodolfo Gómez, Steven Woods, Wang Hui, Graham R. Smith, Daryl P. Shanley, Ian M. Clark, and David A. Young. 2015. “Genome-Wide MicroRNA and Gene Analysis of Mesenchymal Stem Cell Chondrogenesis Identifies an Essential Role and Multiple Targets for miR-140-5p.” Stem Cells (Dayton, Ohio) 33 (11): 3266–80. doi:10.1002/stem.2093.

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.

Duncan, Christopher J. A., Siti M. B. Mohamad, Dan F. Young, Andrew J. Skelton, T. Ronan Leahy, Diane C. Munday, Karina M. Butler, Sofia Morfopoulou, Julianne R. Brown, Mike Hubank, Jeff Connell, Patrick J. Gavin, Cathy McMahon, Eugene Dempsey, Niamh E. Lynch, Thomas S. Jacques, Manoj Valappil, Andrew J. Cant, Judith Breuer, Karin R. Engelhardt, Richard E. Randall, and Sophie Hambleton. 2015. “Human IFNAR2 Deficiency: Lessons for Antiviral Immunity.” Science Translational Medicine 7 (307): 307ra154–54. doi:10.1126/scitranslmed.aac4227.

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.

Jones, Dominic, Mark Wade, Sirintra Nakjang, Lewis Chaytor, James Grey, Craig N. Robson, Luke Gaughan, Dominic Jones, Mark Wade, Sirintra Nakjang, Lewis Chaytor, James Grey, Craig N. Robson, and Luke Gaughan. 2015. “FOXA1 Regulates Androgen Receptor Variant Activity in Models of Castrate-Resistant Prostate Cancer.” Oncotarget 5 (0). http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget&page=article&op=view&path%5B%5D=4927.

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.

Jakubovics, Nicholas S., Jill C. Robinson, Derek S. Samarian, Ethan Kolderman, Sufian A. Yassin, Deepti Bettampadi, Matthew Bashton, and Alexander H. Rickard. 2015. “Critical Roles of Arginine in Growth and Biofilm Development by Streptococcus Gordonii.” Molecular Microbiology 97 (2): 281–300. doi:10.1111/mmi.13023.

O’Neill, Daniel, Dominic Jones, Mark Wade, James Grey, Sirintra Nakjang, Wenrui Guo, Barry R. Davies, Steve R. Wedge, Craig N. Robson, and Luke Gaughan. 2015. “Development and Exploitation of a Novel Mutant Androgen Receptor Modelling Strategy to Identify New Targets for Advanced Prostate Cancer Therapy.” Oncotarget 5 (0). http://www.impactjournals.com/oncotarget/index.php?journal=oncotarget&page=article&op=view&path%5B%5D=4347.

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.

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.

Shepherd, Colin, Andrew J. Skelton, Michael D. Rushton, Louise N. Reynard, and John Loughlin. 2015. “Expression Analysis of the Osteoarthritis Genetic Susceptibility Locus Mapping to an Intron of the MCF2L Gene and Marked by the Polymorphism Rs11842874.” BMC Medical Genetics 16 (1): 108. doi:10.1186/s12881-015-0254-2.

Wilson, C. L., D. Jurk, N. Fullard, P. Banks, A. Page, S. Luli, A. M. Elsharkawy, R. G. Gieling, J. Bagchi Chakraborty, C. Fox, C. Richardson, K. Callaghan, G. E. Blair, N. Fox, A. Lagnado, J. F. Passos, A. J. Moore, G. R. Smith, D. G. Tiniakos, J. Mann, F. Oakley, and D. A. Mann. 2015. “NFκB1 Is a Suppressor of Neutrophil-Driven Hepatocellular Carcinoma.” Nature Communications 6: 6818. doi:10.1038/ncomms7818.

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.

MacLean, Dan, Kentaro Yoshida, Anne Edwards, Lisa Crossman, Bernardo Clavijo, Matt Clark, David Swarbreck, Matthew Bashton, Patrick Chapman, Mark Gijzen, Mario Caccamo, Allan Downie, Sophien Kamoun, and Diane GO Saunders. 2013. “Crowdsourcing Genomic Analyses of Ash and Ash Dieback – Power to the People.” GigaScience 2 (1): 2. doi:10.1186/2047-217X-2-2.

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.

Xu, Y., M. J. Barter, D. C. Swan, K. S. Rankin, A. D. Rowan, M. Santibanez-Koref, J. Loughlin, and D. A. Young. 2012. “Identification of the Pathogenic Pathways in Osteoarthritic Hip Cartilage: Commonality and Discord Between Hip and Knee OA.” Osteoarthritis and Cartilage 20 (9): 1029–38. doi:10.1016/j.joca.2012.05.006.

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.

Pratt, Arthur G., Daniel C. Swan, Sarah Richardson, Gillian Wilson, Catharien M. U. Hilkens, David A. Young, and John D. Isaacs. 2012. “A CD4 T Cell Gene Signature for Early Rheumatoid Arthritis Implicates Interleukin 6-Mediated STAT3 Signalling, Particularly in Anti-Citrullinated Peptide Antibody-Negative Disease.” Annals of the Rheumatic Diseases 71 (8): 1374–81. doi:10.1136/annrheumdis-2011-200968.

Cole-Ezea, Patience, Dan Swan, Daryl Shanley, and John Hesketh. 2012. “Glutathione Peroxidase 4 Has a Major Role in Protecting Mitochondria from Oxidative Damage and Maintaining Oxidative Phosphorylation Complexes in Gut Epithelial Cells.” Free Radical Biology and Medicine 53 (3): 488–97. doi:10.1016/j.freeradbiomed.2012.05.029.

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.

Turcot, Valérie, Alexandra Groom, James C. McConnell, Mark S. Pearce, Catherine Potter, Nicholas D. Embleton, Daniel C. Swan, and Caroline L. Relton. 2012. “Bioinformatic Selection of Putative Epigenetically Regulated Loci Associated with Obesity Using Gene Expression Data.” Gene 499 (1): 99–107. doi:10.1016/j.gene.2012.02.001.

Relton, Caroline L., Alexandra Groom, Beate St. Pourcain, Adrian E. Sayers, Daniel C. Swan, Nicholas D. Embleton, Mark S. Pearce, Susan M. Ring, Kate Northstone, Jon H. Tobias, Joseph Trakalo, Andy R. Ness, Seif O. Shaheen, and George Davey Smith. 2012. “DNA Methylation Patterns in Cord Blood DNA and Body Size in Childhood.” PLoS ONE 7 (3): e31821. doi:10.1371/journal.pone.0031821.

Groom, Alexandra, Catherine Potter, Daniel C. Swan, Ghazaleh Fatemifar, David M. Evans, Susan M. Ring, Valerie Turcot, Mark S. Pearce, Nicholas D. Embleton, George Davey Smith, John C. Mathers, and Caroline L. Relton. 2012. “Postnatal Growth and DNA Methylation Are Associated With Differential Gene Expression of the TACSTD2 Gene and Childhood Fat Mass.” Diabetes 61 (2): 391–400. doi:10.2337/db11-1039.

Browning, Andrew C., Eugene P. Halligan, Elizabeth A. Stewart, Daniel C. Swan, Rosamund Dove, Govindi J. Samaranayake, and Winfried M. Amoaku. 2012. “Comparative Gene Expression Profiling of Human Umbilical Vein Endothelial Cells and Ocular Vascular Endothelial Cells.” British Journal of Ophthalmology 96 (1): 128–32. doi:10.1136/bjophthalmol-2011-300572.

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.

Daniels, Darren J., Christopher Clothier, Daniel C. Swan, and Gabriele Saretzki. 2010. “Immediate and Gradual Gene Expression Changes in Telomerase over-Expressing Fibroblasts.” Biochemical and Biophysical Research Communications 399 (1): 7–13. doi:10.1016/j.bbrc.2010.07.018.

Werner, Andreas, and Daniel Swan. 2010. “What Are Natural Antisense Transcripts Good for?” Biochemical Society Transactions 38 (4): 1144–49. doi:10.1042/BST0381144.

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.

Andrews, Elise, Martin Armstrong, Jonathan Tugwood, Dan Swan, Philip Glaves, Munir Pirmohamed, Guruprasad P. Aithal, Matthew C. Wright, Christopher P. Day, and Ann K. Daly. 2010. “A Role for the Pregnane X Receptor in Flucloxacillin-Induced Liver Injury.” Hepatology (Baltimore, Md.) 51 (5): 1656–64. doi:10.1002/hep.23549.

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.

Varanasi, Satya S., Ole K. Olstad, Daniel C. Swan, Paul Sanderson, Vigdis T. Gautvik, Sjur Reppe, Roger M. Francis, Kaare M. Gautvik, and Harish K. Datta. 2010. “Skeletal Site-Related Variation in Human Trabecular Bone Transcriptome and Signaling.” PloS One 5 (5): e10692. doi:10.1371/journal.pone.0010692.

Jackson, Kelly A., Ruth A. Valentine, Jill A. McKay, Daniel C. Swan, John C. Mathers, and Dianne Ford. 2009. “Analysis of Differential Gene-Regulatory Responses to Zinc in Human Intestinal and Placental Cell Lines.” The British Journal of Nutrition 101 (10): 1474–83. doi:10.1017/S0007114508094634.

Hong, M., K. R. Ryan, P. D. Arkwright, A. R. Gennery, C. Costigan, M. Dominguez, D. W. Denning, V. McConnell, A. J. Cant, M. Abinun, G. P. Spickett, D. C. Swan, C. S. Gillespie, D. A. Young, and D. Lilic. 2009. “Pattern Recognition Receptor Expression Is Not Impaired in Patients with Chronic Mucocutanous Candidiasis with or Without Autoimmune Polyendocrinopathy Candidiasis Ectodermal Dystrophy.” Clinical and Experimental Immunology 156 (1): 40–51. doi:10.1111/j.1365-2249.2009.03873.x.

Carlile, Mark, Daniel Swan, Kelly Jackson, Keziah Preston-Fayers, Benoit Ballester, Paul Flicek, and Andreas Werner. 2009. “Strand Selective Generation of Endo-siRNAs from the Na/phosphate Transporter Gene Slc34a1 in Murine Tissues.” Nucleic Acids Research 37 (7): 2274–82. doi:10.1093/nar/gkp088.

Werner, Andreas, Mark Carlile, and Daniel Swan. 2009. “What Do Natural Antisense Transcripts Regulate?” RNA Biology 6 (1): 43–48.

Ince, Robin A. A., Rasmus S. Petersen, Daniel C. Swan, and Stefano Panzeri. 2009. “Python for Information Theoretic Analysis of Neural Data.” Frontiers in Neuroinformatics 3: 4. doi:10.3389/neuro.11.004.2009.

Greenall, Amanda, Guiyuan Lei, Daniel C. Swan, Katherine James, Liming Wang, Heiko Peters, Anil Wipat, Darren J. Wilkinson, and David Lydall. 2008. “A Genome Wide Analysis of the Response to Uncapped Telomeres in Budding Yeast Reveals a Novel Role for the NAD+ Biosynthetic Gene BNA2 in Chromosome End Protection.” Genome Biology 9 (10): R146. doi:10.1186/gb-2008-9-10-r146.

Waterhouse, J. C., D. C. Swan, and R. R. B. Russell. 2007. “Comparative Genome Hybridization of Streptococcus Mutans Strains.” Oral Microbiology and Immunology 22 (2): 103–10. doi:10.1111/j.1399-302X.2007.00330.x.

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.

Field, Dawn, Bela Tiwari, Tim Booth, Stewart Houten, Dan Swan, Nicolas Bertrand, and Milo Thurston. 2006. “Open Software for Biologists: From Famine to Feast.” Nature Biotechnology 24 (7): 801–3. doi:10.1038/nbt0706-801.

Acknowledged in

The contribution of the Bioinformatics Support Unit has also been acknowledged in the following publications:

Zeybel, Müjdat, Timothy Hardy, Yi K. Wong, John C. Mathers, Christopher R. Fox, Agata Gackowska, Fiona Oakley, Alastair D. Burt, Caroline L. Wilson, Quentin M. Anstee, Matt J. Barter, Steven Masson, Ahmed M. Elsharkawy, Derek A. Mann, and Jelena Mann. 2012. “Multigenerational Epigenetic Adaptation of the Hepatic Wound-Healing Response.” Nature Medicine 18 (9): 1369–77. doi:10.1038/nm.2893.

Noël, Christophe J., Nicia Diaz, Thomas Sicheritz-Ponten, Lucie Safarikova, Jan Tachezy, Petrus Tang, Pier-Luigi Fiori, and Robert P. Hirt. 2010. “Trichomonas Vaginalis Vast BspA-Like Gene Family: Evidence for Functional Diversity from Structural Organisation and Transcriptomics.” BMC Genomics 11: 99. doi:10.1186/1471-2164-11-99.

Leaver, M., P. Domínguez-Cuevas, J. M. Coxhead, R. A. Daniel, and J. Errington. 2009. “Life Without a Wall or Division Machine in Bacillus Subtilis.” Nature 457 (7231): 849–53. doi:10.1038/nature07742.

Lister, Allyson, Varodom Charoensawan, Subhajyoti De, Katherine James, Sarath Chandra Janga, and Julian Huppert. 2009. “Interfacing Systems Biology and Synthetic Biology.” Genome Biology 10 (6): 309. doi:10.1186/gb-2009-10-6-309.

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