Bioinformatics Support Unit




Worrell JC, Leslie J, Smith GR, Zaki MYW, Paish HL, Knox A, James ML, Cartwright TN, O'Reilly S, Kania G, Distler O, Distler JHW, Herrick AL, Jeziorska M, Borthwick LA, Fisher AJ, Mann J, Mann DA, Oakley F. cRel expression regulates distinct transcriptional and functional profiles driving fibroblast matrix production in systemic sclerosis. Rheumatology (Oxford). 2020 Dec 1;59(12):3939-3951. doi: 10.1093/rheumatology/keaa272.

Khazeem MM, Cowell IG, Harkin LF, Casement JW, Austin CA. Transcription of carbonyl reductase 1 is regulated by DNA topoisomerase II beta. FEBS Lett. 2020 Oct;594(20):3395-3405. doi: 10.1002/1873-3468.13904.

Posada J, Valadkhan S, Burge D, Davies K, Tarn J, Casement J, Jobling K, Gallagher P, Wilson D, Barone F, Fisher BA, Ng WF. Improvement of Severe Fatigue Following Nuclease Therapy in Patients With Primary Sjögren's Syndrome: A Randomized Clinical Trial. Arthritis Rheumatol. 2020 Aug 15;73(1):143–50. doi: 10.1002/art.41489.

Saint-Criq V, Delpiano L, Casement J, Onuora JC, Lin J, Gray MA. Choice of Differentiation Media Significantly Impacts Cell Lineage and Response to CFTR Modulators in Fully Differentiated Primary Cultures of Cystic Fibrosis Human Airway Epithelial Cells. Cells. 2020 Sep 21;9(9):2137. doi: 10.3390/cells9092137.

Sathasivam HP, Casement J, Bates T, Sloan P, Thomson P, Robinson M, Kist R. Gene expression changes associated with malignant transformation of oral potentially malignant disorders. J Oral Pathol Med. 2020 Aug 2. doi: 10.1111/jop.13090.

Cytlak U, Resteu A, Pagan S, Green K, Milne P, Maisuria S, McDonald D, Hulme G, Filby A, Carpenter B, Queen R, Hambleton S, Hague R, Lango Allen H, Thaventhiran JED, Doody G, Collin M, Bigley V. Differential IRF8 Transcription Factor Requirement Defines Two Pathways of Dendritic Cell Development in Humans. Immunity. 2020 Aug 18;53(2):353-370.e8. doi: 10.1016/j.immuni.2020.07.003.

Transcriptomic profiling across the nonalcoholic fatty liver disease spectrum reveals gene signatures for steatohepatitis and fibrosis. Govaere O, Cockell S, Tiniakos D, Queen R, Younes R, Vacca M, Alexander L, Ravaioli F, Palmer J, Petta S, Boursier J, Rosso C, Johnson K, Wonders K, Day CP, Ekstedt M, Orešič M, Darlay R, Cordell HJ, Marra F, Vidal-Puig A, Bedossa P, Schattenberg JM, Clément K, Allison M, Bugianesi E, Ratziu V, Daly AK, Anstee QM. Sci Transl Med. 2020 Dec 2;12(572):eaba4448. doi: 10.1126/scitranslmed.aba4448.

Cheung, Kathleen, Marjolein J. Burgers, David A. Young, Simon Cockell, and Louise N. Reynard. 2020. “Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip Arrays in Cartilage.” Epigenetics 15 (6-7): 594–603. doi:10.1080/15592294.2019.1700003.

Collin, Joseph, Rachel Queen, Darin Zerti, Birthe Dorgau, Maria Georgiou, Ivo Djidrovski, Rafiqul Hussain, Jonathan M. Coxhead, Agatha Joseph, Paul Rooney, Steven Lisgo, Francisco Figueiredo, Lyle Armstrong, and Majlinda Lako. 2020. “Co-Expression of SARS-CoV-2 Entry Genes in the Superficial Adult Human Conjunctival, Limbal and Corneal Epithelium Suggests an Additional Route of Entry via the Ocular Surface.” The Ocular Surface, June. doi:10.1016/j.jtos.2020.05.013.

Sorial, A. K., I. M. J. Hofer, M. Tselepi, K. Cheung, E. Parker, D. J. Deehan, S. J. Rice, and J. Loughlin. 2020. “Multi-Tissue Epigenetic Analysis of the Osteoarthritis Susceptibility Locus Mapping to the Plectin Gene PLEC.” Osteoarthritis and Cartilage, June. doi:10.1016/j.joca.2020.06.001.

Clark, Alexander D., Nisha Nair, Amy E. Anderson, Nishanthi Thalayasingam, Najib Naamane, Andrew J. Skelton, Julie Diboll, Anne Barton, Stephen Eyre, John D. Isaacs, Arthur G. Pratt, and Louise N. Reynard. 2020. “Lymphocyte DNA Methylation Mediates Genetic Risk at Shared Immune-Mediated Disease Loci.” The Journal of Allergy and Clinical Immunology 145 (5): 1438–51. doi:10.1016/j.jaci.2019.12.910.

Sungnak, Waradon, Ni Huang, Christophe Bécavin, Marijn Berg, Rachel Queen, Monika Litvinukova, Carlos Talavera-López, Henrike Maatz, Daniel Reichart, Fotios Sampaziotis, Kaylee B. Worlock, Masahiro Yoshida, and Josephine L. Barnes. 2020. “SARS-CoV-2 Entry Factors Are Highly Expressed in Nasal Epithelial Cells Together with Innate Immune Genes.” Nature Medicine 26 (5): 681–87. doi:10.1038/s41591-020-0868-6.

Anstee, Quentin M., Rebecca Darlay, Simon Cockell, Marica Meroni, Olivier Govaere, Dina Tiniakos, Alastair D. Burt, Pierre Bedossa, Jeremy Palmer, Yang-Lin Liu, Guruprasad P. Aithal, Michael Allison, Hannele Yki-Järvinen, Michele Vacca, Jean-Francois Dufour, Pietro Invernizzi, Daniele Prati, Mattias Ekstedt, Stergios Kechagias, Sven Francque, Salvatore Petta, Elisabetta Bugianesi, Karine Clement, Vlad Ratziu, Jörn M. Schattenberg, Luca Valenti, Christopher P. Day, Heather J. Cordell, Ann K. Daly, and EPoS Consortium Investigators. 2020. “Genome-Wide Association Study of Non-Alcoholic Fatty Liver and Steatohepatitis in a Histologically-Characterised Cohort.” Journal of Hepatology, April. doi:10.1016/j.jhep.2020.04.003.

Cheung, Kathleen, Matthew J. Barter, Julia Falk, Carole J. Proctor, Louise N. Reynard, and David A. Young. 2020. “Histone ChIP-Seq Identifies Differential Enhancer Usage During Chondrogenesis as Critical for Defining Cell-Type Specificity.” FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology 34 (4): 5317–31. doi:10.1096/fj.201902061RR.

Barter, Matt J., Catherine Bui, Kathleen Cheung, Julia Falk, Rodolfo Gómez, Andrew J. Skelton, Hannah R. Elliott, Louise N. Reynard, and David A. Young. 2020. “DNA Hypomethylation During MSC Chondrogenesis Occurs Predominantly at Enhancer Regions.” Scientific Reports 10 (1): 1169. doi:10.1038/s41598-020-58093-5.



Zerti, Darin, Joseph Collin, Rachel Queen, Simon J. Cockell, and Majlinda Lako. 2019. “Understanding the Complexity of Retina and Pluripotent Stem Cell Derived Retinal Organoids with Single Cell RNA Sequencing: Current Progress, Remaining Challenges and Future Prospective.” Current Eye Research, December. doi:10.1080/02713683.2019.1697453.

O’Keefe, Hannah, Rachel Queen, Phillip Lord, and Joanna L. Elson. 2019. “What Can a Comparative Genomics Approach Tell Us About the Pathogenicity of mtDNA Mutations in Human Populations?” Evolutionary Applications 12 (10): 1912–30. doi:10.1111/eva.12851.

Davies, Helen R., Kirsty Hodgson, Edward Schwalbe, Jonathan Coxhead, Naomi Sinclair, Xueqing Zou, Simon Cockell, Akhtar Husain, Serena Nik-Zainal, and Neil Rajan. 2019. “Epigenetic Modifiers DNMT3A and BCOR Are Recurrently Mutated in CYLD Cutaneous Syndrome.” Nature Communications 10 (1): 4717. doi:10.1038/s41467-019-12746-w.

Rice, S. J., K. Cheung, L. N. Reynard, and J. Loughlin. 2019. ‘Discovery and Analysis of Methylation Quantitative Trait Loci (MQTLs) Mapping to Novel Osteoarthritis Genetic Risk Signals’. Osteoarthritis and Cartilage 27 (10): 1545–56. doi:10.1016/j.joca.2019.05.017.
Phillips, Helen M., Catherine A. Stothard, Wasay M. Shaikh Qureshi, Anastasia I. Kousa, J. Alberto Briones-Leon, Ramada R. Khasawneh, Chloe O’Loughlin, Rachel Sanders, Silvia Mazzotta, Rebecca Dodds, Kerstin Seidel, Timothy Bates, Mitsushiro Nakatomi, Simon J. Cockell, Jürgen E. Schneider, Timothy J. Mohun, René Maehr, Ralf Kist, Heiko Peters, and Simon D. Bamforth. 2019. ‘Pax9 Is Required for Cardiovascular Development and Interacts with Tbx1 in the Pharyngeal Endoderm to Control 4th Pharyngeal Arch Artery Morphogenesis’. Development (Cambridge, England) 146 (18). doi:10.1242/dev.177618.
Munkley, Jennifer, Li Ling, S. R. Gokul Krishnan, Gerald Hysenaj, Emma Scott, Caroline Dalgliesh, Htoo Zarni Oo, Teresa Mendes Maia, Kathleen Cheung, Ingrid Ehrmann, Karen E. Livermore, Hanna Zielinska, Oliver Thompson, Bridget Knight, Paul McCullagh, John McGrath, Malcolm Crundwell, Lorna W. Harries, Mads Daugaard, Simon Cockell, Nuno L. Barbosa-Morais, Sebastian Oltean, and David J. Elliott. 2019. ‘Androgen-Regulated Transcription of ESRP2 Drives Alternative Splicing Patterns in Prostate Cancer’. ELife 8 (September). doi:10.7554/eLife.47678.
Baker, Kenneth F., Andrew J. Skelton, Dennis W. Lendrem, Adam Scadeng, Ben Thompson, Arthur G. Pratt, and John D. Isaacs. 2019. ‘Predicting Drug-Free Remission in Rheumatoid Arthritis: A Prospective Interventional Cohort Study’. Journal of Autoimmunity, July, 102298. doi:10.1016/j.jaut.2019.06.009.
Ridgley, Laura A., Amy E. Anderson, Nicola J. Maney, Najib Naamane, Andrew J. Skelton, Catherine A. Lawson, Paul Emery, John D. Isaacs, Ruaidhrí J. Carmody, and Arthur G. Pratt. 2019. ‘IL-6 Mediated Transcriptional Programming of Naïve CD4+ T Cells in Early Rheumatoid Arthritis Drives Dysregulated Effector Function’. Frontiers in Immunology 10: 1535. doi:10.3389/fimmu.2019.01535.

Collin, Joseph, Darin Zerti, Rachel Queen, Tiago Santos-Ferreira, Roman Bauer, Jonathan Coxhead, Rafiqul Hussain, David Steel, Carla Mellough, Marius Ader, Evelyne Sernagor, Lyle Armstrong, and Majlinda Lako. 2019. “CRX Expression in Pluripotent Stem Cell-Derived Photoreceptors Marks a Transplantable Subpopulation of Early Cones.” Stem Cells (Dayton, Ohio) 37 (5): 609–22. doi:10.1002/stem.2974.

Collin, Joseph, Rachel Queen, Darin Zerti, Birthe Dorgau, Rafiqul Hussain, Jonathan Coxhead, Simon Cockell, and Majlinda Lako. 2019. “Deconstructing Retinal Organoids: Single Cell RNA-Seq Reveals the Cellular Components of Human Pluripotent Stem Cell-Derived Retina.” Stem Cells (Dayton, Ohio) 37 (5): 593–98. doi:10.1002/stem.2963.

Govaere, Olivier, Simon Cockell, Matthias Van Haele, Jasper Wouters, Wouter Van Delm, Kathleen Van den Eynde, Arianna Bianchi, Rudy van Eijsden, Werner Van Steenbergen, Diethard Monbaliu, Frederik Nevens, and Tania Roskams. 2019. “High-Throughput Sequencing Identifies Aetiology-Dependent Differences in Ductular Reaction in Human Chronic Liver Disease.” The Journal of Pathology 248 (1): 66–76. doi:10.1002/path.5228.

Kounatidou, Evangelia, Sirintra Nakjang, Stuart R. C. McCracken, Scott M. Dehm, Craig N. Robson, Dominic Jones, and Luke Gaughan. 2019. “A Novel CRISPR-Engineered Prostate Cancer Cell Line Defines the AR-V Transcriptome and Identifies PARP Inhibitor Sensitivities.” Nucleic Acids Research, April. doi:10.1093/nar/gkz286.

Ajekigbe, B., K. Cheung, Y. Xu, A. J. Skelton, A. Panagiotopoulos, J. Soul, T. E. Hardingham, D. J. Deehan, M. J. Barter, and D. A. Young. 2019. “Identification of Long Non-Coding RNAs Expressed in Knee and Hip Osteoarthritic Cartilage.” Osteoarthritis and Cartilage 27 (4): 694–702. doi:10.1016/j.joca.2018.12.015.

Mellough, Carla B., Joseph Collin, Rachel Queen, Gerrit Hilgen, Birthe Dorgau, Darin Zerti, Majed Felemban, Kathryn White, Evelyne Sernagor, and Majlinda Lako. 2019. “Systematic Comparison of Retinal Organoid Differentiation from Human Pluripotent Stem Cells Reveals Stage Specific, Cell Line, and Methodological Differences.” Stem Cells Translational Medicine, March. doi:10.1002/sctm.18-0267.

Chaytor, Lewis, Matthew Simcock, Sirintra Nakjang, Richard Heath, Laura Walker, Craig Robson, Dominic Jones, and Luke Gaughan. 2019. “The Pioneering Role of GATA2 in Androgen Receptor Variant Regulation Is Controlled by Bromodomain and Extraterminal Proteins in Castrate-Resistant Prostate Cancer.” Molecular Cancer Research: MCR, March. doi:10.1158/1541-7786.MCR-18-1231.

Anderson, Amy E., Nicola J. Maney, Nisha Nair, Dennis W. Lendrem, Andrew J. Skelton, Julie Diboll, Philip M. Brown, Graham R. Smith, Ruaidhrí J. Carmody, Anne Barton, John D. Isaacs, and Arthur G. Pratt. 2019. “Expression of STAT3-Regulated Genes in Circulating CD4+ T Cells Discriminates Rheumatoid Arthritis Independently of Clinical Parameters in Early Arthritis.” Rheumatology (Oxford, England), February. doi:10.1093/rheumatology/kez003.

Rice, Sarah J., Maria Tselepi, Antony K. Sorial, Guillaume Aubourg, Colin Shepherd, David Almarza, Andrew J. Skelton, Ioanna Pangou, David Deehan, Louise N. Reynard, and John Loughlin. 2019. “Prioritization of PLEC and GRINA as Osteoarthritis Risk Genes Through the Identification and Characterization of Novel Methylation Quantitative Trait Loci.” Arthritis & Rheumatology (Hoboken, N.J.), February. doi:10.1002/art.40849.

Ehrmann, Ingrid, James H. Crichton, Matthew R. Gazzara, Katherine James, Yilei Liu, Sushma Nagaraja Grellscheid, Tomaž Curk, Dirk de Rooij, Jannetta S. Steyn, Simon Cockell, Ian R. Adams, Yoseph Barash, and David J. Elliott. 2019. “An Ancient Germ Cell-Specific RNA-Binding Protein Protects the Germline from Cryptic Splice Site Poisoning.” eLife 8 (January). doi:10.7554/eLife.39304.


Bojic, Sanja, Dean Hallam, Nuno Alcada, Ali Ghareeb, Rachel Queen, Sagoo Pervinder, Harley Buck, Aya Amitai Lange, Gustavo Figueiredo, Paul Rooney, Miodrag Stojkovic, Alex Shortt, Francisco C. Figueiredo, and Majlinda Lako. 2018. “CD200 Expression Marks a Population of Quiescent Limbal Epithelial Stem Cells with Holoclone Forming Ability.” Stem Cells (Dayton, Ohio) 36 (11): 1723–35. doi:10.1002/stem.2903.

Szołtysek, Katarzyna, Patryk Janus, Gracjana Zając, Tomasz Stokowy, Anna Walaszczyk, Wiesława Widłak, Bartosz Wojtaś, Bartłomiej Gielniewski, Simon Cockell, Neil D. Perkins, Marek Kimmel, and Piotr Widlak. 2018. “RRAD, IL4I1, CDKN1A, and SERPINE1 Genes Are Potentially Co-Regulated by NF-κB and P53 Transcription Factors in Cells Exposed to High Doses of Ionizing Radiation.” BMC Genomics 19 (1): 813. doi:10.1186/s12864-018-5211-y.

Danilenko, M., K. Hodgson, R. Stones, A. Husain, M. Zangarini, G. Veal, and N. Rajan. 2018. “Diverse Assays from a Single Skin Punch Biopsy to Assess Topical Drug Intervention.” The British Journal of Dermatology, October. doi:10.1111/bjd.17353.

Martinez-Soria, Natalia, Lynsey McKenzie, Julia Draper, Anetta Ptasinska, Hasan Issa, Sandeep Potluri, Helen J. Blair, Anna Pickin, Asmida Isa, Paulynn Suyin Chin, Ricky Tirtakusuma, Daniel Coleman, Sirintra Nakjang, Salam Assi, Victoria Forster, Mojgan Reza, Ed Law, Philip Berry, Dorothee Mueller, Alex Elder, Simon N. Bomken, Deepali Pal, James M. Allan, Gareth J. Veal, Peter N. Cockerill, Christian Wichmann, Josef Vormoor, Georges Lacaud, Constanze Bonifer, and Olaf Heidenreich. 2018. “The Oncogenic Transcription Factor RUNX1/ETO Corrupts Cell Cycle Regulation to Drive Leukemic Transformation.” Cancer Cell 34 (4): 626–642.e8. doi:10.1016/j.ccell.2018.08.015.

Acres, Meghan J., Florian Gothe, Angela Grainger, Andrew J. Skelton, David J. Swan, Joseph D. P. Willet, Suzy Leech, Sonya Galcheva, Violeta Iotova, Sophie Hambleton, and Karin R. Engelhardt. 2018. “Signal Transducer and Activator of Transcription 5B Deficiency Due to a Novel Missense Mutation in the Coiled-Coil Domain.” The Journal of Allergy and Clinical Immunology, September. doi:10.1016/j.jaci.2018.08.032.

Danilenko, Marina, Elaine Stamp, Deborah D. Stocken, Akhtar Husain, Monique Zangarini, Amy Cranston, Robert Stones, Naomi Sinclair, Kirsty Hodgson, Susan A. Bowett, David Roblin, Silvio Traversa, Ruth Plummer, Gareth Veal, James A. A. Langtry, Alan Ashworth, John Burn, and Neil Rajan. 2018. “Targeting Tropomyosin Receptor Kinase in Cutaneous CYLD Defective Tumors with Pegcantratinib: The TRAC Randomized Clinical Trial.” JAMA Dermatology 154 (8): 913–21. doi:10.1001/jamadermatol.2018.1610.

O’Keefe, Hannah, Rachel A. Queen, Surita Meldau, Phillip Lord, and Joanna L. Elson. 2018. “Haplogroup Context Is Less Important in the Penetrance of Mitochondrial DNA Complex I Mutations Compared to Mt-tRNA Mutations.” Journal of Molecular Evolution, July. doi:10.1007/s00239-018-9855-7.

Macdonald, Christopher D., Adrian M. D. Falconer, Chun Ming Chan, David J. Wilkinson, Andrew Skelton, Louise Reynard, Gary J. Litherland, G. Nicholas Europe-Finner, and Andrew D. Rowan. 2018. “Cytokine-Induced Cysteine- Serine-Rich Nuclear Protein-1 (CSRNP1) Selectively Contributes to MMP1 Expression in Human Chondrocytes.” PloS One 13 (11): e0207240. doi:10.1371/journal.pone.0207240.

Guyet, Aurelie, Martyn Dade-Robertson, Anil Wipat, John Casement, Wendy Smith, Helen Mitrani, and Meng Zhang. 2018. “Mild Hydrostatic Pressure Triggers Oxidative Responses in Escherichia Coli.” PloS One 13 (7): e0200660. doi:10.1371/journal.pone.0200660.

RA-MAP Consortium. 2018. “Novel Methodology to Discern Predictors of Remission and Patterns of Disease Activity over Time Using Rheumatoid Arthritis Clinical Trials Data.” RMD Open 4 (2): e000721. doi:10.1136/rmdopen-2018-000721.

Janus, Patryk, Katarzyna Szołtysek, Gracjana Zając, Tomasz Stokowy, Anna Walaszczyk, Wiesława Widłak, Bartosz Wojtaś, Bartłomiej Gielniewski, Marta Iwanaszko, Rosemary Braun, Simon Cockell, Neil D. Perkins, Marek Kimmel, and Piotr Widlak. 2018. “Pro-Inflammatory Cytokine and High Doses of Ionizing Radiation Have Similar Effects on the Expression of NF-kappaB-Dependent Genes.” Cellular Signalling 46 (June): 23–31. doi:10.1016/j.cellsig.2018.02.011.

Shepherd, Colin, Dongxing Zhu, Andrew J. Skelton, Jennifer Combe, Harrison Threadgold, Linyi Zhu, Tonia L. Vincent, Paul Stuart, Louise N. Reynard, and John Loughlin. 2018. “Functional Characterisation of the Osteoarthritis Genetic Risk Residing at ALDH1A2 Identifies Rs12915901 as a Key Target Variant.” Arthritis & Rheumatology (Hoboken, N.J.), May. doi:10.1002/art.40545.

McClurg, Urszula L., Nay C. T. H. Chit, Mahsa Azizyan, Joanne Edwards, Arash Nabbi, Karl T. Riabowol, Sirintra Nakjang, Stuart R. McCracken, and Craig N. Robson. 2018. “Molecular Mechanism of the TP53-MDM2-AR-AKT Signalling Network Regulation by USP12.” Oncogene, May. doi:10.1038/s41388-018-0283-3.

McClurg, Urszula L., Mahsa Azizyan, Daniel T. Dransfield, Nivedita Namdev, Nay C. T. H. Chit, Sirintra Nakjang, and Craig N. Robson. 2018. “The Novel Anti-Androgen Candidate Galeterone Targets Deubiquitinating Enzymes, USP12 and USP46, to Control Prostate Cancer Growth and Survival.” Oncotarget 9 (38): 24992–25007. doi:10.18632/oncotarget.25167.

Robinson, J. C., N. Rostami, J. Casement, W. Vollmer, A. H. Rickard, and N. S. Jakubovics. 2018. “ArcR Modulates Biofilm Formation in the Dental Plaque Colonizer Streptococcus Gordonii.” Molecular Oral Microbiology 33 (2): 143–54. doi:10.1111/omi.12207.

Dean, P., K. M. Sendra, T. A. Williams, A. K. Watson, P. Major, S. Nakjang, E. Kozhevnikova, A. V. Goldberg, E. R. S. Kunji, R. P. Hirt, and T. M. Embley. 2018. “Transporter Gene Acquisition and Innovation in the Evolution of Microsporidia Intracellular Parasites.” Nature Communications 9 (1): 1709. doi:10.1038/s41467-018-03923-4.

James, Katherine, Chimwemwe Chipeta, Antony Parker, Stephen Harding, Simon J. Cockell, Colin S. Gillespie, Jennifer Hallinan, Francesca Barone, Simon J. Bowman, Wan-Fai Ng, Benjamin A. Fisher, and UK Primary Sjögren’s Syndrome Registry. 2018. “B-Cell Activity Markers Are Associated with Different Disease Activity Domains in Primary Sjögren’s Syndrome.” Rheumatology (Oxford, England), March. doi:10.1093/rheumatology/key063.

Thalayasingam, Nishanthi, Nisha Nair, Andrew J. Skelton, Jonathan Massey, Amy E. Anderson, Alexander D. Clark, Julie Diboll, Dennis W. Lendrem, Louise N. Reynard, Heather J. Cordell, Stephen Eyre, John D. Isaacs, Anne Barton, and Arthur G. Pratt. 2018. “CD4+ and B Lymphocyte Expression Quantitative Traits at Rheumatoid Arthritis Risk Loci in Patients with Untreated Early Arthritis: Implications for Causal Gene Identification.” Arthritis & Rheumatology (Hoboken, N.J.) 70 (3): 361–70. doi:10.1002/art.40393.

Paish, Hannah L., Nicholas S. Kalson, Graham R. Smith, Alicia Del Carpio Pons, Thomas E. Baldock, Nicholas Smith, Katarzyna Swist-Szulik, David J. Weir, Michelle Bardgett, David J. Deehan, Derek A. Mann, and Lee A. Borthwick. 2018. “Fibroblasts Promote Inflammation and Pain via IL-1α Induction of the Monocyte Chemoattractant Chemokine (C-C Motif) Ligand 2.” The American Journal of Pathology 188 (3): 696–714. doi:10.1016/j.ajpath.2017.11.007.

Brown, S. M., M. Arefi, R. Stones, P. S. Loo, S. Barnard, C. Bloxham, N. Stefanos, J. a. A. Langtry, S. Worthy, E. Calonje, A. Husain, and N. Rajan. 2018. “Inherited Pulmonary Cylindromas: Extending the Phenotype of CYLD Mutation Carriers.” The British Journal of Dermatology, March. doi:10.1111/bjd.16573.

Grey, James, Dominic Jones, Laura Wilson, Sirintra Nakjang, Jake Clayton, Richard Temperley, Emma Clark, Luke Gaughan, and Craig Robson. 2018. “Differential Regulation of the Androgen Receptor by Protein Phosphatase Regulatory Subunits.” Oncotarget 9 (3): 3922–35. doi:10.18632/oncotarget.22883.

Carroll, Bernadette, Elsje G. Otten, Diego Manni, Rhoda Stefanatos, Fiona M. Menzies, Graham R. Smith, Diana Jurk, Niall Kenneth, Simon Wilkinson, Joao F. Passos, Johannes Attems, Elizabeth A. Veal, Elisa Teyssou, Danielle Seilhean, Stéphanie Millecamps, Eeva-Liisa Eskelinen, Agnieszka K. Bronowska, David C. Rubinsztein, Alberto Sanz, and Viktor I. Korolchuk. 2018. “Oxidation of SQSTM1/P62 Mediates the Link Between Redox State and Protein Homeostasis.” Nature Communications 9 (1): 256. doi:10.1038/s41467-017-02746-z.

Cooles, Faye A. H., Amy E. Anderson, Andrew Skelton, Arthur G. Pratt, Mariola S. Kurowska-Stolarska, Iain McInnes, Catharien M. U. Hilkens, and John D. Isaacs. 2018. “Phenotypic and Transcriptomic Analysis of Peripheral Blood Plasmacytoid and Conventional Dendritic Cells in Early Drug Naïve Rheumatoid Arthritis.” Frontiers in Immunology 9: 755. doi:10.3389/fimmu.2018.00755.

Cope, Andrew P., Michael R. Barnes, Alexandra Belson, Michael Binks, Sarah Brockbank, Francisco Bonachela-Capdevila, Claudio Carini, Benjamin A. Fisher, Carl S. Goodyear, Paul Emery, Michael R. Ehrenstein, Neil Gozzard, Ray Harris, Sally Hollis, Sarah Keidel, Marc Levesque, Catharina Lindholm, Michael F. McDermott, Iain B. McInnes, Christopher M. Mela, Gerry Parker, Simon Read, Ayako Wakatsuki Pedersen, Frederique Ponchel, Duncan Porter, Ravi Rao, Anthony Rowe, Peter Schulz-Knappe, Matthew A. Sleeman, Deborah Symmons, Peter C. Taylor, Brian Tom, Wayne Tsuji, Denny Verbeeck, John D. Isaacs, and RA-MAP Consortium. 2018. “The RA-MAP Consortium: A Working Model for Academia-Industry Collaboration.” Nature Reviews. Rheumatology 14 (1): 53–60. doi:10.1038/nrrheum.2017.200.

Danilenko, Marina, Robert Stones, and Neil Rajan. 2018. “Transcriptomic Profiling of Human Skin Biopsies in the Clinical Trial Setting: A Protocol for High Quality RNA Extraction from Skin Tumours.” Wellcome Open Research 3: 45. doi:10.12688/wellcomeopenres.14360.1.


Proctor, Carole J., and Graham R. Smith. 2017. “Computer Simulation Models as a Tool to Investigate the Role of microRNAs in Osteoarthritis.” PLOS ONE 12 (11): e0187568. doi:10.1371/journal.pone.0187568.

Madakashira, Bhavani, Laura Corbett, Chi Zhang, Pier Paoli, John W. Casement, Jelena Mann, Kirsten C. Sadler, and Derek A. Mann. 2017. “Variant Histone H2afv Reprograms DNA Methylation During Early Zebrafish Development.” Epigenetics, November, 1–14. doi:10.1080/15592294.2017.1359382.

Pease, Louise I., Peter D. Clegg, Carole J. Proctor, Daryl J. Shanley, Simon J. Cockell, and Mandy J. Peffers. 2017. “Cross Platform Analysis of Transcriptomic Data Identifies Ageing Has Distinct and Opposite Effects on Tendon in Males and Females.” Scientific Reports 7 (1): 14443. doi:10.1038/s41598-017-14650-z.

Barter, Matt J., Rodolfo Gomez, Sam Hyatt, Kat Cheung, Andrew Skelton, Yaobo Xu, Ian Clark, and David A. Young. 2017. “Long Noncoding RNA ROCR Contributes to SOX9 Expression and Chondrogenic Differentiation of Human Mesenchymal Stem Cells.” Development (Cambridge, England), October. doi:10.1242/dev.152504.

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.

Schwalbe, Edward C., Janet C. Lindsey, Sirintra Nakjang, Stephen Crosier, Amanda J. Smith, Debbie Hicks, Gholamreza Rafiee, Rebecca M. Hill, Alice Iliasova, Thomas Stone, Barry Pizer, Antony Michalski, Abhijit Joshi, Stephen B. Wharton, Thomas S. Jacques, Simon Bailey, Daniel Williamson, and Steven C. Clifford. 2017. “Novel Molecular Subgroups for Clinical Classification and Outcome Prediction in Childhood Medulloblastoma: A Cohort Study.” The Lancet. Oncology 18 (7): 958–71. doi:10.1016/S1470-2045(17)30243-7.

Duncan, Christopher J. A., Emma Dinnigan, Rachel Theobald, Angela Grainger, Andrew J. Skelton, Rafiqul Hussain, Joseph D. P. Willet, David J. Swan, Jonathan Coxhead, Matthew F. Thomas, Julian Thomas, Veena Zamvar, Mary A. Slatter, Andrew J. Cant, Karin R. Engelhardt, and Sophie Hambleton. 2017. “Early-Onset Autoimmune Disease Due to a Heterozygous Loss-of-Function Mutation in TNFAIP3 (A20).” Annals of the Rheumatic Diseases, June. doi:10.1136/annrheumdis-2016-210944.

Widdrington, John D., Aurora Gomez-Duran, Jannetta S. Steyn, Angela Pyle, Marie-Helene Ruchaud-Sparagano, Jonathan Scott, Simon V. Baudouin, Anthony J. Rostron, John Simpson, and Patrick F. Chinnery FMedSci. 2017. “Mitochondrial DNA Depletion Induces Innate Immune Dysfunction Rescued by Interferon-γ.” The Journal of Allergy and Clinical Immunology, June. doi:10.1016/j.jaci.2017.04.048.

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.

Russell, Lisa J., Lisa Jones, Amir Enshaei, Stefano Tonin, Sarra L. Ryan, Jeyanthy Eswaran, Sirintra Nakjang, Elli Papaemmanuil, Jose M. C. Tubio, Adele K. Fielding, Ajay Vora, Peter J. Campbell, Anthony V. Moorman, and Christine J. Harrison. 2017. “Characterisation of the Genomic Landscape of CRLF2-Rearranged Acute Lymphoblastic Leukemia.” Genes, Chromosomes and Cancer 56 (5): 363–72. doi:10.1002/gcc.22439.

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.

Noble, Richard A., Natalie Bell, Helen Blair, Arti Sikka, Huw Thomas, Nicole Phillips, Sirintra Nakjang, Satomi Miwa, Rachel Crossland, Vikki Rand, Despina Televantou, Anna Long, Hector C. Keun, Chris M. Bacon, Simon Bomken, Susan E. Critchlow, and Stephen R. Wedge. 2017. “Inhibition of Monocarboxylate Transporter 1 by AZD3965 as a Novel Therapeutic Approach for the Treatment of Diffuse Large B-Cell Lymphoma and Burkitt Lymphoma.” Haematologica, April, haematol.2016.163030. doi:10.3324/haematol.2016.163030.

Queen, Rachel A., Jannetta S. Steyn, Phillip Lord, and Joanna L. Elson. 2017. “Mitochondrial DNA Sequence Context in the Penetrance of Mitochondrial T-RNA Mutations: A Study Across Multiple Lineages with Diagnostic Implications.” PloS One 12 (11): e0187862. doi:10.1371/journal.pone.0187862.


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.

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.


Elder, Alex, Helen Blair, Katherine Dormon, Simon Bomken, Simon J. Cockell, Olaf Heidenreich, and Josef Vormoor. 2015. “High Abundance of Acute Lymphoblastic Leukaemia Founder Clones Does Not Translate to Functional Heterogeneity.” Blood 126 (23): 844–44.

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): 307ra154–307ra154. 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.

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).

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).

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 Colin S Gillespie. 2014. “Bioconductor Tools for Microarray Data Analysis.” In Microarray Image and Data Analysis, 459–79. Digital Imaging and Computer Vision. CRC Press.

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): 1144–9. 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.