Staff Profile

Background

My background is in experimental molecular biology, particularly the scaffolding of signal transduction processes. Since leaving the lab to pursue a Bioinformatics career, I have gained an MRes degree in the subject, and spent 15 years in the Bioinformatics Support Unit providing practical support to a wide array of researchers. I led the BSU for 9 years (2011-2020), before being appointed as Senior Lecturer in Bioinformatics in the School of Biomedical, Nutritional and Sports Sciences.

Roles and Responsibilities

Senior Lecturer in Bioinformatics in the School of Biomedical, Nutritional and Sport Sciences.

Director of Research, School of Biomedical, Nutritional and Sport Sciences.

Qualifications

B.Sc. (Hons) - Biochemistry and Genetics - University of Nottingham, 1999
Ph.D. - Genetics - University of Leicester, 2004
M.Res. - Bioinformatics and Computational Biology - University of Leeds, 2005

Research Interests

I have been a professional bioinformatician for more than 15 years, during which time I have contributed to a large number of collaborative projects as a researcher and an investigator. My recent research career has seen me involved as a co-investigator on a number of large multi-omics investigations of complex disease. Many of these projects have used bulk RNA-Seq to characterise pathological states or to stratify disease, and increasingly these studies are looking to use single-cell and spatial transcriptomics to refine the detail of these systems even further.

My research revolves around a small number of central themes, all involving the analysis of biological data:

• Integration of disparate biological data
• Molecular characterisation of complex disease
• High-throughput sequencing analysis, particulatly functional genomics techniques such as RNA-Seq, ChIP-Seq etc

In recent years, I have been involved in a number of large projects connected to one or more of these themes, including the following:

• Psoriasis Stratification to Optimise Relevant Therapy (PSORT) - MRC, co-Investigator
• Liver Investigation: Testing Marker Utility in Steatohepatitis (LITMUS) - EU (IMI), co-Investigator
• Elucidating Pathways of Steatohepatitis (EPoS) - EU (H2020), co-Investigator
• An in silico based approach to improve the efficacy and precision of drug REPurpOsing TRIALs for a mechanism-based patient cohort with predominant cerebro-cardiovascular phenotypes (REPO-TRIAL) - EU (H2020), co-Investigator
• Strategic Training Awards for Research Skills - Newcastle University Bioinformatics Skills Schools (NUBASS) - BBSRC, Principal Investigator

My teaching responsibilities are:

Module Leadership

• CSC8309 – Genome Scale Data Analytics
• MMB8052 – Bioinformatics for Biomedical Scientists

Postgraduate Teaching

• CVR8004 – Clinical Assessment and Investigation

Undergraduate Teaching

• CMB1011 – Professional and Practical Skills for Bioscientists
• CMB2000 – Essential Skills in Biomedical Research
• BGM2062 – Advanced Protein Analysis
• BGM2063 – Approaches to Analysis of Genes and Genomes
• BMS3025 – Bioinformatics
• PED3005 – Advanced Pharmacogenetics

Previous teaching

• CSC8325 - An Introduction to Bioinformatics Theory and Practice (2019 - 2023), CSC8326 – Advanced Bioinformatics Theory and Practice (2019 - 2023), CSC8313 – Bioinformatics Theory and Practice (2005-2019), MMB8023 – Systems Biology MRes strand (2011 – 2018), GNM8007 – Bioinformatics, Interpretation, Statistics and Data Quality Assurance (2017 – 2018)

Bioinformatics Training

I have prepared and delivered training courses in bioinformatics and programming to life science researchers for many years.

During Coronavirus crisis of 2020 I produced the live-streamed “Lockdown Learning” series. My YouTube channel has >6,000 subscribers and my tutorial videos have >280,000 views.

• Articles

  • Vaughan AJ, McMeekin LJ, Hine K, Stubbs IW, Codadu NK, Cockell S, Hill JT, Cowell R, Trevelyan AJ, Parrish RR. RNA Sequencing Demonstrates Ex Vivo Neocortical Transcriptomic Changes Induced by Epileptiform Activity in Male and Female Mice. eNeuro 2024, 11(5), ENEURO.0520-23.2024.
  • Govaere O, Cockell SJ, Zatorska M, Wonders K, Tiniakos D, Frey AM, Palmowksi P, Walker R, Porter A, Trost M, Anstee QM, Daly AK. Pharmacogene expression during progression of metabolic dysfunction-associated steatotic liver disease: Studies on mRNA and protein levels and their relevance to drug treatment. Biochemical Pharmacology 2024, 228, 116249.
  • Sabatini S, Sen P, Carli F, Pezzica S, Rosso C, Lembo E, Verrastro O, Daly A, Govaere O, Cockell S, Hyotylainen T, Mingrone G, Bugianesi E, Anstee QM, Oresic M, Gastaldelli A. Hepatic glucose production rises with the histological severity of metabolic dysfunction-associated steatohepatitis. Cell Reports Medicine 2024, 5(11), 101820.
  • Vacca V, Kamzolas I, Mørch Harder L, Oakley F, Trautwein C, Hatting M, Ross T, Bernardo B, Oldenburger A, Toftegaard Hjuler S, Ksiazek I, Linden D, Schuppan D, Rodriguez-Cuenca S, Manuela Tonini M, Castañeda TR, Kannt A, Rodrigues CMP, Cockell S, Govaere O, Daly AK, Allison M, Honnens de Lichtenberg K, Kim YO, Lindblom A, Oldam S, Andréasson A-C, Schlerman F, Marioneaux J, Sanyal A, Afonso MB, Younes R, Amano Y, Friedman SL, Wang S, Bhattacharya D, Simon E, Paradis V, Burt A, Grypari IM, Davies S, Driessen A, Yashiro H, Pors S, Worm Andersen M, Feigh M, Yunis C, Bedossa P, Stewart M, Cater HL, Wells S, Schattenberg JM, Anstee QM, The LITMUS Investigators, Tiniakos D, Perfield JW, Petsalaki E, Davidsen P, Vidal-Puig A. An unbiased ranking of murine dietary models based on their proximity to human metabolic dysfunction-associated steatotic liver disease (MASLD). Nature Metabolism 2024, 6, 1178-1196.
  • Siachisumo C, Luzzi S, Aldalaqan S, Hysenaj G, Dalgliesh C, Cheung K, Gazzara M, Yonchev ID, James K, Kheirollahi Chadegani M, Ehrmann I, Smith GR, Cockell SJ, Munkley J, Barash Y, Wilson SA, Elliott DJ. An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression. eLife 2024, 12, RP89705.
  • Queen R, Crosier M, Eley L, Kerwin J, Turner JE, Yu J, Alqahtani A, Dhanaseelan T, Overman L, Soetjoadi H, Baldock R, Coxhead J, Boczonadi V, Laude A, Cockell SJ, Kane MA, Lisgo S, Henderson DJ. Spatial transcriptomics reveals novel genes during the remodelling of the embryonic human arterial valves. PLoS Genetics 2023, 19(11).
  • Zormpas E, Queen R, Comber A, Cockell SJ. Mapping the transcriptome: Realizing the full potential of spatial data analysis. Cell 2023, 186(26), 5677 - 5689.
  • Govaere O, Hasoon M, Alexander L, Cockell S, Tiniakos D, Ekstedt M, Schattenberg JM, Boursier J, Bugianesi E, Ratziu V, LITMUS Investigators, Daly AK, Anstee QM. A proteo-transcriptomic map of non-alcoholic fatty liver disease signatures. Nature Metabolism 2023, 5, 572-578.
  • Hanrath AT, Hatton CF, Gothe F, Browne C, Vowles J, Leary P, Cockell SJ, Cowley SA, James WS, Hambleton S, Duncan CJA. Type I Interferon receptor (IFNAR2) deficiency reveals Zika virus cytopathicity in human macrophages and microglia. Frontiers in Immunology 2022, 13, 1035532.
  • Datta HK, Kringen MK, Tuck SP, Salpingidou G, Olstad OK, Gautvik KM, Cockell SJ, Gautvik VT, Prediger M, Wu JJ, Birch MA, Reppe S. Mechanical-Stress-Related Epigenetic Regulation of ZIC1 Transcription Factor in the Etiology of Postmenopausal Osteoporosis. International Journal of Molecular Sciences 2022, 23(6), 2957.
  • James K, Alsobhe A, Cockell SJ, Wipat A, Pocock M. Integration of probabilistic functional networks without an external Gold Standard. BMC Bioinformatics 2022, 23, 302.
  • Johnson K, Leary PJ, Govaere O, Barter MJ, Charlton SH, Cockell SJ, Tiniakos D, Zatorska M, Bedossa P, Brosnan MJ, Cobbold JF, Ekstedt M, Aithal GP, Clement K, Schattenberg JM, Boursier J, Ratziu V, Bugianesi E, Anstee QM, Daly AK, LITMUS Consortium Investigators. Increased serum miR-193a-5p during non-alcoholic fatty liver disease progression: Diagnostic and mechanistic relevance. JHEP Reports 2022, 4(2), 100409.
  • Donaghy PC, Cockell SJ, Martin-Ruiz C, Coxhead J, Kane J, Erskine D, Koss D, Taylor JP, Morris CM, O'Brien JT, Thomas AJ. Blood mRNA expression in Alzheimer’s disease and dementia with Lewy bodies. American Journal of Geriatric Psychiatry 2022, 30(9), 964-975.
  • Oud MS, Smits RM, Smith HE, Mastrorosa FK, Holt GS, Houston BJ, de Vries PF, Alobaidi BKS, Batty LE, Ismail H, Greenwood J, Sheth H, Mikulasova A, Astuti GDN, Gilissen C, McEleny K, Turner H, Coxhead J, Cockell S, Braat DDM, Fleischer K, D'Hauwers KWM, Schaafsma E, Consortium GEMINI, Nagirnaja L, Conrad DF, Friedrich C, Kliesch S, Aston KI, Riera-Escamilla A, Krausz C, Gonzaga-Jauregui C, Santibanez-Koref M, Elliott DJ, Vissers LELM, Tuttelmann F, O'Bryan MK, Ramos L, Xavier MJ, van der Heijden GW, Veltman JA. A de novo paradigm for male infertility. Nature Communications 2022, 13(154).
  • Kozumi K, Kodama T, Murai H, Sakane S, Govaere O, Cockell S, Motooka D, Kakita N, Yamada Y, Kondo Y, Tahata Y, Yamada R, Hikita H, Sakamori R, Kamada Y, Daly AK, Anstee QM, Tatsumi T, Morii E, Takehara T. Transcriptomics Identify Thrombospondin-2 as a Biomarker for Nonalcoholic Steatohepatitis and Advanced Liver Fibrosis. Hepatology 2021, 74(5), 2452-2466.
  • Addison R, Weatherhead SC, Pawitri A, Smith GR, Rider A, Grantham HJ, Cockell SJ, Reynolds NJ. Therapeutic wavelengths of ultraviolet B radiation activate apoptotic, circadian rhythm, redox signalling and key canonical pathways in psoriatic epidermis. Redox Biology 2021, 41, 101924.
  • Pfister D, Gonzalo N, Nunez N, Pinyol R, Govaere O, Pinter M, Szydlowska M, Gupta R, Qiu M, Deczkowska A, Weiner A, Muller F, Sinha A, Friebel E, Engleitner T, Lenggenhager D, Moncsek A, Heide D, Stirm K, Kosla J, Kotsiliti E, Leone V, Dudek M, Yousuf S, Inverso D, Singh I, Teijeiro A, Castet F, Montironi C, Haber PK, Tiniakos D, Bedossa P, Cockell S, Younes R, Vacca M, Marra F, Schattenberg JM, Allison M, Bugianesi E, Ratziu R, Pressiani T, DAlessio A, Personeni N, Rimassa L, Daly AK, Scheiner B, Pomej K, Kirstein MM, Vogel A, PeckRadosavljevic M, Hucke F, Finkelmeier F, Waidmann O, Trojan J, Schulze K, Wege H, Koch S, Weinmann A, Bueter M, Rossler F, Siebenhuner A, DeDosso S, Mallm JP, Umansky V, Jugold M, Luedde T, Schietinger A, Schirmacher P, Emu B, Augustin HG, Billeter A, MullerStich B, Kikuchi H, Duda DG, Kutting F, Waldschmidt DT, Ebert MP, Rahbari N, Mei HE, Schulz AR, Ringelhan M, Malek N, Spahn S, Bitzer M, deGalarreta MR, Lujambio A, Dufour JF, Marron TU, Kaseb A, Kudo M, Huang YH, Djouder N, Wolter K, Zender L, Marche PN, Decaens T, Pinato DJ, Rad R, Mertens JC, Weber A, Unger K, Meissner F, Roth S, Jilkova ZM, Claassen M, Anstee QM, Amit I, Knolle P, Becher B, Llovet JM, Heikenwalder M. NASH limits anti-tumor surveillance in immunotherapy-treated HCC. Nature 2021, 592, 450-456.
  • 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, Oresic M, Darlay R, Cordell H, Marra F, Vidal-Puig A, Bedossa P, Schattenberg JM, Clément K, Allison M, Bugianesi E, Ratziu V, Daly AK, Anstee QM. Transcriptomic profiling across the nonalcoholic fatty liver disease spectrum reveals gene signatures for steatohepatitis and fibrosis. Science Translational Medicine 2020, 12(572), eaba4448.
  • Ball SL, Cockell SJ, Wilson JA, Mann DA, Fisher AJ. Microarray analysis of primary epithelial and fibroblast cells in chronic rhinosinusitis without nasal polyps. Rhinology 2020, 58(6), 581-587.
  • Anstee QM, Darlay R, Cockell S, Meroni M, Govaere O, Tiniakos D, Burt AD, Bedossa P, Palmer J, Liu YL, Aithal GP, Allison M, Yki-Järvinen H, Vacca M, Dufour JF, Invernizzi P, Prati D, Ekstedt M, Kechagias S, Francque S, Petta S, Bugianesi E, Clement K, Ratziu V, Schattenberg JM, Valenti L, Day CP, Cordell HJ, Daly AK. Genome-Wide Association Study of Non-Alcoholic Fatty Liver and Steatohepatitis in a Histologically-Characterised Cohort. Journal of Hepatology 2020, 73(3), 505-515.
  • Govaere O, Cockell S, Van Haele M, Wouters J, Van Delm W, Van den Eynde K, Bianchi A, van Eijsden R, Van Steenbergen W, Monbaliu D, Nevens F, Roskams T. High-throughput sequencing identifies aetiology-dependent differences in ductular reaction in human chronic liver disease. Journal of Pathology 2019, 248(1), 66-76.
  • Davies HR, Hodgson K, Schwalbe E, Coxhead J, Sinclair N, Zou X, Cockell S, Husain A, Nik-Zainal S, Rajan N. Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome. Nature Communications 2019, 10, 4717.
  • Collin J, Queen R, Zerti D, Dorgau B, Hussain R, Coxhead J, Cockell S, Lako M. Deconstructing Retinal Organoids: Single cell RNA-Seq reveals the cellular components of human pluripotent stem cell-derived retina. Stem Cells (Durham) 2019, 37(5), 593-598.
  • Cheung K, Burgers MJ, Young DA, Cockell S, Reynard LN. Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage. Epigenetics 2019, 15(6-7), 594-603.
  • Munkley J, Li L, Krishnan SRG, Hysenaj G, Scott E, Dalgliesh C, Oo HZ, Maia TM, Cheung K, Ehrmann I, Livermore KE, Zielinska H, Thompson O, Knight B, McCullagh P, McGrath J, Crundwell M, Harries LW, Daugaard M, Cockell S, Barbosa-Morais NL, Oltean S, Elliott DJ. Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer. eLife 2019, 8, e47678.
  • Ehrmann I, Crichton JH, Gazzara MR, James K, Liu Y, Grellscheid SN, Curk T, de Rooij D, Steyn JS, Cockell S, Adams IR, Barash Y, Elliott DJ. An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning. eLife 2019, 8, e39304.
  • Phillips HM, Stothard CA, Shaikh Qureshi WM, Kousa AI, BrionesLeon JA, Khasawneh RR, Sanders R, O'Loughlin C, Mazzotta S, Dodds R, Seidel K, Bates T, Nakatomi M, Cockell SJ, Schneider JE, Mohun TJ, Maehr R, Kist R, Peters H, Bamforth SD. Pax9 is required for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to control 4^th pharyngeal arch artery morphogenesis. Development 2019, 146, dev177618.
  • Janus P, Szoltysek K, Zajac G, Stokowy T, Walaszczyk A, Widlak W, Wojtas B, Gielniewski B, Iwanaszko M, Braun R, Cockell S, Perkins ND, Kimmel M, Widlak P. Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes. Cellular Signalling 2018, 46, 23-31.
  • James K, Chipeta C, Parker A, Harding S, Cockell SJ, Gillespie CS, Hallinan J, Barone F, Bowman SJ, Ng W-F, Fisher BA, for the UK Primary Sjögren's Syndrome Registry. B-cell activity markers are associated with different disease activity domains in primary Sjögren's syndrome. Rheumatology 2018, 57(7), 1222-1227.
  • Szoltysek K, Janus P, Zajac G, Stokowy T, Walaszczyk A, Widlak W, Wojtas B, Gielniewski B, Cockell S, Perkins ND, Kimmel M, Widlak P. 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 2018, 19(1), 813.
  • James K, Gamba P, Cockell SJ, Zenkin N. Misincorporation by RNA polymerase is a major source of transcription pausing in vivo. Nucleic Acids Research 2017, 45(3), 1105-1113.
  • James K, Cockell SJ, Zenkin N. Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics. Methods 2017, 120, 76-84.
  • Pease LI, Clegg PD, Proctor CJ, Shanley DJ, Cockell SJ, Peffers MJ. Cross platform analysis of transcriptomic data identifies ageing has distinct and opposite effects on tendon in males and females. Scientific Reports 2017, 7(1), 14443.
  • Elder A, Bomken S, Wilson I, Blair HJ, Cockell S, Ponthan F, Dormon K, Pal D, Heidenreich O, Vormoor J. Abundant and equipotent founder cells establish and maintain acute lymphoblastic leukaemia. Leukemia 2017, 31, 2577-2586.
  • Hardyman J, Tyson J, Jackson K, Aldridge C, Cockell S, Wakeling L, Valentine RA, Ford D. 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 2016, 8(3), 337-343.
  • Méplan C, Johnson IT, Polley ACJ, Cockell S, Bradburn DM, Commane DM, Arasaradnam RP, Mulholland F, Zupanic A, Mathers JC, Hesketh J. Transcriptomics and proteomics show that selenium affects inflammation, cytoskeleton, and cancer pathways in human rectal biopsies. The FASEB Journal 2016, 30(8), 2812-2825.
  • Hunter JE, Butterworth JA, Zhao B, Sellier H, Campbell KJ, Thomas HD, Bacon CM, Cockell SJ, Gewurz BE, Perkins ND. The NF-κB subunit c-Rel regulates Bach2 tumour suppressor expression in B-cell lymphoma. Oncogene 2016, 35(26), 3476-3484.
  • Mullen J, Cockell SJ, Tipney H, Woollard PM, Wipat A. Mining integrated semantic networks for drug repositioning opportunities. PeerJ 2016, 4, e1558.
  • Khundakar AA, Hanson PS, Erskine D, Lax NZ, Roscamp J, Karyka E, Tsefou E, Singh P, Cockell SJ, Gribben A, Ramsay L, Blain PJ, Mosimann UP, Lett DJ, Elstner M, Turnbull DM, Xiang CC, Brownstein MJ, O'Brien JT, Taylor JP, Attems J, Thomas AJ, McKeith IG, Morris CM. Analysis of primary visual cortex in dementia with Lewy bodies indicates GABAergic involvement associated with recurrent complex visual hallucinations. Acta Neuropathologica Communications 2016, 4, 66.
  • Mullen J, Cockell SJ, Woollard P, Wipat A. An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations. PLoS One 2016, 11(5), e0155811.
  • Moles A, Butterworth JA, Sanchez A, Hunter JE, Leslie J, Sellier H, Tiniakos D, Cockell SJ, Mann DA, Oakley F, Perkins ND. A RelA(p65) Thr505 phospho-site mutation reveals an important mechanism regulating NF-kB dependent liver regeneration and cancer. Oncogene 2016, 35(35), 4623-4632.
  • Ogo OA, Tyson J, Cockell SJ, Howard A, Valentine RA, Ford D. 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). Molecular and Cell Biology 2015, 35(6), 977-987.
  • Wakeling LA, Ions LJ, Escolme SM, Cockell SJ, Su T, Dey M, Hampton EV, Jenkins G, Wainwright LJ, McKay JA, Ford D. SIRI1 effects DNA methylation of polycomb protein target genes, a hotspot of the epigenetic shift observed in ageing. Human Genomics 2015, 9, 14.
  • Dubarry M, Lawless C, Banks AP, Cockell S, Lydall D. Genetic Networks Required to Coordinate Chromosome Replication by DNA Polymerases α, δ, and ε in Saccharomyces cerevisiae. G3: Genes, Genomes, Genetics 2015, 5(10), 2187-2197.
  • Gabriel AS, Lafta FM, Schwalbe EC, Nakjang S, Cockell SJ, Iliasova A, Enshaei A, Schwab C, Rand V, Clifford SC, Kinsey SE, Mitchell CD, Vora A, Harrison CJ, Moorman AV, Strathdee G. Epigenetic landscape correlates with genetic subtype but does not predict outcome in childhood acute lymphoblastic leukemia. Epigenetics 2015, 10(8), 717-726.
  • James K, Al-Ali S, Tarn J, Cockell SJ, Gillespie CS, Hindmarsh V, Locke J, Mitchell S, Lendrem D, Bowman S, Price E, Pease CT, Emery P, Lanyon P, Hunter JA, Gupta M, Bombardieri M, Sutcliffe N, Pitzalis C, McLaren J, Cooper A, Regan M, Giles I, Isenberg D, Saravanan V, Coady D, Dasgupta B, McHugh N, Young-Min S, Moots R, Gendi N, Akil M, Griffiths B, The UK Primary Sjögren’s Syndrome registry, Wipat A, Newton J, Jones DE, Isaacs J, Hallinan J, Ng W-F. A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome. PLoS ONE 2015, 10(12), e0143970.
  • Probert PM, Chung GW, Cockell SJ, Agius L, Mosesso P, White SA, Oakley F, Brown CD, Wright MC. Utility of B-13 Progenitor-Derived Hepatocytes in Hepatotoxicity and Genotoxicity Studies. Toxicological Sciences 2014, 137(2), 350-370.
  • Iannetti A, Ledoux AC, Tudhope SJ, Sellier H, Zhao B, Mowla S, Moore A, Hummerich H, Gewurz BE, Cockell SJ, Jat PS, Willmore E, Perkins ND. Regulation of p53 and Rb Links the Alternative NF-kappaB Pathway to EZH2 Expression and Cell Senescence. PLoS Genetics 2014, 10(9), e1004642.
  • Werner A, Cockell S, Falconer J, Carlile M, Alnumeir S, Robinson J. Contribution of natural antisense transcription to an endogenous siRNA signature in human cells. BMC Genomics 2014, 15, 19.
  • Flanagan K, Cockell S, Harwood C, Hallinan J, Nakjang S, Lawry B, Wipat A. A distributed computational search strategy for the identification of diagnostics targets: Application to finding aptamer targets for methicillin-resistant staphylococci. Journal of Integrative Bioinformatics 2014, 11(2), 242.
  • Werner Andreas, Cockell Simon, Falconer Jane, Alnumeir Sammer, Robinson John. Production of small genic RNAs and endogenous siRNAs from sense/antisense transcripts in human cells. Genome Biology 2013. Submitted.
  • Lord P, Cockell S, Stevens R. Three Steps to Heaven: Semantic Publishing in a Real World Workflow. Future Internet 2012, 4(4), 1004-1015.
  • Lee KC, Padget K, Curtis Hannah, Cowell IG, Moiani D, Sondka Z, Morris NK, Jackson GH, Cockell SJ, Tainer JA, Austin CA. MRE11 facilitates the removal of human topoisomerase II complexes from genomic DNA. Biology Open 2012, 1(9), 863-873.
  • Weile J, James K, Hallinan J, Cockell SJ, Lord P, Wipat A, Wilkinson DJ. Bayesian integration of networks without gold standards. Bioinformatics 2012, 28(11), 1495-1500.
  • Stadler LKJ, Hoffmann T, Tomlinson DC, Song Q, Lee T, Busby M, Nyathi Y, Gendra E, Tiede C, Flanagan K, Cockell SJ, Wipat A, Harwood C, Wagner SD, Knowles MA, Davis JJ, Keegan N, KoFerrigno P. 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 2011, 24(9), 751-763.
  • Weile J, Pocock M, Cockell SJ, Lord P, Dewar JM, Holstein EM, Wilkinson D, Lydall D, Hallinan J, Wipat A. Customizable views on semantically integrated networks for systems biology. Bioinformatics 2011, 27(9), 1299-1306.
  • Parnell LD, Lindenbaum P, Shameer K, Dall'Olio GM, Swan DC, Jensen LJ, Cockell SJ, Pedersen BS, Mangan ME, Miller CA, Albert I. BioStar: An Online Question & Answer Resource for the Bioinformatics Community. PLoS Computational Biology 2011, 7(10), e1002216.
  • Emami K, Morris NJ, Cockell SJ, Golebiowska G, Shu QY, Gatehouse AMR. 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 2010, 58(11), 6912-6922.
  • Cockell SJ, Weile J, Lord P, Wipat C, Andriychenko D, Pocock M, Wilkinson D, Young M, Wipat A. An integrated dataset for in silico drug discovery. Journal of Integrative Bioinformatics 2010, 7(3), 116.
  • Cockell SJ, Baldo O, Jackson RM. Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking. Bioinformatics 2007, 23(5), 573-581.

• Book Chapter

  • Cockell S, Bashton M, Gillespie CS. Bioconductor tools for microarray data analysis. In: Rueda, L, ed. Microarray Image and Data Analysis: Theory and Practice. Boca Raton: CRC Press, 2014.

• Conference Proceedings (inc. Abstracts)

  • James K, Cockell SJ, Gillespie CS, Assi LK, Bowman S, Griffiths B, Ng WF, UKPSSR. Serum Free Light Chains are Associated with Clinical Disease Activity of Primary Sjögren's Syndrome in the Cutaneous, Biological and Renal Domains. In: The 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell.
  • Al-Ali S, Skelton A, Cockell S, Tarn J, James K, Bowman SJ, Griffiths B, Locke J, Young D, Ng WF, UKPSSR. Identification of Whole Blood Gene Expression Signature in Primary Sjogren's Syndrome Associated Lymphoma. In: 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell Publishing Ltd.
  • Elder A, Blair H, Dormon K, Bomken S, Cockell SJ, Heidenreich O, Vormoor J. High Abundance of Acute Lymphoblastic Leukaemia Founder Clones Does Not Translate to Functional Heterogeneity. In: 57th ASH Annual Meeting. 2015, Orlando, USA: American Society of Hematology.
  • James K, Al-Ali S, Tarn J, Cockell SJ, Gillespie CS, Bowman S, Isaacs J, Jones DE, Newton J, Price E, Wipat A, Hallinan J, Ng WF, UKPSSR. Gene Set Enrichment Analysis Across Multiple Expression Studies Reveals a Core Subset of Primary Sjögren's Syndrome-Related Genes. In: The 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell.
  • James K, Al-Ali S, Tarn J, Cockell SJ, Gillespie CS, Bowman S, Isaacs J, Jones DE, Newton J, Price E, Wipat A, Hallinan J, Ng WF, UKPSSR. A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome. In: The 13th International Symposium on Sjögren's Syndrome. 2015, Bergen, Norway: Wiley-Blackwell.
  • Tarn J, Cockell S, Gillespie C, Al-Ali S, James K, Locke J, Bowman S, Griffiths B, Young D, Ng WF. Whole Blood microRNA Signature for Primary Sjogren's Syndrome-Related Lymphoma. In: ACR/ARHP Annual Meeting. 2014, Boston, MA, USA: Wiley-Blackwell Publishing.
  • Al-Ali S, Cockell S, Skelton A, James K, Tarn J, Young D, Griffiths B, Bowman S, Locke J, Ng WF. Identification of Whole Blood Gene Expression Signature in Primary Sjogren's Syndrome Associated Lymphoma. In: ACR/ARHP Annual Meeting. 2014, Boston, MA, USA: Wiley-Blackwell Publishing.
  • James K, Cockell SJ, Gillespie CS, Assi L, Bowman S, Griffiths B, Ng WF, UKPSSR. Baff and B2m, but not Free Light Chains, Correlate with Disease Activity in Primary Sjögren's Syndrome (PSS). In: Annual European Congress of Rheumatology. 2014, Paris, France: BMJ Group.
  • Reppe S, Olstad OK, Cockell SJ, Sanderson P, Gautvik VT, Gautvik KM, Datta H. Transcriptome Profiling Reveals that Postmenopausal Osteoporosis and Bone Density Correlate with Fat Metabolism but not Adiposity. In: 2013 Annual Meeting of the American Society for Bone and Mineral Research. 2013, Baltimore, MD, USA: Wiley-Blackwell.
  • Nesbitt V, Pitceathly R, Cockell S, Poulton J, Rahman S, Hanna M, Taylor R, Chinnery P, Turnbull D, McFarland R. The Medical Research Council Neuromuscular Centre for Translational Research Mitochondrial Disease Patient Cohort Study UK: From Conceptualisation to Utilisation. In: Association of British Neurologists (ABN) joint meeting with the Royal College of Physicians (RCP). 2013, London, UK: BMJ Publishing Group.
  • Pratt AG, Brown PM, Cockell SJ, Wilson G, Isaacs JD. A CD4+T-Cell Gene Expression Signature Predicts Drug Survival on Methotrexate Monotherapy in Early Rheumatoid Arthritis. In: 33rd European Workshop for Rheumatology Research. 2013, Prague, Czech Republic: BMJ Publishing Group.
  • Nesbitt V, Pitceathly R, Cockell S, Poulton J, Rahman S, Hanna M, Turnbull D, McFarland R. The medical research council neuromuscular centre for translational research mitochondrial disease patient cohort study UK: from conceptualisation to utilisation. In: United Kingdom Neuromuscular Translational Research Conference. 2012, Newcastle upon Tyne: Elsevier Ltd.
  • Pratt AG, Brown PM, Cockell SJ, Wilson G, Isaacs JD. A CD4+T-Cell Gene Expression Signature Predicts Drug Survival On Methotrexate Monotherapy in Early Rheumatoid Arthritis. In: Annual Scientific Meeting of the American College of Rheumatology (ACR). 2012, Washington, DC, USA: John Wiley & Sons, Inc.

• Letters

  • Masi AC, Fofanova TY, Lamb CA, Auchtung JM, Britton RA, Estes MK, Ramani S, Cockell S, Coxhead J, Embleton ND, Berrington JE, Petrosino JF, Stewart CJ. Distinct gene expression profiles between human preterm- and adult-derived intestinal organoids exposed to Enterococcus faecalis: A pilot study. Gut 2022, 71(10), 2141-2143.
  • Hoogland C, O'Gorman M, Bogard P, Gibson F, Berth M, Cockell SJ, Ekefjard A, Forsstrom-Olsson O, Kapferer A, Nilsson M, Martinez-Bartolome S, Albar JP, Echevarria-Zomeno S, Martinez-Gomariz M, Joets J, Binz PA, Taylor CF, Dowsey A, Jones AR. Guidelines for reporting the use of gel image informatics in proteomics. Nature Biotechnology 2010, 28(7), 655-656.

• Report

  • Misirli G, Hallinan JS, Pocock M, Cockell SJ, Weile J, Wipat A. BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology. Newcastle upon Tyne: School of Computing Science, University of Newcastle upon Tyne, 2011. School of Computing Science Technical Report Series 1237.

• Reviews

  • James K, Wipat A, Cockell SJ. Expanding Interactome Analyses beyond Model Eukaryotes. Briefings in Functional Genomics 2022, 21(4), 243-269.
  • Zerti Z, Collin J, Queen R, Cockell SJ, Lako M. Understanding the complexity of retinal and pluripotent stem cell derived retinal organoids with single cell RNA sequencing: current progress, remaining challenges and future prospectives. Current Eye Research 2020, 45(3), 385-396.