Publications by Dr Simon Cockell - ePrints

Browsing publications by Dr Simon Cockell.

Newcastle Authors	Title	Year
Chile Siachisumo Dr Sara Luzzi Saad Aldalaqan Dr Gerald Hysenaj Caroline Dalgliesh et al.	An anciently diverged family of RNA binding proteins maintain correct splicing of a class of ultra-long exons through cryptic splice site repression	2024
Professor Fiona Oakley Dr Simon Cockell Dr Olivier Govaere Professor Ann Daly Professor Arun Sanyal et al.	An unbiased ranking of murine dietary models based on their proximity to human metabolic dysfunction-associated steatotic liver disease (MASLD)	2024
Dr Olivier Govaere Dr Simon Cockell Michalina Zatorska Kristy Wonders Professor Dina Tiniakos et al.	Pharmacogene expression during progression of metabolic dysfunction-associated steatotic liver disease: Studies on mRNA and protein levels and their relevance to drug treatment	2024
Neela Codadu Dr Simon Cockell Professor Andrew Trevelyan Dr Ryley Parrish	RNA Sequencing Demonstrates Ex Vivo Neocortical Transcriptomic Changes Induced by Epileptiform Activity in Male and Female Mice	2024
Dr Olivier Govaere Dr Megan Hasoon Dr Simon Cockell Dr Dina Tiniakos Professor Ann Daly et al.	A proteo-transcriptomic map of non-alcoholic fatty liver disease signatures	2023
Lefteris Zormpas Dr Rachel Queen Dr Simon Cockell	Mapping the transcriptome: Realizing the full potential of spatial data analysis	2023
Dr Rachel Queen Moira Crosier Dr Lorraine Eley Dr Janet Kerwin Jasmin Turner et al.	Spatial transcriptomics reveals novel genes during the remodelling of the embryonic human arterial valves	2023
Hannah Smith Francesco Kumara Mastrorosa Dr Giles Holt Dr Brendan Houston Dr Bilal Alobaidi et al.	A de novo paradigm for male infertility	2022
Dr Paul Donaghy Dr Simon Cockell Dr Carmen Martin-Ruiz Dr Jonathan Coxhead Dr Joseph Kane et al.	Blood mRNA expression in Alzheimer’s disease and dementia with Lewy bodies	2022
Andrea Masi Professor Chris Lamb Dr Simon Cockell Dr Jonathan Coxhead Professor Nicholas Embleton et al.	Distinct gene expression profiles between human preterm- and adult-derived intestinal organoids exposed to Enterococcus faecalis: A pilot study	2022
Dr Katherine James Professor Anil Wipat Dr Simon Cockell	Expanding Interactome Analyses beyond Model Eukaryotes	2022
Dr Katherine Johnson Dr Peter Leary Dr Olivier Govaere Dr Matthew Barter Sarah Charlton et al.	Increased serum miR-193a-5p during non-alcoholic fatty liver disease progression: Diagnostic and mechanistic relevance	2022
Dr Katherine James Aoesha Alsobhe Dr Simon Cockell Professor Anil Wipat Dr Matthew Pocock et al.	Integration of probabilistic functional networks without an external Gold Standard	2022
Dr Harish Datta Dr Stephen Tuck Dr Simon Cockell Michael Prediger Dr Mark Birch et al.	Mechanical-Stress-Related Epigenetic Regulation of ZIC1 Transcription Factor in the Etiology of Postmenopausal Osteoporosis	2022
Dr Aidan Hanrath Catherine Hatton Dr Florian Gothe Connie Browne Dr Simon Cockell et al.	Type I Interferon receptor (IFNAR2) deficiency reveals Zika virus cytopathicity in human macrophages and microglia	2022
Dr Olivier Govaere Dr Dina Tiniakos Professor Pierre Bedossa Dr Simon Cockell Dr Massimo Younes et al.	NASH limits anti-tumor surveillance in immunotherapy-treated HCC	2021
Rachel Roberts Dr Sophie Weatherhead Dika Pawitri Dr Graham Smith Dr Ashley Rider et al.	Therapeutic wavelengths of ultraviolet B radiation activate apoptotic, circadian rhythm, redox signalling and key canonical pathways in psoriatic epidermis	2021
Dr Olivier Govaere Dr Simon Cockell Professor Ann Daly Professor Quentin Anstee	Transcriptomics Identify Thrombospondin-2 as a Biomarker for Nonalcoholic Steatohepatitis and Advanced Liver Fibrosis	2021
Professor Quentin Anstee Dr Rebecca Darlay Dr Simon Cockell Dr Olivier Govaere Dr Dina Tiniakos et al.	Genome-Wide Association Study of Non-Alcoholic Fatty Liver and Steatohepatitis in a Histologically-Characterised Cohort	2020
Stephen Ball Dr Simon Cockell Emerita Professor Janet Wilson Professor Derek Mann Professor Andrew Fisher et al.	Microarray analysis of primary epithelial and fibroblast cells in chronic rhinosinusitis without nasal polyps	2020
Dr Olivier Govaere Dr Simon Cockell Dr Dina Tiniakos Dr Rachel Queen Dr Massimo Younes et al.	Transcriptomic profiling across the nonalcoholic fatty liver disease spectrum reveals gene signatures for steatohepatitis and fibrosis	2020
Dr Rachel Queen Dr Simon Cockell Professor Majlinda Lako	Understanding the complexity of retinal and pluripotent stem cell derived retinal organoids with single cell RNA sequencing: current progress, remaining challenges and future prospectives	2020
Dr Helen Phillips Catherine Stothard Dr Wasay Shaikh Qureshi Dr Alberto Briones Leon Ramada Khasawneh et al.	Pax9 is required for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to control 4^th pharyngeal arch artery morphogenesis	2019
Dr Ingrid Ehrmann Dr Katherine James Yilei Liu Dr Sushma Grellscheid Dr Jannetta Steyn et al.	An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning	2019
Dr Jennifer Munkley SR Gokul Krishnan Gerald Hysenaj Dr Emma Scott Caroline Dalgliesh et al.	Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer	2019
Kat Cheung Marjolein Burgers Professor David Young Dr Simon Cockell Dr Louise Reynard et al.	Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage	2019
Dr Joseph Collin Dr Rachel Queen Dr Darin Zerti Dr Birthe Hilgen Raf Hussain et al.	Deconstructing Retinal Organoids: Single cell RNA-Seq reveals the cellular components of human pluripotent stem cell-derived retina	2019
Dr Kirsty Hodgson Dr Ed Schwalbe Dr Jonathan Coxhead Naomi Sinclair Dr Simon Cockell et al.	Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome	2019
Dr Olivier Govaere Dr Simon Cockell Dr Arianna Bianchi	High-throughput sequencing identifies aetiology-dependent differences in ductular reaction in human chronic liver disease	2019
Dr Katarzyna Szoltysek Dr Simon Cockell Professor Neil Perkins	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	2018
Dr Katherine James Dr Simon Cockell Dr Colin Gillespie Dr Jennifer Hallinan Dr Francesca Barone et al.	B-cell activity markers are associated with different disease activity domains in primary Sjögren's syndrome	2018
Dr Katarzyna Szoltysek Dr Anna Walaszczyk Dr Simon Cockell	Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes	2018
Dr Alex Elder Dr Simon Bomken Dr Ian Wilson Dr Helen Blair Dr Simon Cockell et al.	Abundant and equipotent founder cells establish and maintain acute lymphoblastic leukaemia	2017
Dr Louise Pease Dr Carole Proctor Dr Daryl Shanley Dr Simon Cockell	Cross platform analysis of transcriptomic data identifies ageing has distinct and opposite effects on tendon in males and females	2017
Dr Katherine James Dr Simon Cockell Professor Nikolay Zenkin	Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics	2017
Dr Katherine James Dr Pamela Gamba Dr Simon Cockell Professor Nikolay Zenkin	Misincorporation by RNA polymerase is a major source of transcription pausing in vivo	2017
Dr Anna Moles Fernandez Dr Jacqueline Butterworth Dr Jill Hunter Dr Jack Leslie Helene Sellier et al.	A RelA(p65) Thr505 phospho-site mutation reveals an important mechanism regulating NF-kB dependent liver regeneration and cancer	2016
Joseph Mullen Dr Simon Cockell Professor Anil Wipat	An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations	2016
Dr Ahmad Khundakar Dr Peter Hanson Dr Daniel Erskine Dr Nichola Lax Evangelia Karyka et al.	Analysis of primary visual cortex in dementia with Lewy bodies indicates GABAergic involvement associated with recurrent complex visual hallucinations	2016
Joseph Mullen Dr Simon Cockell Professor Anil Wipat	Mining integrated semantic networks for drug repositioning opportunities	2016
Dr Jill Hunter Dr Jacqueline Butterworth Helene Sellier Huw Thomas Dr Christopher Bacon et al.	The NF-κB subunit c-Rel regulates Bach2 tumour suppressor expression in B-cell lymphoma	2016
Dr Catherine Meplan Dr Simon Cockell David Bradburn Dr Daniel Commane Dr Ramesh Arasaradnam et al.	Transcriptomics and proteomics show that selenium affects inflammation, cytoskeleton, and cancer pathways in human rectal biopsies	2016
Dr Joy Hardyman-Carlile Dr John Tyson Dr Kelly Jackson Christine Aldridge Dr Simon Cockell et al.	Zinc sensing by metal-responsive transcription factor 1 (MTF1) controls metallothionein and ZnT1 expression to buffer the sensitivity of the transcriptome response to zinc	2016
Dr Katherine James Shereen Al-Ali Dr Jessica Tarn Dr Simon Cockell Dr Colin Gillespie et al.	A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren’s Syndrome	2015
Jessica Tarn Dr Simon Cockell Dr Colin Gillespie Emerita Professor Julia Newton Professor Anil Wipat et al.	A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome	2015
Dr Al Gabriel Fadhel Alsaid Naji Dr Ed Schwalbe Dr Sirintra Nakjang Dr Simon Cockell et al.	Epigenetic landscape correlates with genetic subtype but does not predict outcome in childhood acute lymphoblastic leukemia	2015
Shereen Al-Ali Dr Jessica Tarn Dr Simon Cockell Dr Colin Gillespie Professor John Isaacs et al.	Gene Set Enrichment Analysis Across Multiple Expression Studies Reveals a Core Subset of Primary Sjögren's Syndrome-Related Genes	2015
Dr Marion Dubarry Dr Conor Lawless Dr Andrew Banks Dr Simon Cockell Professor David Lydall et al.	Genetic Networks Required to Coordinate Chromosome Replication by DNA Polymerases α, δ, and ε in Saccharomyces cerevisiae	2015
Dr Alex Elder Dr Helen Blair Katie Dormon Dr Simon Bomken Dr Simon Cockell et al.	High Abundance of Acute Lymphoblastic Leukaemia Founder Clones Does Not Translate to Functional Heterogeneity	2015
Shereen Al-Ali Dr Simon Cockell Dr Jessica Tarn Dr Katherine James Sarah Bowman et al.	Identification of Whole Blood Gene Expression Signature in Primary Sjogren's Syndrome Associated Lymphoma	2015
Dr Simon Cockell Dr Colin Gillespie Professor Fai Ng	Serum Free Light Chains are Associated with Clinical Disease Activity of Primary Sjögren's Syndrome in the Cutaneous, Biological and Renal Domains	2015
Dr Luisa Wakeling Laura Ions Suzie Escolme Dr Simon Cockell Tianhong Su et al.	SIRI1 effects DNA methylation of polycomb protein target genes, a hotspot of the epigenetic shift observed in ageing	2015
Ogo Ogo Dr John Tyson Dr Simon Cockell Dr Alison Howard Professor Ruth Valentine et al.	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)	2015
Dr Keith Flanagan Dr Simon Cockell Professor Colin Harwood Dr Jennifer Hallinan Dr Sirintra Nakjang et al.	A distributed computational search strategy for the identification of diagnostics targets: Application to finding aptamer targets for methicillin-resistant staphylococci	2014
Dr Simon Cockell Dr Colin Gillespie Professor Fai Ng	Baff and B2m, but not Free Light Chains, Correlate with Disease Activity in Primary Sjögren's Syndrome (PSS)	2014
Dr Simon Cockell Dr Matthew Bashton Dr Colin Gillespie	Bioconductor tools for microarray data analysis	2014
Dr Andreas Werner Dr Simon Cockell Dr Jane Falconer Mark Carlile Dr Sammer Alnumeir et al.	Contribution of natural antisense transcription to an endogenous siRNA signature in human cells	2014
Shereen Al-Ali Dr Simon Cockell Andrew Skelton Dr Katherine James Dr Jessica Tarn et al.	Identification of Whole Blood Gene Expression Signature in Primary Sjogren's Syndrome Associated Lymphoma	2014
Dr Alessio Iannetti Dr Adeline Ledoux Dr Susan Tudhope Helene Sellier Adam Moore et al.	Regulation of p53 and Rb Links the Alternative NF-kappaB Pathway to EZH2 Expression and Cell Senescence	2014
Dr Phillip Probert Git Chung Dr Simon Cockell Professor Loranne Agius Steven White et al.	Utility of B-13 Progenitor-Derived Hepatocytes in Hepatotoxicity and Genotoxicity Studies	2014
Dr Jessica Tarn Dr Simon Cockell Dr Colin Gillespie Shereen Al-Ali Dr Katherine James et al.	Whole Blood microRNA Signature for Primary Sjogren's Syndrome-Related Lymphoma	2014
Dr Arthur Pratt Dr Philip Brown Dr Simon Cockell Gillian Wilson Professor John Isaacs et al.	A CD4+T-Cell Gene Expression Signature Predicts Drug Survival on Methotrexate Monotherapy in Early Rheumatoid Arthritis	2013
Dr Victoria Nesbitt Dr Robert Pitceathly Dr Simon Cockell Professor Michael Hanna Professor Patrick Chinnery et al.	The Medical Research Council Neuromuscular Centre for Translational Research Mitochondrial Disease Patient Cohort Study UK: From Conceptualisation to Utilisation	2013
Dr Simon Cockell Dr Harish Datta	Transcriptome Profiling Reveals that Postmenopausal Osteoporosis and Bone Density Correlate with Fat Metabolism but not Adiposity	2013
Dr Arthur Pratt Dr Philip Brown Dr Simon Cockell Gillian Wilson Professor John Isaacs et al.	A CD4+T-Cell Gene Expression Signature Predicts Drug Survival On Methotrexate Monotherapy in Early Rheumatoid Arthritis.	2012
Jochen Weile Dr Katherine James Dr Jennifer Hallinan Dr Simon Cockell Dr Phillip Lord et al.	Bayesian integration of networks without gold standards	2012
Dr Kay Padget Hannah Curtis Dr Ian Cowell Dr Zbyslaw Sondka Dr Nick Morris et al.	MRE11 facilitates the removal of human topoisomerase II complexes from genomic DNA	2012
Dr Victoria Nesbitt Dr Robert Pitceathly Dr Simon Cockell Professor Michael Hanna Emeritus Professor Doug Turnbull et al.	The medical research council neuromuscular centre for translational research mitochondrial disease patient cohort study UK: from conceptualisation to utilisation	2012
Dr Phillip Lord Dr Simon Cockell	Three Steps to Heaven: Semantic Publishing in a Real World Workflow	2012
Dr Goksel Misirli Dr Jennifer Hallinan Dr Matthew Pocock Dr Simon Cockell Jochen Weile et al.	BacillOndex: An Integrated Data Resource for Systems and Synthetic Biology	2011
Dr Daniel Swan Dr Simon Cockell	BioStar: An Online Question & Answer Resource for the Bioinformatics Community	2011
Jochen Weile Dr Matthew Pocock Dr Simon Cockell Dr Phillip Lord James Dewar et al.	Customizable views on semantically integrated networks for systems biology	2011
Dr Simon Cockell Dr Phillip Lord	Kcite - A tool for producing citations and bibliographies in WordPress posts	2011
Dr Simon Cockell Dr Phillip Lord	Mathjax-Latex Wordpress Plugin	2011
Dr Simon Cockell Professor Anil Wipat Professor Colin Harwood Dr Neil Keegan	Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant.	2011
Dr Simon Cockell Jochen Weile Dr Phillip Lord Dmytro Andriychenko Dr Matthew Pocock et al.	An integrated dataset for in silico drug discovery	2010
Dr Kaveh Emami Dr Nick Morris Dr Simon Cockell Professor Angharad MR Gatehouse	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	2010
Dr Frank Gibson Dr Simon Cockell	Guidelines for reporting the use of gel image informatics in proteomics	2010
Dr Simon Cockell	Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking	2007