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Blog Post number 4
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Blog Post number 1
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publications
Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking
Published in Bioinformatics (Oxford, England), 2007
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Recommended citation: Simon Cockell, Baldo Oliva, Richard Jackson, "Structure-based evaluation of in silico predictions of protein-protein interactions using Comparative Docking." Bioinformatics (Oxford, England), 2007.
An integrated dataset for in silico drug discovery
Published in Journal of Integrative Bioinformatics, 2010
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Recommended citation: Simon Cockell, Jochen Weile, Phillip Lord, Claire Wipat, Dmytro Andriychenko, Matthew Pocock, Darren Wilkinson, Malcolm Young, Anil Wipat, "An integrated dataset for in silico drug discovery." Journal of Integrative Bioinformatics, 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
Published in Journal of Agricultural and Food Chemistry, 2010
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Recommended citation: Kaveh Emami, Nicholas Morris, Simon Cockell, Gabriela Golebiowska, Qing-Yao Shu, Angharad 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." Journal of Agricultural and Food Chemistry, 2010.
Guidelines for reporting the use of gel image informatics in proteomics
Published in Nature Biotechnology, 2010
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Recommended citation: Christine Hoogland, Martin O'Gorman, Philippe Bogard, Frank Gibson, Matthias Berth, Simon Cockell, Andreas Ekefjärd, Ola Forsstrom-Olsson, Anna Kapferer, Mattias Nilsson, Salvador Martínez-Bartolomé, Juan Albar, Sira Echevarría-Zomeño, Montserrat Martínez-Gomariz, Johann Joets, Pierre-Alain Binz, Chris Taylor, Andrew Dowsey, Andrew Jones, "Guidelines for reporting the use of gel image informatics in proteomics." Nature Biotechnology, 2010.
Customizable views on semantically integrated networks for systems biology
Published in Bioinformatics (Oxford, England), 2011
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Recommended citation: Jochen Weile, Matthew Pocock, Simon Cockell, Phillip Lord, James Dewar, Eva-Maria Holstein, Darren Wilkinson, David Lydall, Jennifer Hallinan, Anil Wipat, "Customizable views on semantically integrated networks for systems biology." Bioinformatics (Oxford, England), 2011.
Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant
Published in Protein engineering, design & selection: PEDS, 2011
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Recommended citation: Lukas Stadler, Toni Hoffmann, Darren Tomlinson, Qifeng Song, Tracy Lee, Michael Busby, Yvonne Nyathi, Elisenda Gendra, Christian Tiede, Keith Flanagan, Simon Cockell, Anil Wipat, Colin Harwood, Simon Wagner, Margaret Knowles, Jason Davis, Neil Keegan, Paul Ferrigno, "Structure-function studies of an engineered scaffold protein derived from Stefin A. II: Development and applications of the SQT variant." Protein engineering, design & selection: PEDS, 2011.
BioStar: an online question & answer resource for the bioinformatics community
Published in PLoS computational biology, 2011
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Recommended citation: Laurence Parnell, Pierre Lindenbaum, Khader Shameer, Giovanni Dall'Olio, Daniel Swan, Lars Jensen, Simon Cockell, Brent Pedersen, Mary Mangan, Christopher Miller, Istvan Albert, "BioStar: an online question & answer resource for the bioinformatics community." PLoS computational biology, 2011.
Bayesian integration of networks without gold standards
Published in Bioinformatics (Oxford, England), 2012
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Recommended citation: Jochen Weile, Katherine James, Jennifer Hallinan, Simon Cockell, Phillip Lord, Anil Wipat, Darren Wilkinson, "Bayesian integration of networks without gold standards." Bioinformatics (Oxford, England), 2012.
MRE11 facilitates the removal of human topoisomerase II complexes from genomic DNA
Published in Biology Open, 2012
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Recommended citation: Ka Lee, Kay Padget, Hannah Curtis, Ian Cowell, Davide Moiani, Zbyslaw Sondka, Nicholas Morris, Graham Jackson, Simon Cockell, John Tainer, Caroline Austin, "MRE11 facilitates the removal of human topoisomerase II complexes from genomic DNA." Biology Open, 2012.
Contribution of natural antisense transcription to an endogenous siRNA signature in human cells
Published in BMC genomics, 2014
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Recommended citation: Andreas Werner, Simon Cockell, Jane Falconer, Mark Carlile, Sammer Alnumeir, John Robinson, "Contribution of natural antisense transcription to an endogenous siRNA signature in human cells." BMC genomics, 2014.
Utility of B-13 progenitor-derived hepatocytes in hepatotoxicity and genotoxicity studies
Published in Toxicological Sciences: An Official Journal of the Society of Toxicology, 2014
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Recommended citation: Philip Probert, Git Chung, Simon Cockell, Loranne Agius, Pasquale Mosesso, Steven White, Fiona Oakley, Colin Brown, Matthew Wright, "Utility of B-13 progenitor-derived hepatocytes in hepatotoxicity and genotoxicity studies." Toxicological Sciences: An Official Journal of the Society of Toxicology, 2014.
A distributed computational search strategy for the identification of diagnostics targets: application to finding aptamer targets for methicillin-resistant staphylococci
Published in Journal of Integrative Bioinformatics, 2014
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Recommended citation: Keith Flanagan, Simon Cockell, Colin Harwood, Jennifer Hallinan, Sirintra Nakjang, Beth Lawry, Anil Wipat, "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.
A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome
Published in PloS One, 2015
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Recommended citation: Katherine James, Shereen Al-Ali, Jessica Tarn, Simon Cockell, Colin Gillespie, Victoria Hindmarsh, James Locke, Sheryl Mitchell, Dennis Lendrem, Simon Bowman, Elizabeth Price, Colin Pease, Paul Emery, Peter Lanyon, John 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, Anil Wipat, Julia Newton, David Jones, John Isaacs, Jennifer Hallinan, Wan-Fai Ng, "A Transcriptional Signature of Fatigue Derived from Patients with Primary Sjögren's Syndrome." PloS One, 2015.
Epigenetic landscape correlates with genetic subtype but does not predict outcome in childhood acute lymphoblastic leukemia
Published in Epigenetics, 2015
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Recommended citation: Alem Gabriel, Fadhel Lafta, Edward Schwalbe, Sirintra Nakjang, Simon Cockell, Alice Iliasova, Amir Enshaei, Claire Schwab, Vikki Rand, Steven Clifford, Sally Kinsey, Chris Mitchell, Ajay Vora, Christine Harrison, Anthony Moorman, Gordon Strathdee, "Epigenetic landscape correlates with genetic subtype but does not predict outcome in childhood acute lymphoblastic leukemia." Epigenetics, 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
Published in Molecular and Cellular Biology, 2015
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Recommended citation: Ogo Ogo, John Tyson, Simon Cockell, Alison Howard, Ruth Valentine, Dianne Ford, "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, 2015.
SIRT1 affects DNA methylation of polycomb group protein target genes, a hotspot of the epigenetic shift observed in ageing
Published in Human Genomics, 2015
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Recommended citation: Luisa Wakeling, Laura Ions, Suzanne Escolme, Simon Cockell, Tianhong Su, Madhurima Dey, Emily Hampton, Gail Jenkins, Linda Wainwright, Jill McKay, Dianne Ford, "SIRT1 affects DNA methylation of polycomb group protein target genes, a hotspot of the epigenetic shift observed in ageing." Human Genomics, 2015.
Genetic Networks Required to Coordinate Chromosome Replication by DNA Polymerases α, δ, and ε in Saccharomyces cerevisiae
Published in G3 (Bethesda, Md.), 2015
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Recommended citation: Marion Dubarry, Conor Lawless, A. Banks, Simon Cockell, David Lydall, "Genetic Networks Required to Coordinate Chromosome Replication by DNA Polymerases α, δ, and ε in Saccharomyces cerevisiae." G3 (Bethesda, Md.), 2015.
Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells
Published in Biology Open, 2015
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Recommended citation: Catriona Manville, Kayleigh Smith, Zbyslaw Sondka, Holly Rance, Simon Cockell, Ian Cowell, Ka Lee, Nicholas Morris, Kay Padget, Graham Jackson, Caroline Austin, "Genome-wide ChIP-seq analysis of human TOP2B occupancy in MCF7 breast cancer epithelial cells." Biology Open, 2015.
An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations
Published in PloS One, 2016
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Recommended citation: Joseph Mullen, Simon Cockell, Peter Woollard, Anil Wipat, "An Integrated Data Driven Approach to Drug Repositioning Using Gene-Disease Associations." PloS One, 2016.
Mining integrated semantic networks for drug repositioning opportunities
Published in PeerJ, 2016
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Recommended citation: Joseph Mullen, Simon Cockell, Hannah Tipney, Peter Woollard, Anil Wipat, "Mining integrated semantic networks for drug repositioning opportunities." PeerJ, 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
Published in Metallomics: Integrated Biometal Science, 2016
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Recommended citation: J. Hardyman, J. Tyson, K. Jackson, C. Aldridge, S. Cockell, L. Wakeling, R. Valentine, D. Ford, "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: Integrated Biometal Science, 2016.
Analysis of primary visual cortex in dementia with Lewy bodies indicates GABAergic involvement associated with recurrent complex visual hallucinations
Published in Acta Neuropathologica Communications, 2016
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Recommended citation: Ahmad Khundakar, Peter Hanson, Daniel Erskine, Nichola Lax, Joseph Roscamp, Evangelia Karyka, Eliona Tsefou, Preeti Singh, Simon Cockell, Andrew Gribben, Lynne Ramsay, Peter Blain, Urs Mosimann, Deborah Lett, Matthias Elstner, Douglass Turnbull, Charles Xiang, Michael Brownstein, John O'Brien, John-Paul Taylor, Johannes Attems, Alan Thomas, Ian McKeith, Christopher Morris, "Analysis of primary visual cortex in dementia with Lewy bodies indicates GABAergic involvement associated with recurrent complex visual hallucinations." Acta Neuropathologica Communications, 2016.
The NF-κB subunit c-Rel regulates Bach2 tumour suppressor expression in B-cell lymphoma
Published in Oncogene, 2016
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Recommended citation: J. Hunter, J. Butterworth, B. Zhao, H. Sellier, K. Campbell, H. Thomas, C. Bacon, S. Cockell, B. Gewurz, N. Perkins, "The NF-κB subunit c-Rel regulates Bach2 tumour suppressor expression in B-cell lymphoma." Oncogene, 2016.
Transcriptomics and proteomics show that selenium affects inflammation, cytoskeleton, and cancer pathways in human rectal biopsies
Published in FASEB journal: official publication of the Federation of American Societies for Experimental Biology, 2016
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Recommended citation: Catherine Méplan, Ian Johnson, Abigael Polley, Simon Cockell, David Bradburn, Daniel Commane, Ramesh Arasaradnam, Francis Mulholland, Anze Zupanic, John Mathers, John Hesketh, "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, 2016.
A RelA(p65) Thr505 phospho-site mutation reveals an important mechanism regulating NF-κB-dependent liver regeneration and cancer
Published in Oncogene, 2016
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Recommended citation: A. Moles, J. Butterworth, A. Sanchez, J. Hunter, J. Leslie, H. Sellier, D. Tiniakos, S. Cockell, D. Mann, F. Oakley, N. Perkins, "A RelA(p65) Thr505 phospho-site mutation reveals an important mechanism regulating NF-κB-dependent liver regeneration and cancer." Oncogene, 2016.
Misincorporation by RNA polymerase is a major source of transcription pausing in vivo
Published in Nucleic Acids Research, 2017
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Recommended citation: Katherine James, Pamela Gamba, Simon Cockell, Nikolay Zenkin, "Misincorporation by RNA polymerase is a major source of transcription pausing in vivo." Nucleic Acids Research, 2017.
Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics
Published in Methods (San Diego, Calif.), 2017
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Recommended citation: Katherine James, Simon Cockell, Nikolay Zenkin, "Deep sequencing approaches for the analysis of prokaryotic transcriptional boundaries and dynamics." Methods (San Diego, Calif.), 2017.
Influence of Genetic Variations in Selenoprotein Genes on the Pattern of Gene Expression after Supplementation with Brazil Nuts
Published in Nutrients, 2017
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Recommended citation: Janaina Donadio, Marcelo Rogero, Simon Cockell, John Hesketh, Silvia Cozzolino, "Influence of Genetic Variations in Selenoprotein Genes on the Pattern of Gene Expression after Supplementation with Brazil Nuts." Nutrients, 2017.
Cross platform analysis of transcriptomic data identifies ageing has distinct and opposite effects on tendon in males and females
Published in Scientific Reports, 2017
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Recommended citation: Louise Pease, Peter Clegg, Carole Proctor, Daryl Shanley, Simon Cockell, Mandy Peffers, "Cross platform analysis of transcriptomic data identifies ageing has distinct and opposite effects on tendon in males and females." Scientific Reports, 2017.
Abundant and equipotent founder cells establish and maintain acute lymphoblastic leukaemia
Published in Leukemia, 2017
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Recommended citation: A. Elder, S. Bomken, I. Wilson, H. Blair, S. Cockell, F. Ponthan, K. Dormon, D. Pal, O. Heidenreich, J. Vormoor, "Abundant and equipotent founder cells establish and maintain acute lymphoblastic leukaemia." Leukemia, 2017.
Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes
Published in Cellular Signalling, 2018
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Recommended citation: Patryk Janus, Katarzyna Szołtysek, Gracjana Zając, Tomasz Stokowy, Anna Walaszczyk, Wiesława Widłak, Bartosz Wojtaś, Bartłomiej Gielniewski, Marta Iwanaszko, Rosemary Braun, Simon Cockell, Neil Perkins, Marek Kimmel, Piotr Widlak, "Pro-inflammatory cytokine and high doses of ionizing radiation have similar effects on the expression of NF-kappaB-dependent genes." Cellular Signalling, 2018.
B-cell activity markers are associated with different disease activity domains in primary Sjögren's syndrome
Published in Rheumatology (Oxford, England), 2018
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Recommended citation: Katherine James, Chimwemwe Chipeta, Antony Parker, Stephen Harding, Simon Cockell, Colin Gillespie, Jennifer Hallinan, Francesca Barone, Simon Bowman, Wan-Fai Ng, Benjamin Fisher, "B-cell activity markers are associated with different disease activity domains in primary Sjögren's syndrome." Rheumatology (Oxford, England), 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
Published in BMC genomics, 2018
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Recommended citation: Katarzyna Szołtysek, Patryk Janus, Gracjana Zając, Tomasz Stokowy, Anna Walaszczyk, Wiesława Widłak, Bartosz Wojtaś, Bartłomiej Gielniewski, Simon Cockell, Neil Perkins, Marek Kimmel, Piotr Widlak, "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.
An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning
Published in eLife, 2019
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Recommended citation: Ingrid Ehrmann, James Crichton, Matthew Gazzara, Katherine James, Yilei Liu, Sushma Grellscheid, Tomaž Curk, Dirk Rooij, Jannetta Steyn, Simon Cockell, Ian Adams, Yoseph Barash, David Elliott, "An ancient germ cell-specific RNA-binding protein protects the germline from cryptic splice site poisoning." eLife, 2019.
Deconstructing Retinal Organoids: Single Cell RNA-Seq Reveals the Cellular Components of Human Pluripotent Stem Cell-Derived Retina
Published in Stem Cells (Dayton, Ohio), 2019
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Recommended citation: Joseph Collin, Rachel Queen, Darin Zerti, Birthe Dorgau, Rafiqul Hussain, Jonathan Coxhead, Simon Cockell, Majlinda Lako, "Deconstructing Retinal Organoids: Single Cell RNA-Seq Reveals the Cellular Components of Human Pluripotent Stem Cell-Derived Retina." Stem Cells (Dayton, Ohio), 2019.
High-throughput sequencing identifies aetiology-dependent differences in ductular reaction in human chronic liver disease
Published in The Journal of Pathology, 2019
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Recommended citation: Olivier Govaere, Simon Cockell, Matthias Van, Jasper Wouters, Wouter Van, Kathleen Eynde, Arianna Bianchi, Rudy Eijsden, Werner Van, Diethard Monbaliu, Frederik Nevens, Tania Roskams, "High-throughput sequencing identifies aetiology-dependent differences in ductular reaction in human chronic liver disease." The Journal of Pathology, 2019.
Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer
Published in eLife, 2019
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Recommended citation: Jennifer Munkley, Ling Li, S. Krishnan, Gerald Hysenaj, Emma Scott, Caroline Dalgliesh, Htoo Oo, Teresa Maia, Kathleen Cheung, Ingrid Ehrmann, Karen Livermore, Hanna Zielinska, Oliver Thompson, Bridget Knight, Paul McCullagh, John McGrath, Malcolm Crundwell, Lorna Harries, Mads Daugaard, Simon Cockell, Nuno Barbosa-Morais, Sebastian Oltean, David Elliott, "Androgen-regulated transcription of ESRP2 drives alternative splicing patterns in prostate cancer." eLife, 2019.
Pax9 is required for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to control 4th pharyngeal arch artery morphogenesis
Published in Development (Cambridge, England), 2019
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Recommended citation: Helen Phillips, Catherine Stothard, Wasay Shaikh, Anastasia Kousa, J. Briones-Leon, Ramada Khasawneh, Chloe O'Loughlin, Rachel Sanders, Silvia Mazzotta, Rebecca Dodds, Kerstin Seidel, Timothy Bates, Mitsushiro Nakatomi, Simon Cockell, Jürgen Schneider, Timothy Mohun, René Maehr, Ralf Kist, Heiko Peters, Simon Bamforth, "Pax9 is required for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to control 4th pharyngeal arch artery morphogenesis." Development (Cambridge, England), 2019.
Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome
Published in Nature Communications, 2019
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Recommended citation: Helen Davies, Kirsty Hodgson, Edward Schwalbe, Jonathan Coxhead, Naomi Sinclair, Xueqing Zou, Simon Cockell, Akhtar Husain, Serena Nik-Zainal, Neil Rajan, "Epigenetic modifiers DNMT3A and BCOR are recurrently mutated in CYLD cutaneous syndrome." Nature Communications, 2019.
Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage
Published in Epigenetics, 2020
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Recommended citation: Kathleen Cheung, Marjolein Burgers, David Young, Simon Cockell, Louise Reynard, "Correlation of Infinium HumanMethylation450K and MethylationEPIC BeadChip arrays in cartilage." Epigenetics, 2020.
Understanding the complexity of retina and pluripotent stem cell derived retinal organoids with single cell RNA sequencing: current progress, remaining challenges and future prospective
Published in Current Eye Research, 2020
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Recommended citation: Darin Zerti, Joseph Collin, Rachel Queen, Simon Cockell, Majlinda Lako, "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, 2020.
Genome-wide association study of non-alcoholic fatty liver and steatohepatitis in a histologically characterised cohort☆
Published in Journal of Hepatology, 2020
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Recommended citation: Quentin Anstee, Rebecca Darlay, Simon Cockell, Marica Meroni, Olivier Govaere, Dina Tiniakos, Alastair Burt, Pierre Bedossa, Jeremy Palmer, Yang-Lin Liu, Guruprasad 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 Schattenberg, Luca Valenti, Christopher Day, Heather Cordell, Ann Daly, "Genome-wide association study of non-alcoholic fatty liver and steatohepatitis in a histologically characterised cohort☆." Journal of Hepatology, 2020.
Microarray analysis of primary epithelial and fibroblast cells in chronic rhinosinusitis without nasal polyps
Published in Rhinology, 2020
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Recommended citation: S. Ball, S. Cockell, J. Wilson, D. Mann, A. Fisher, "Microarray analysis of primary epithelial and fibroblast cells in chronic rhinosinusitis without nasal polyps." Rhinology, 2020.
Transcriptomic profiling across the nonalcoholic fatty liver disease spectrum reveals gene signatures for steatohepatitis and fibrosis
Published in Science Translational Medicine, 2020
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Recommended citation: Olivier Govaere, Simon Cockell, Dina Tiniakos, Rachel Queen, Ramy Younes, Michele Vacca, Leigh Alexander, Federico Ravaioli, Jeremy Palmer, Salvatore Petta, Jerome Boursier, Chiara Rosso, Katherine Johnson, Kristy Wonders, Christopher Day, Mattias Ekstedt, Matej Orešič, Rebecca Darlay, Heather Cordell, Fabio Marra, Antonio Vidal-Puig, Pierre Bedossa, Jörn Schattenberg, Karine Clément, Michael Allison, Elisabetta Bugianesi, Vlad Ratziu, Ann Daly, Quentin Anstee, "Transcriptomic profiling across the nonalcoholic fatty liver disease spectrum reveals gene signatures for steatohepatitis and fibrosis." Science Translational Medicine, 2020.
NASH limits anti-tumour surveillance in immunotherapy-treated HCC
Published in Nature, 2021
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Recommended citation: Dominik Pfister, Nicolás Núñez, Roser Pinyol, Olivier Govaere, Matthias Pinter, Marta Szydlowska, Revant Gupta, Mengjie Qiu, Aleksandra Deczkowska, Assaf Weiner, Florian Müller, Ankit Sinha, Ekaterina Friebel, Thomas Engleitner, Daniela Lenggenhager, Anja Moncsek, Danijela Heide, Kristin Stirm, Jan Kosla, Eleni Kotsiliti, Valentina Leone, Michael Dudek, Suhail Yousuf, Donato Inverso, Indrabahadur Singh, Ana Teijeiro, Florian Castet, Carla Montironi, Philipp Haber, Dina Tiniakos, Pierre Bedossa, Simon Cockell, Ramy Younes, Michele Vacca, Fabio Marra, Jörn Schattenberg, Michael Allison, Elisabetta Bugianesi, Vlad Ratziu, Tiziana Pressiani, Antonio D'Alessio, Nicola Personeni, Lorenza Rimassa, Ann Daly, Bernhard Scheiner, Katharina Pomej, Martha Kirstein, Arndt Vogel, Markus Peck-Radosavljevic, Florian Hucke, Fabian Finkelmeier, Oliver Waidmann, Jörg Trojan, Kornelius Schulze, Henning Wege, Sandra Koch, Arndt Weinmann, Marco Bueter, Fabian Rössler, Alexander Siebenhüner, Sara De, Jan-Philipp Mallm, Viktor Umansky, Manfred Jugold, Tom Luedde, Andrea Schietinger, Peter Schirmacher, Brinda Emu, Hellmut Augustin, Adrian Billeter, Beat Müller-Stich, Hiroto Kikuchi, Dan Duda, Fabian Kütting, Dirk-Thomas Waldschmidt, Matthias Ebert, Nuh Rahbari, Henrik Mei, Axel Schulz, Marc Ringelhan, Nisar Malek, Stephan Spahn, Michael Bitzer, Marina Galarreta, Amaia Lujambio, Jean-Francois Dufour, Thomas Marron, Ahmed Kaseb, Masatoshi Kudo, Yi-Hsiang Huang, Nabil Djouder, Katharina Wolter, Lars Zender, Parice Marche, Thomas Decaens, David Pinato, Roland Rad, Joachim Mertens, Achim Weber, Kristian Unger, Felix Meissner, Susanne Roth, Zuzana Jilkova, Manfred Claassen, Quentin Anstee, Ido Amit, Percy Knolle, Burkhard Becher, Josep Llovet, Mathias Heikenwalder, "NASH limits anti-tumour surveillance in immunotherapy-treated HCC." Nature, 2021.
Therapeutic wavelengths of ultraviolet B radiation activate apoptotic, circadian rhythm, redox signalling and key canonical pathways in psoriatic epidermis
Published in Redox Biology, 2021
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Recommended citation: Rachel Addison, Sophie Weatherhead, Anandika Pawitri, Graham Smith, Ashley Rider, Henry Grantham, Simon Cockell, Nick Reynolds, "Therapeutic wavelengths of ultraviolet B radiation activate apoptotic, circadian rhythm, redox signalling and key canonical pathways in psoriatic epidermis." Redox Biology, 2021.
Network medicine for disease module identification and drug repurposing with the NeDRex platform
Published in Nature Communications, 2021
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Recommended citation: Sepideh Sadegh, James Skelton, Elisa Anastasi, Judith Bernett, David Blumenthal, Gihanna Galindez, Marisol Salgado-Albarrán, Olga Lazareva, Keith Flanagan, Simon Cockell, Cristian Nogales, Ana Casas, Harald Schmidt, Jan Baumbach, Anil Wipat, Tim Kacprowski, "Network medicine for disease module identification and drug repurposing with the NeDRex platform." Nature Communications, 2021.
Transcriptomics Identify Thrombospondin-2 as a Biomarker for NASH and Advanced Liver Fibrosis
Published in Hepatology (Baltimore, Md.), 2021
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Recommended citation: Kazuhiro Kozumi, Takahiro Kodama, Hiroki Murai, Sadatsugu Sakane, Olivier Govaere, Simon Cockell, Daisuke Motooka, Naruyasu Kakita, Yukinori Yamada, Yasuteru Kondo, Yuki Tahata, Ryoko Yamada, Hayato Hikita, Ryotaro Sakamori, Yoshihiro Kamada, Ann Daly, Quentin Anstee, Tomohide Tatsumi, Eiichi Morii, Tetsuo Takehara, "Transcriptomics Identify Thrombospondin-2 as a Biomarker for NASH and Advanced Liver Fibrosis." Hepatology (Baltimore, Md.), 2021.
Distinct gene expression profiles between human preterm-derived and adult-derived intestinal organoids exposed to Enterococcus faecalis: a pilot study
Published in Gut, 2021
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Recommended citation: Andrea Masi, Tatiana Fofanova, Christopher Lamb, Jennifer Auchtung, Robert Britton, Mary Estes, Sasirekha Ramani, Simon Cockell, Jonathan Coxhead, Nicholas Embleton, Janet Berrington, Joseph Petrosino, Christopher Stewart, "Distinct gene expression profiles between human preterm-derived and adult-derived intestinal organoids exposed to Enterococcus faecalis: a pilot study." Gut, 2021.
A de novo paradigm for male infertility
Published in Nature Communications, 2022
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Recommended citation: M. Oud, R. Smits, H. Smith, F. Mastrorosa, G. Holt, B. Houston, P. Vries, B. Alobaidi, L. Batty, H. Ismail, J. Greenwood, H. Sheth, A. Mikulasova, G. Astuti, C. Gilissen, K. McEleny, H. Turner, J. Coxhead, S. Cockell, D. Braat, K. Fleischer, K. D'Hauwers, E. Schaafsma, L. Nagirnaja, D. Conrad, C. Friedrich, S. Kliesch, K. Aston, A. Riera-Escamilla, C. Krausz, C. Gonzaga-Jauregui, M. Santibanez-Koref, D. Elliott, L. Vissers, F. Tüttelmann, M. O'Bryan, L. Ramos, M. Xavier, G. Heijden, J. Veltman, "A de novo paradigm for male infertility." Nature Communications, 2022.
Type I interferon receptor (IFNAR2) deficiency reveals Zika virus cytopathicity in human macrophages and microglia
Published in Frontiers in Immunology, 2022
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Recommended citation: Aidan Hanrath, Catherine Hatton, Florian Gothe, Cathy Browne, Jane Vowles, Peter Leary, Simon Cockell, Sally Cowley, William James, Sophie Hambleton, Christopher Duncan, "Type I interferon receptor (IFNAR2) deficiency reveals Zika virus cytopathicity in human macrophages and microglia." Frontiers in Immunology, 2022.
Increased serum miR-193a-5p during non-alcoholic fatty liver disease progression: Diagnostic and mechanistic relevance
Published in JHEP reports: innovation in hepatology, 2022
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Recommended citation: Katherine Johnson, Peter Leary, Olivier Govaere, Matthew Barter, Sarah Charlton, Simon Cockell, Dina Tiniakos, Michalina Zatorska, Pierre Bedossa, M. Brosnan, Jeremy Cobbold, Mattias Ekstedt, Guruprasad Aithal, Karine Clément, Jörn Schattenberg, Jerome Boursier, Vlad Ratziu, Elisabetta Bugianesi, Quentin Anstee, Ann Daly, "Increased serum miR-193a-5p during non-alcoholic fatty liver disease progression: Diagnostic and mechanistic relevance." JHEP reports: innovation in hepatology, 2022.
Mechanical-Stress-Related Epigenetic Regulation of ZIC1 Transcription Factor in the Etiology of Postmenopausal Osteoporosis
Published in International Journal of Molecular Sciences, 2022
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Recommended citation: Harish Datta, Marianne Kringen, Stephen Tuck, Georgia Salpingidou, Ole Olstad, Kaare Gautvik, Simon Cockell, Vigdis Gautvik, Michael Prediger, Jun Wu, Mark Birch, Sjur Reppe, "Mechanical-Stress-Related Epigenetic Regulation of ZIC1 Transcription Factor in the Etiology of Postmenopausal Osteoporosis." International Journal of Molecular Sciences, 2022.
Expanding interactome analyses beyond model eukaryotes
Published in Briefings in Functional Genomics, 2022
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Recommended citation: Katherine James, Anil Wipat, Simon Cockell, "Expanding interactome analyses beyond model eukaryotes." Briefings in Functional Genomics, 2022.
Integration of probabilistic functional networks without an external Gold Standard
Published in BMC bioinformatics, 2022
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Recommended citation: Katherine James, Aoesha Alsobhe, Simon Cockell, Anil Wipat, Matthew Pocock, "Integration of probabilistic functional networks without an external Gold Standard." BMC bioinformatics, 2022.
Blood mRNA Expression in Alzheimer's Disease and Dementia With Lewy Bodies
Published in The American Journal of Geriatric Psychiatry: Official Journal of the American Association for Geriatric Psychiatry, 2022
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Recommended citation: Paul Donaghy, Simon Cockell, Carmen Martin-Ruiz, Jonathan Coxhead, Joseph Kane, Daniel Erskine, David Koss, John-Paul Taylor, Christopher Morris, John O'Brien, Alan Thomas, "Blood mRNA Expression in Alzheimer's Disease and Dementia With Lewy Bodies." The American Journal of Geriatric Psychiatry: Official Journal of the American Association for Geriatric Psychiatry, 2022.
Quantitative modeling of human liver reveals dysregulation of glycosphingolipid pathways in nonalcoholic fatty liver disease
Published in iScience, 2022
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Recommended citation: Partho Sen, Olivier Govaere, Tim Sinioja, Aidan McGlinchey, Dawei Geng, Vlad Ratziu, Elisabetta Bugianesi, Jörn Schattenberg, Antonio Vidal-Puig, Michael Allison, Simon Cockell, Ann Daly, Tuulia Hyötyläinen, Quentin Anstee, Matej Orešič, "Quantitative modeling of human liver reveals dysregulation of glycosphingolipid pathways in nonalcoholic fatty liver disease." iScience, 2022.
talks
Talk 1 on Relevant Topic in Your Field
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Conference Proceeding talk 3 on Relevant Topic in Your Field
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teaching
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Teaching experience 2
Workshop, University 1, Department, 2015
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