Dr Mark Dunning

Clinical Medicine, School of Medicine and Population Health

Bioinformatics Core Director

m.j.dunning@sheffield.ac.uk

The Medical School

Full contact details

Dr Mark Dunning
Clinical Medicine, School of Medicine and Population Health
The Medical School
Beech Hill Road
Sheffield
S10 2RX

Profile

I obtained my PhD in the Statistics and Computational Biology group of Simon Tavare at The University of Cambridge. As part of my thesis I developed open-source software for the analysis of Illumina microarray data, which is available through the Bioconductor project.

I joined the Bioinformatics Core at Cancer Research Uk Cambridge Institute and played a key role in the analysis of gene expression profiles as part of the METABRIC project, which identified and described new subtypes of breast cancer. I also participated in the pilot phases of the International Cancer Genome Consortium (ICGC) project by developing computational pipelines to process the whole-genome sequencing data from Oesophageal cancer patients.

During my time in the Bioinformatics Core I also developed a passion for teaching and commenced a role dedicated to organising and delivering Bioinformatics training courses, with the aim of empowering wet-lab scientists to begin to explore data for themselves and foster more-productive collaborations with Bioinformaticians.

I have a strong commitment to reproducible research and making my research outputs available to other researchers, and indeed members of the public who may have funded the research in the first place. For instance, I recently developed and deployed a Shiny application that allows interested parties to query various prostate cancer datasets.

In keeping with my open access principles, the code underlying the application is available via github and utilises data sets that can be downloaded from Bioconductor. I have also recently investigated technologies such as Galaxy and Docker to ease the deployment of software and facilitate reproducible research.

Qualifications

2015 – 2017: Bioinformatics Training Co-ordinator, Cancer Research Uk, Cambridge Institute
2009 – 2015: Bioinformatics Analyst / Senior Bioinformatics Analyst, Cancer Research Uk Cambridge Institute
2005 – 2009: PhD (Oncology) University of Cambridge
2004 – 2005: Msc (Data Analysis, Networks and Nonlinear Dynamics) University of York
1999 – 2004: Bsc (Mathematics and Computer Science) University of York

Current PhD Opportunities:

Deconvoluting the spatial multi-omic landscape of high-grade glioma to target post-surgical residual disease

Research interests

High-throughput technologies such as next generation sequencing (NGS) can routinely produce massive amounts of data that can be used for tasks such as identifying biological samples with aberrant expression patterns or allow us to describe all variants in a genome.

However, such datasets pose new challenges in the way the data have to be analysed, annotated and interpreted which are not trivial and are daunting to the wet-lab biologist.

My interests lie in making the analysis of high-throughput datasets accessible to the non-bioinformatician; via specialised training courses and by developing computational pipelines and workflow.

I am currently exploring technologies that facilitate reproducible research and promote an open attitude to scientific research, and endeavour to make my talks, code, and analyses available whenever.

Current projects

From October 2017 I will be establishing a Bioinformatics Core service at The University of Sheffield to support researchers in the planning, analysis, interpretation and management of their data.

I will also be developing and organising training courses covering the analysis skills essential to the being a modern, data-literate scientist.

Publications

Journal articles

Payne T, Burgess T, Bradley S, Roscoe S, Sassani M, Dunning MJ, Hernandez D, Scholz S, McNeill A, Taylor R , Su L et al (2023) Multimodal assessment of mitochondrial function in Parkinson's disease. Brain, 147(1), 267-280. View this article in WRRO
López-Guajardo A, Zafar A, Al Hennawi K, Rossi V, Alrwaili A, Medcalf JD, Dunning M, Nordgren N, Pettersson T, Estabrook ID , Hawkins RJ et al (2023) Regulation of cellular contractile force, shape and migration of fibroblasts by oncogenes and Histone deacetylase 6. Frontiers in Molecular Biosciences, 10.
Payne T, Appleby M, Buckley E, van Gelder LMA, Mullish BH, Sassani M, Dunning MJ, Hernandez D, Scholz SW, McNeill A , Libri V et al (2023) A Double‐Blind, Randomized, Placebo‐Controlled Trial of Ursodeoxycholic Acid (UDCA) in Parkinson's Disease. Movement Disorders.
Barrow R, Wilkinson J, He Y, Callaghan M, Brüning-Richardson A, Dunning M & Stead L (2022) SpheroidAnalyseR—an online platform for analyzing data from 3D spheroids or organoids grown in 96-well plates. Journal of Biological Methods, 9(4).
Tonge JJ, Notley SV, Dunning MJ, López-Guajardo A, Medcalf JD, Heldin P, Panoutsos G & Gad AKB (2022) Hyaluronan nanoscale clustering and Hyaluronan synthase 2 expression are linked to the invasion of child fibroblasts and infantile fibrosarcoma in vitro and in vivo. Scientific Reports, 12, 1-10. View this article in WRRO
Souilhol C, Tardajos Ayllon B, Li X, Diagbouga MR, Zhou Z, Canham L, Roddie H, Pirri D, Chambers EV, Dunning MJ , Ariaans M et al (2022) JAG1-NOTCH4 mechanosensing drives atherosclerosis.. Sci Adv, 8(35), eabo7958.
Kariotis S, Jammeh E, Swietlik EM, Pickworth JA, Rhodes CJ, Otero P, Wharton J, Iremonger J, Dunning MJ, Pandya D , Mascarenhas TS et al (2021) Biological heterogeneity in idiopathic pulmonary arterial hypertension identified through unsupervised transcriptomic profiling of whole blood. Nature Communications, 12. View this article in WRRO
Solano BS, Föll MC, Gallardo-Alba C, Erxleben A, Rasche H, Hiltemann S, Fahrner M, Dunning MJ, Schulz MH, Scholtz B , Clements D et al (2021) Fostering accessible online education using Galaxy as an e-learning platform. PLoS Computational Biology, 17(5). View this article in WRRO
Shah KM, Dunning MJ, Gartland A & Wilkinson JM (2021) Distinct concentration-dependent molecular pathways regulate bone cell responses to cobalt and chromium exposure from joint replacement prostheses. International Journal of Molecular Sciences, 22(10).
Rhodes CJ, Otero-Núñez P, Wharton J, Swietlik EM, Kariotis S, Harbaum L, Dunning MJ, Elinoff JM, Errington N, Thomson AAR , Iremonger J et al (2020) Whole blood RNA profiles associated with pulmonary arterial hypertension and clinical outcome. American Journal of Respiratory and Critical Care Medicine. View this article in WRRO
Yatai KB, Dunning MJ & Wang D (2020) Consensus genomic subtypes of muscle-invasive bladder cancer : a step in the right direction but still a long way to go. European Urology, 77(4), 434-435. View this article in WRRO
Hamilton N, Rutherford HA, Petts JJ, Isles HM, Weber T, Henneke M, Gärtner J, Dunning MJ & Renshaw SA (2020) The failure of microglia to digest developmental apoptotic cells contributes to the pathology of RNASET2-deficient leukoencephalopathy. Glia. View this article in WRRO
Westbrook JA, Wood SL, Cairns DA, McMahon K, Gahlaut R, Thygesen H, Shires M, Roberts S, Marshall H, Oliva M , Dunning MJ et al (2019) Identification and validation of DOCK4 as a potential biomarker for risk of bone metastasis development in patients with early breast cancer. The Journal of Pathology, 247(3), 381-391. View this article in WRRO
Bakht MK, Derecichei I, Li Y, Ferraiuolo R-M, Dunning M, Oh SW, Hussein A, Youn H, Stringer KF, Jeong CW , Cheon GJ et al (2019) Neuroendocrine differentiation of prostate cancer leads to PSMA suppression. Endocrine-Related Cancer, 131-146.
Jurmeister S, Ramos-Montoya A, Sandi C, Pértega-Gomes N, Wadhwa K, Lamb AD, Dunning MJ, Attig J, Carroll JS, Fryer LG , Felisbino SL et al (2018) Identification of potential therapeutic targets in prostate cancer through a cross-species approach.. EMBO Molecular Medicine, 10(3).
Lalonde E, Alkallas R, Chua MLK, Fraser M, Haider S, Meng A, Zheng J, Yao CQ, Picard V, Orain M , Hovington H et al (2017) Translating a Prognostic DNA Genomic Classifier into the Clinic: Retrospective Validation in 563 Localized Prostate Tumors. European Urology, 72(1), 22-31.
Dunning MJ, Vowler SL, Lalonde E, Ross-Adams H, Boutros P, Mills IG, Lynch AG & Lamb AD (2017) Mining Human Prostate Cancer Datasets: The “camcAPP” Shiny App. EBioMedicine, 17, 5-6.
Ross-Adams H, Lamb AD, Dunning MJ, Halim S, Lindberg J, Massie CM, Egevad LA, Russell R, Ramos-Montoya A, Vowler SL , Sharma NL et al (2017) Corrigendum to “Integration of Copy Number and Transcriptomics Provides Risk Stratification in Prostate Cancer: A Discovery and Validation Cohort Study” [EBioMedicine 2 (9) (2015) 1133–1144]. EBioMedicine, 17, 238-238.
Shaw GL, Whitaker H, Corcoran M, Dunning MJ, Luxton H, Kay J, Massie CE, Miller JL, Lamb AD, Ross-Adams H , Russell R et al (2016) The Early Effects of Rapid Androgen Deprivation on Human Prostate Cancer. European Urology, 70(2), 214-218.
Whitington T, Gao P, Song W, Ross-Adams H, Lamb AD, Yang Y, Svezia I, Klevebring D, Mills IG, Karlsson R , Halim S et al (2016) Gene regulatory mechanisms underpinning prostate cancer susceptibility. Nature Genetics, 48(4), 387-397.
Ross-Adams H, Lamb AD, Dunning MJ, Halim S, Lindberg J, Massie CM, Egevad LA, Russell R, Ramos-Montoya A, Vowler SL , Sharma NL et al (2015) Integration of copy number and transcriptomics provides risk stratification in prostate cancer: A discovery and validation cohort study. EBioMedicine, 2(9), 1133-1144.
Uribe-Lewis S, Stark R, Carroll T, Dunning MJ, Bachman M, Ito Y, Stojic L, Halim S, Vowler SL, Lynch AG , Delatte B et al (2015) 5-hydroxymethylcytosine marks promoters in colon that resist DNA hypermethylation in cancer. Genome Biology, 16(1).
Massie CE, Spiteri I, Ross-Adams H, Luxton H, Kay J, Whitaker HC, Dunning MJ, Lamb AD, Ramos-Montoya A, Brewer DS , Cooper CS et al (2015) HES5 silencing is an early and recurrent change in prostate tumourigenesis. Endocrine-Related Cancer, 22(2), 131-144.
Vollan HKM, Rueda OM, Chin S-F, Curtis C, Turashvili G, Shah S, Lingjaerde OC, Yuan Y, Ng CK, Dunning MJ , Dicks E et al (2015) A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer. Molecular Oncology, 9(1), 115-127.
Lalonde E, Ishkanian AS, Sykes J, Fraser M, Ross-Adams H, Erho N, Dunning MJ, Halim S, Lamb AD, Moon NC , Zafarana G et al (2014) Tumour genomic and microenvironmental heterogeneity for integrated prediction of 5-year biochemical recurrence of prostate cancer: a retrospective cohort study. The Lancet Oncology, 15(13), 1521-1532.
Ali HR, Rueda OM, Chin S-F, Curtis C, Dunning MJ, Aparicio SAJR & Caldas C (2014) Genome-driven integrated classification of breast cancer validated in over 7,500 samples. Genome Biology, 15(8).
Weaver JMJ, Ross-Innes CS, Shannon N, Lynch AG, Forshew T, Barbera M, Murtaza M, Ong C-AJ, Lao-Sirieix P, Dunning MJ , Smith L et al (2014) Ordering of mutations in preinvasive disease stages of esophageal carcinogenesis. Nature Genetics, 46(8), 837-843.
Weaver J, Ross-Innes C, Shannon N, Lynch A, Murtaza M, Forshew T, Dunning M, Underwood T, Hardwick R, Eldridge M , Edwards P et al (2014) PTU-153 The Timing Of Oncogenic Events In The Evolution Of The Oesophageal Adenocarcinoma Genome And Implications For Clinical Diagnostics. Gut, 63(Suppl 1), A105.2-A106.
Sir J-H, Pütz M, Daly O, Morrison CG, Dunning M, Kilmartin JV & Gergely F (2013) Loss of centrioles causes chromosomal instability in vertebrate somatic cells. The Journal of Cell Biology, 203(5), 747-756.
Earl HM, Chin S-F, Dunning M, Iddawela M, Rueda O, Russell R, Jones L, Vallier A-L, Hughes-Davies L, Abraham J , Chan S et al (2013) Neo-tAnGo science: A translational study of PAM 50 sub-typing in sequential fresh tissue samples during neoadjuvant chemotherapy.. Journal of Clinical Oncology, 31(15_suppl), 1015-1015.
Dawson S-J, Tsui DWY, Murtaza M, Biggs H, Rueda OM, Chin S-F, Dunning MJ, Gale D, Forshew T, Mahler-Araujo B , Rajan S et al (2013) Analysis of Circulating Tumor DNA to Monitor Metastatic Breast Cancer. New England Journal of Medicine, 368(13), 1199-1209.
(2012) A Correction to the Research Article Titled: "Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling" by Y. Yuan, H. Failmezger, O. M. Rueda, H. R. Ali, S. Graf, S.-F. Chin, R. F. Schwarz, C. Curtis, M. J. Dunning, H. Bardwell, N. Johnson, S. Doyle, G. Turashvili, E. Provenzano, S. Aparicio, C. Caldas, F. Markowetz. Science Translational Medicine, 4(161), 161er6-161er6.
Yuan Y, Failmezger H, Rueda OM, Ali HR, Graf S, Chin S-F, Schwarz RF, Curtis C, Dunning MJ, Bardwell H , Johnson N et al (2012) Quantitative Image Analysis of Cellular Heterogeneity in Breast Tumors Complements Genomic Profiling. Science Translational Medicine, 4(157), 157ra143-157ra143.
Weaver JMJ, Shannon NB, Smith M, Dunning M, Ong CA, Ross-Innes C, Underwood T, Lynch A, Eldridge M, Caldas C , Edwards P et al (2012) OC-008 Defining the genetic landscape of oesophageal adenocarcinoma by next-generation sequencing. Gut, 61(Suppl 2), A3.3-A4.
Maia A-T, Antoniou AC, O'Reilly M, Samarajiwa S, Dunning M, Kartsonaki C, Chin S-F, Curtis CN, McGuffog L, Domchek SM , Easton DF et al (2012) Effects of BRCA2 cis-regulation in normal breast and cancer risk amongst BRCA2 mutation carriers. Breast Cancer Research, 14(2).
Curtis C, Shah SP, Chin S-F, Turashvili G, Rueda OM, Dunning MJ, Speed D, Lynch AG, Samarajiwa S, Yuan Y , Gräf S et al (2012) The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups. Nature, 486(7403), 346-352.
Ross-Innes CS, Stark R, Teschendorff AE, Holmes KA, Ali HR, Dunning MJ, Brown GD, Gojis O, Ellis IO, Green AR , Ali S et al (2012) Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature, 481(7381), 389-393.
Holland DG, Burleigh A, Git A, Goldgraben MA, Perez‐Mancera PA, Chin S, Hurtado A, Bruna A, Ali HR, Greenwood W , Dunning MJ et al (2011) ZNF703 is a common Luminal B breast cancer oncogene that differentially regulates luminal and basal progenitors in human mammary epithelium. EMBO Molecular Medicine, 3(3), 167-180.
Lynch AG, Hadfield J, Dunning MJ, Osborne M, Thorne NP & Tavaré S (2010) The cost of reducing starting RNA quantity for Illumina BeadArrays: A bead-level dilution experiment. BMC Genomics, 11(1).
Dunning MJ, Curtis C, Barbosa-Morais NL, Caldas C, Tavaré S & Lynch AG (2010) The importance of platform annotation in interpreting microarray data. The Lancet Oncology, 11(8), 717-717.
Smith ML, Dunning MJ, Tavaré S & Lynch AG (2010) Identification and correction of previously unreported spatial phenomena using raw Illumina BeadArray data. BMC Bioinformatics, 11(1).
Barbosa-Morais NL, Dunning MJ, Samarajiwa SA, Darot JFJ, Ritchie ME, Lynch AG & Tavaré S (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Research, 38(3), e17-e17.
Curtis C, Lynch AG, Dunning MJ, Spiteri I, Marioni JC, Hadfield J, Chin S-F, Brenton JD, Tavaré S & Caldas C (2009) The pitfalls of platform comparison: DNA copy number array technologies assessed. BMC Genomics, 10(1), 588-588.
Lynch AG, Dunning MJ, Iddawela M, Barbosa-Morais NL & Ritchie ME (2009) Considerations for the processing and analysis of GoldenGate-based two-colour Illumina platforms. Statistical Methods in Medical Research, 18(5), 437-452.
Cairns JM, Dunning MJ, Ritchie ME, Russell R & Lynch AG (2008) BASH: a tool for managing BeadArray spatial artefacts. Bioinformatics, 24(24), 2921-2922.
Git A, Spiteri I, Blenkiron C, Dunning MJ, Pole JCM, Chin S-F, Wang Y, Smith J, Livesey FJ & Caldas C (2008) PMC42, a breast progenitor cancer cell line, has normal-like mRNA and microRNA transcriptomes. Breast Cancer Research, 10(3).
Dunning MJ, Ritchie ME, Barbosa-Morais NL, Tavaré S & Lynch AG (2008) Spike-in validation of an Illumina-specific variance-stabilizing transformation. BMC Research Notes, 1(1), 18-18.
Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavaré S & Ritchie ME (2008) Statistical issues in the analysis of Illumina data. BMC Bioinformatics, 9(1).
Stranger BE, Nica AC, Forrest MS, Dimas A, Bird CP, Beazley C, Ingle CE, Dunning M, Flicek P, Koller D , Montgomery S et al (2007) Population genomics of human gene expression. Nature Genetics, 39(10), 1217-1224.
Dunning MJ, Smith ML, Ritchie ME & Tavare S (2007) beadarray: R classes and methods for Illumina bead-based data. Bioinformatics, 23(16), 2183-2184.
Stranger BE, Forrest MS, Dunning M, Ingle CE, Beazley C, Thorne N, Redon R, Bird CP, de Grassi A, Lee C , Tyler-Smith C et al (2007) Relative Impact of Nucleotide and Copy Number Variation on Gene Expression Phenotypes. Science, 315(5813), 848-853.
Blenkiron C, Goldstein LD, Thorne NP, Spiteri I, Chin S-F, Dunning MJ, Barbosa-Morais NL, Teschendorff AE, Green AR, Ellis IO , Tavaré S et al (2007) MicroRNA expression profiling of human breast cancer identifies new markers of tumor subtype. Genome Biology, 8(10), R214-R214.
Keatinge M, Gegg ME, Watson L, Mortiboys H, Li N, Dunning M, Ailani D, Bui H, van Rens A, Lefeber DJ , Schapira AHV et al () Unexpected phenotypic and molecular changes of combined glucocerebrosidase and acid sphingomyelinase deficiency. Disease Models & Mechanisms.
Hamilton N, Rutherford HA, Isles HM, Petts JJ, Weber T, Henneke M, Gärtner J, Dunning M & Renshaw SA () Failure to clear developmental apoptosis contributes to the pathology of RNASET2-deficient leukoencephalopathy. View this article in WRRO
Wood E, Parker MD, Dunning MJ, Hesketh S, Wang D, Pink R & Fratter C () Clinical long-read sequencing of the human mitochondrial genome for mitochondrial disease diagnostics. View this article in WRRO
Dunning MJ, Vowler SL, Lalonde E, Ross-Adams H, Mills IG, Lynch AG & Lamb AD () Mining human prostate cancer datasets: The “camcAPP” shiny app.
Lynch AG, Chin S-F, Dunning MJ, Caldas C, Tavaré S & Curtis C () Calling Sample Mix-Ups in Cancer Population Studies. PLoS ONE, 7(8), e41815-e41815.
Ritchie ME, Dunning MJ, Smith ML, Shi W & Lynch AG () BeadArray Expression Analysis Using Bioconductor. PLoS Computational Biology, 7(12), e1002276-e1002276.

Datasets

Dunning M & Tazi-Ahnini R Alopecia areata patients show deficiency of FOXP3+CD39+ T regulatory cells and clonotypic restriction of Treg TCRbeta-chain, which highlights the immunopathological aspect of the disease.

Preprints

Pirri D, Tian S, Tardajos-Ayllon B, Irving S, Donati F, Allen SP, Mammoto T, Vilahur G, Miller C, Schenkel T , Chambers EV et al (2023) EPAS1 Attenuates Atherosclerosis Initiation at Disturbed Flow Sites through Endothelial Fatty Acid Uptake, Cold Spring Harbor Laboratory.
Xavier JM, Magno R, Russell R, de Almeida BP, Jacinta-Fernandes A, Duarte A, Dunning M, Samarajiwa S, O’Reilly M, Rocha CL , Rosli N et al (2022) Mapping of cis-regulatory variants by differential allelic expression analysis identifies candidate risk variants and target genes of 27 breast cancer risk loci, Cold Spring Harbor Laboratory.
Barrow R, Wilkinson JN, He Y, Callaghan M, Brüning-Richardson A, Dunning M & Stead LF (2022) SpheroidAnalyseR – an online platform for analysing data from 3D spheroids or organoids grown in 96-well plates, Cold Spring Harbor Laboratory.
Serrano-Solano B, Erxleben A, Gallardo-Alba C, Rasche H, Hiltemann S, Föll M, Fahrner M, Dunning MJ, Schulz M, Scholtz B , Clements D et al (2020) Fostering Accessible Online Education Using Galaxy as an e-learning Platform, MDPI AG.
Tonge JJ, Notley SV, Dunning MJ, López-Guajardo A, Medcalf JD, Heldin P, Panoutsos G & Gad AKB () Hyaluronan nanoscale clustering and Hyaluronan synthase 2 expression are linked to the invasion of child fibroblasts and infantile fibrosarcoma in vitro and in vivo, Research Square Platform LLC.
Souilhol C, Li X, Canham L, Roddie H, Pirri D, Ayllon BT, Chambers EV, Dunning MJ, Ariaans M, Li J , Fang Y et al () JAG1-NOTCH4 Mechanosensing Drives Atherosclerosis, Cold Spring Harbor Laboratory.
Keatinge M, Gegg ME, Watson L, Mortiboys H, Li N, Dunning M, Ailani D, Bui H, van Rens A, Lefeber DJ , MacDonald RB et al () Unexpected opposing biological effect of genetic risk factors for Parkinson’s disease, Cold Spring Harbor Laboratory.

School of Medicine and Population Health