Dunning, Mark, Dr

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
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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.

Current PhD Opportunities:

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

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 ��߲ݴ�ý 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

Pirri D, Tian S, Tardajos-Ayllon B, Irving S, Donati F, Allen SP, Mammoto T, Vilahur G, Kabir L, Bennett J , Rasool Y et al (2024) . Circ Res.
Wood SL, Lopez-Guajardo A, Oliva MR, Collins M, Pham K, Dunning M, Chambers EV & Brown JE (2024) . Journal of Bone Oncology, 45, 100566-100566.
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) . Brain, 147(1), 267-280.
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) . 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) . Movement Disorders.
Barrow R, Wilkinson J, He Y, Callaghan M, Brüning-Richardson A, Dunning M & Stead L (2022) . Journal of Biological Methods, 9(4).
Tonge JJ, Notley SV, Dunning MJ, López-Guajardo A, Medcalf JD, Heldin P, Panoutsos G & Gad AKB (2022) . Scientific Reports, 12, 1-10.
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) . 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) . Nature Communications, 12.
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) . PLoS Computational Biology, 17(5).
Shah KM, Dunning MJ, Gartland A & Wilkinson JM (2021) . 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) . American Journal of Respiratory and Critical Care Medicine.
Yatai KB, Dunning MJ & Wang D (2020) . European Urology, 77(4), 434-435.
Hamilton N, Rutherford HA, Petts JJ, Isles HM, Weber T, Henneke M, Gärtner J, Dunning MJ & Renshaw SA (2020) . Glia.
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) . The Journal of Pathology, 247(3), 381-391.
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) . 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) . 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) . European Urology, 72(1), 22-31.
Dunning MJ, Vowler SL, Lalonde E, Ross-Adams H, Boutros P, Mills IG, Lynch AG & Lamb AD (2017) . 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) . 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) . 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) . 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) . 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) . 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) . 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) . 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) . The Lancet Oncology, 15(13), 1521-1532.
Ali HR, Rueda OM, Chin S-F, Curtis C, Dunning MJ, Aparicio SAJR & Caldas C (2014) . 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) . 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) . Gut, 63(Suppl 1), A105.2-A106.
Sir J-H, Pütz M, Daly O, Morrison CG, Dunning M, Kilmartin JV & Gergely F (2013) . 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) . 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) . New England Journal of Medicine, 368(13), 1199-1209.
(2012) . 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) . 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) . 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) . 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) . 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) . 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) . EMBO Molecular Medicine, 3(3), 167-180.
Lynch AG, Hadfield J, Dunning MJ, Osborne M, Thorne NP & Tavaré S (2010) . BMC Genomics, 11(1).
Dunning MJ, Curtis C, Barbosa-Morais NL, Caldas C, Tavaré S & Lynch AG (2010) . The Lancet Oncology, 11(8), 717-717.
Smith ML, Dunning MJ, Tavaré S & Lynch AG (2010) . BMC Bioinformatics, 11(1).
Barbosa-Morais NL, Dunning MJ, Samarajiwa SA, Darot JFJ, Ritchie ME, Lynch AG & Tavaré S (2010) . 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) . BMC Genomics, 10(1), 588-588.
Lynch AG, Dunning MJ, Iddawela M, Barbosa-Morais NL & Ritchie ME (2009) . Statistical Methods in Medical Research, 18(5), 437-452.
Cairns JM, Dunning MJ, Ritchie ME, Russell R & Lynch AG (2008) . 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) . Breast Cancer Research, 10(3).
Dunning MJ, Ritchie ME, Barbosa-Morais NL, Tavaré S & Lynch AG (2008) . BMC Research Notes, 1(1), 18-18.
Dunning MJ, Barbosa-Morais NL, Lynch AG, Tavaré S & Ritchie ME (2008) . 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) . Nature Genetics, 39(10), 1217-1224.
Dunning MJ, Smith ML, Ritchie ME & Tavare S (2007) . 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) . 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) . 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 () . Disease Models & Mechanisms.
Hamilton N, Rutherford HA, Isles HM, Petts JJ, Weber T, Henneke M, Gärtner J, Dunning M & Renshaw SA () .
Wood E, Parker MD, Dunning MJ, Hesketh S, Wang D, Pink R & Fratter C () .
Dunning MJ, Vowler SL, Lalonde E, Ross-Adams H, Mills IG, Lynch AG & Lamb AD () .
Lynch AG, Chin S-F, Dunning MJ, Caldas C, Tavaré S & Curtis C () . PLoS ONE, 7(8), e41815-e41815.
Ritchie ME, Dunning MJ, Smith ML, Shi W & Lynch AG () . PLoS Computational Biology, 7(12), e1002276-e1002276.

Conference proceedings papers

Ashford BA, Appleby-Mallinder CS, Dawson C, Matuszyk MM, Heath PR, Wei W, Dunning MJ, Boche D, Simpson JE & Highley JR (2023) Inflammatory pathology in human motor neuron disease. JOURNAL OF PATHOLOGY, Vol. 261 (pp S5-S5)

Datasets

Dunning M & Tazi-Ahnini R .

Preprints

Gelder KL, Carruthers NA, Ball SS, Dunning M, Craggs TD, Twelvetrees AE & Bose DA (2024) , Cold Spring Harbor Laboratory.
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) , 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) , Cold Spring Harbor Laboratory.
Barrow R, Wilkinson JN, He Y, Callaghan M, Brüning-Richardson A, Dunning M & Stead LF (2022) , 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) , MDPI AG.
Tonge JJ, Notley SV, Dunning MJ, López-Guajardo A, Medcalf JD, Heldin P, Panoutsos G & Gad AKB () , 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 () , 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 () , Cold Spring Harbor Laboratory.

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School of Medicine and Population Health