Michael Barnes

Michael Barnes

Director of Bioinformatics, Centre for Transaltional Bioinformatics

Michael holds a B.Sc. in Applied Biology and Ph.D. in Molecular Genetics from Cardiff University. After completing a postdoctoral fellowship at University of Wales, Bangor, he joined GlaxoSmithKline to lead a computational biology team focused on the use of genetic, genomic and chemogenomic approaches for drug discovery and patient stratification. At GSK he championed pre-competitive collaboration among pharma and academia, and co-led an EFPIA team of pharmaceutical companies to gain €10M Innovative Medicines Initiative (IMI) funding for the OpenPhacts project (www.openphacts.org), which constructed “an open pharmacological space” - a suite of public bio- and cheminformatics resources for drug discovery. Michael now serves on the scientific advisory board of the OpenPhacts project. Michael is also passionate about improving the translational and collaborative interface between industry and academia. After fourteen years at GSK, Michael joined the William Harvey Research Institute (WHRI) in 2012 as the Director of Bioinformatics. His team now collaborate with all research areas of the WHRI and also many researchers at the Blizard Institute, bringing a focus on the application of computational biology and bioinformatics to improve translational research.

Michael is an investigator at the London Farr Institute and also serves on the board and exec of eMedLab (emedlab.ac.uk), a ground breaking cloud computing facility funded by the MRC. He is also a co-investigator on several stratified medicine projects, including MRC PSORT (Psoriasis), MRC RA-Map (RA), MRC MATURA (RA) and MRC Target (Giant Cell Arteritis).

The centre for Translational Bioinformatics team are working across diverse domains, including genomics, drug discovery, stratified medicine, high performance computing and health informatics with a unified objective to drive forward translation into the clinic. He serves on the MRC Methodology Research Panel and the MRC Stratified Medicine panel and also advises on a number of project boards, including the MRC-eMedLab HPC facility, the IMI etriks project, IMI OpenPHACTS and the F1000 faculty (Bioinformatics). He has published widely and also edited the successful John Wiley Book, Bioinformatics for Geneticists. He also holds a visiting Senior Lecturer post at the Institute of Psychiatry, Kings College London.

Summary of Research

Dr Barnes has broad computational biology research interests spanning the translational research and  drug discovery continuum, from genetic and genomic methods for target identification to clinical informatics and patient stratification.  Active research projects in his team fall into the following key areas:

Pathway analysis of Genetic and Genomic data: Genome wide association studies (GWAS) and exome studies of complex trait pathology and drug response, including, Hypertension, Arrhythmia and Cardiovascular disease.

Exome and Whole Genome Re-sequencing: NGS pipeline development, Re-sequencing studies, causal variant identification and functional analysis.

Multi-Omics and Stratified Medicine: RNA-seq based transcriptomic analysis, proteomics and epigenomics for biomarker identification and stratification of medicine response in Inflammatory diseases.

Trauma Injury Research: Transcriptomic and epigenomic analysis of early response to trauma injury as determinant of patient clinical trajectory in critical care. 

Chemogenomics and Drug Discovery: Target identification and druggability assessment, Chemogenomic analysis and connectivity map analysis. Drug Repositioning.

Clinical Informatics: Development of Clinical datamarts to support translational research and stratified medicine. Currently developing i2b2 and TranSMART based systems.

Cloud Computing: Development of virtual machine infrastructure for flexible scientific cloud computing across omics and clinical informatics applications

Members of the Group

Research staff: Claudia Cabrera; David Watson; Evan Tzanis; Aaron Lee; Kevin Blighe; Sharmila Rana

Key Publications

For a full list of publist publications click here

Jia Z, Liu Y, Guan N, Bo X, Luo Z, Barnes MR. (2016) Cogena, a novel tool for co-expressed gene-set enrichment analysis, applied to drug repositioning and drug mode of action discovery. BMC Genomics. 17(1):414.

Howard SR, Guasti L, Ruiz-Babot G, Mancini A, David A, Storr HL, Metherell LA, Sternberg MJ, Cabrera CP, Warren HR, Barnes MR, Quinton R, de Roux N, Young J, Guiochon-Mantel A, Wehkalampi K, André V, Gothilf Y, Cariboni A, Dunkel L. (2016) IGSF10 mutations dysregulate gonadotropin-releasing hormone neuronal migration resulting in delayed puberty. EMBO Mol Med. 8(6):626-42.

Narasimhan VM, Hunt KA, Mason D, Baker CL, Karczewski KJ, Barnes MR, Barnett AH, Bates C, Bellary S, Bockett NA, Giorda K, Griffiths CJ, Hemingway H, Jia Z, Kelly MA, Khawaja HA, Lek M, McCarthy S, McEachan R, O'Donnell-Luria A, Paigen K, Parisinos CA, Sheridan E, Southgate L, Tee L, Thomas M, Xue Y, Schnall-Levin M, Petkov PM, Tyler-Smith C, Maher ER, Trembath RC, MacArthur DG, Wright J, Durbin R, van Heel DA. (2016) Health and population effects of rare gene knockouts in adult humans with related parents. Science. 352(6284):474-7

Sordi R, Nandra KK, Chiazza F, Johnson FL, Cabrera CP, Torrance HD, Yamada N, Patel NS, Barnes MR, Brohi K, Collino M, Thiemermann C. (2016) Artesunate Protects Against the Organ Injury and Dysfunction Induced by Severe Hemorrhage and Resuscitation. Ann Surg. 2016 Feb 1.

Griffiths CE, Barnes MR, Burden AD, Nestle FO, Reynolds NJ, Smith CH, Warren RB, Barker JN (2015) Establishing an Academic-Industrial Stratified Medicine Consortium: Psoriasis Stratification to Optimize Relevant Therapy. J Invest Dermatol. 135(12):2903-7.

Gagliano SA, Ravji R, Barnes MR, Weale ME, Knight J. (2015) Smoking Gun or Circumstantial Evidence? Comparison of Statistical Learning Methods using Functional Annotations for Prioritizing Risk Variants. Sci Rep. 5:13373.

Jia Z, Zhang X, Guan N, Bo X, Barnes MR*, Luo Z*. (2015) Gene Ranking of RNA-Seq Data via Discriminant Non-Negative Matrix Factorization. PLoS One. 10(9):e0137782.

Lanktree MB, Elbers CC, Li Y, Zhang G, Duan Q, Karczewski KJ, Guo Y, Tragante V, North KE, Cushman M, Asselbergs FW, Wilson JG, Lange LA, Drenos F, Reiner AP, Barnes MR, Keating BJ. (2015) Genetic meta-analysis of 15,901 African Americans identifies variation in EXOC3L1 is associated with HDL concentration. J Lipid Res. 56(9):1781-6.

Rodriguez S, Gaunt TR, Guo Y, Zheng J, Barnes MR* et al (2015) Lipids, obesity and gallbladder disease in women: insights from genetic studies using the cardiovascular gene-centric 50K SNP array. Eur J Hum Genet. Apr 29.

Postmus I*, Trompet S*, Deshmukh HA*, Barnes MR*, et al (2014) Pharmacogenetic meta-analysis of genome-wide association studies of LDL cholesterol response to statins. Nature Comm, 5:5068

Gagliano SA, Barnes MR, Weale ME, Knight J. (2014) A Bayesian method to incorporate hundreds of functional characteristics with association evidence to improve variant prioritization. PLoS One 9(5):e98122

Tragante V, Barnes MR, et al (2014) Gene-centric Meta-analysis in 87,736 Individuals of European Ancestry Identifies Multiple Blood-Pressure-Related Loci. Am J Hum Genet. 94(3):349-60

Yoneyama S*, Guo Y*, Lanktree MB*, Barnes MR*, et al (2014). Gene-centric meta-analyses for central adiposity traits in up to 57 412 individuals of European descent confirm known loci and reveal several novel associations. Hum Mol Genet. 2014 Jan 6.

Sanseau, P, Agarwal P, Barnes MR, Pastinen T, Richards JB, Cardon LR, Mooser V. “Use of genome-wide association studies for drug repositioning“. Nature Biotech., (2012), 30(4),317-320

Barnes MR, Harland L, Foord SM, et al. (2009) Lowering industry firewalls: pre-competitive informatics initiatives in drug discovery. Nat Rev Drug Discov. 8(9):701-8

*Baranzini SE, Galwey NW, Wang J, Khankhanian P, Lindberg R, Pelletier D, Wu W, Uitdehaag BM, Kappos L; GeneMSA Consortium, Polman CH, Matthews PM, Hauser SL, Gibson RA, Oksenberg JR, Barnes MR (2009) Pathway and network-based analysis of genome-wide association studies in multiple sclerosis. Hum Mol Genet. 18(11):2078-90

Sponsors

National Institute for Health Research   Medical Research Council

Collaborators

Internal: Prof Mark Caulfield (WHRI); Prof Costantino Pitzalis (WHRI); Prof Leo Dunkel (WHRI); Prof Patricia Munroe (WHRI); Prof David Kelsell (Blizard); Prof Amrita Ahluwalia (WHRI); Prof Karim Brohi (Blizard); Prof David Van Heel (Blizard); Prof Silvia Marino (Blizard); Prof Sussan Nourshagh (WHRI); Prof Rupert Pearse (WHRI); Prof Steffen Petersen (WHRI); Prof Adam Timmis (WHRI);  Dr Michael O'Dwyer (WHRI); Dr Myles Lewis (WHRI);

External: Prof Nick Reynolds (Newcastle); Prof John Issacs (Newcastle); Prof Christopher Griiffiths (Manchester); Prof Ann Morgan (Leeds); Prof Folkert Asselbergs (UCL); Dr Brendan Keating (UPENN); Prof Jo Knight (Lancaster); Dr Michael Weale (KCL); Dr Gerome Breen (Institute of Psychaitry, KCL); Prof Gerhard Ecker (University of Vienna).

 

Contact

Michael R. Barnes, BSc, Phd
Director of Bioinformatics
Barts and The London NIHR Biomedical Research Unit
William Harvey Research Institute
Charterhouse Square
London, EC1M 6BQ
T: +44 (0) 20 7882 2059
E: This email address is being protected from spambots. You need JavaScript enabled to view it.

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