Professor Mark Viant

Professor Mark Viant

School of Biosciences
Professor of Metabolomics
Director of Phenome Centre Birmingham and NERC Biomolecular Analysis Facility - Metabolomics Node
Past President of the International Metabolomics Society

Contact details

Telephone
+44 (0)121 41 42219
Fax
+44 (0)121 41 45925
Email
m.viant@bham.ac.uk
Address
School of Biosciences
University of Birmingham
Edgbaston
Birmingham
B15 2TT
UK

60 second video iconProfessor Mark Viant’s expertise lies in the field of metabolomics. His research spans from method development in analytical chemistry and bioinformatics through to the application of metabolomics to environmental toxicology.

Qualifications

BSc Chemistry (University of Southampton)

PhD Chemical Physics (University of Southampton)

Biography

On completion of a BSc in Chemistry (1991) and PhD in Chemical Physics (1994), both at the University of Southampton, Viant spent almost a decade in the USA, initially as a Royal Commission for the Exhibition of 1851 Postdoctoral Researcher at the University of California (UC) Berkeley (chemistry) and subsequently as a postdoctoral researcher and then independent faculty member at UC Davis (environmental toxicology). Here, he pioneered the application of metabolomics to environmental health issues in aquatic organisms.

In 2003 he relocated to the University of Birmingham as a NERC Advanced Fellow with the remit to further develop metabolomics in environmental toxicology. With funding from the NERC, BBSRC, MRC, Wellcome Trust, Wolfson Foundation, EU, Environment Agency and several US agencies, Viant has established a large and active research group in environmental metabolomics. In 2008 he was appointed to Reader in Metabolomics, in 2009 became the Director of the NERC Biomolecular Analysis Facility for Metabolomics, and in 2010 secured his current Chair in Metabolomics. He served as the President of the international Metabolomics Society 2012-2014, gaining Lifetime Honorary Fellowship in 2015. His achievements in metabolomics research have recently been recognised by the University of Birmingham’s highest award, the Joseph Chamberlain Award for Academic Advancement (2013).

Teaching

I teach metabolomics on a range of undergraduate and postgraduate courses.

Postgraduate supervision

For a list of possible PhD projects offered by Professor Viant www.findaphd.com/search/customlink.asp?inst=birm-Biol&supersurname=Viant

Doctoral research

PhD title
PhD in Chemical Physics

Research

Metabolomics & Systems Toxicology Laboratory website: more.bham.ac.uk/viant

Systems Toxicology

By exploiting the exceptional capability of metabolomics to conduct untargeted measurements of small molecule biochemistry, our Metabolomics & Systems Toxicology Laboratory specialises in discovering toxicity pathways of chemicals, drugs and nanomaterials in human and environmental toxicology. This strategy is applied to discover and validate metabolic Key Events to accelerate the creation of Adverse Outcome Pathways (AOPs). Related research projects include the applications of metabolomics for chemical grouping and read-across, and to probe the metabolism of the exposure chemicals, which we term untargeted toxicokinetics.

Metabolomics Method Development

Underpinning this translational toxicology research, our Metabolomics & Systems Toxicology Laboratoryalso focuses on developing analytical and bio-/chemo-informatic methods in metabolomics. This includes novel methods to automate sample preparation using liquid handling robots through to developments in high resolution mass spectrometry, all focused towards applications in higher throughput, higher sensitivity toxicology.

Informatics research projects include optimising standardisable methods to process mass spectrometry data and to identify metabolites, and developing transparent and reproducible Galaxy workflows.

Deep Metabolome Annotation

Deep Metabolome Annotation (DMA) is a flagship project in the Metabolomics & Systems Toxicology Laboratory, which is attempting the most extensive experimental characterisation of a complex model organism metabolome to date, utilising a range of analytical methods from LC-MS, GC-MS, DIMSn to NMR spectroscopy. Daphnia magna is the first organismal metabolome to be deeply annotated, which is a freshwater crustacean that is a sentinel species for ecotoxicology and more recently adopted as an NIH model organism for human health.

Metabolomics Standardisation in Regulatory Toxicology

To facilitate the translation of metabolomics into regulatory toxicology, projects are underway with the European Centre for Ecotoxicology and Toxicology of Chemicals (ECETOC) and the OECD to define best practice for analytical and computational metabolomics, including method performance criteria and minimal reporting standards. The draft of the first guidance document has been completed for the Metabolomics standaRds Initiative in Toxicology (MERIT) project. An OECD Guidance Document describing a metabolomics reporting framework (MRF) is anticipated by 2020.  


Mark Viant describes, in 60 seconds, his research in the area of measuring environmental stress by studying animals at the molecular level

Other activities

Chair of Model Organism Metabolomes Task Group of the international Metabolomics Society (2015-present).

Member of Data Quality Task Group of the international Metabolomics Society (2014-present).

Member of the OECD Expert Advisory Group on Molecular Screening and Toxicogenomics (EAGMST) (2014-present).

Editorial Board of Nature Publishing Group's journal Scientific Data (2013-present).

Member of Data Standards Task Group of the international Metabolomics Society (2013-present).

President of the international Metabolomics Society (2012-2014).

Editorial Board of the journal Metabolomics (2004-present).

Publications

M. R. Viant, I. J. Kurland, M. R. Jones, W. B. Dunn, How close are we to complete annotation of metabolomes?, Curr. Opin. Chem. Biol. 158, 252-262 (2017)

R. J. M. Weber, T. N. Lawson, R. M. Salek, T. M. D. Ebbels, R. C. Glen, R. Goodacre, J. L. Griffin, K. Haug, A. Koulman, P. Moreno, M. Ralser, C. Steinbeck, W. B. Dunn, M. R. Viant, Computational tools and workflows in metabolomics: An international survey highlights the opportunity for harmonisation through Galaxy, Metabolomics 13, 12 (2017)

R. L. Davidson, R. J. M. Weber, H. Liu, A. Sharma-Oates, M. R. Viant, Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data, GigaScience 5, 1-9 (2016)

J. Bradbury, G. Genta-Jouve, J. W. Allwood, W. B. Dunn, R. Goodacre, J. D. Knowles, S. He, M. R. Viant, MUSCLE: automated multi-objective evolutionary optimization of targeted LC-MS/MS analysis, Bioinformatics 31, 975-977 (2015)

J. A. Kirwan, R. J. M. Weber, D. I. Broadhurts, M. R. Viant, Direct infusion mass spectrometry metabolomics dataset: a benchmark for data processing and quality control. Scientific Data 1, 240012 (2014)

L. Mirbahai, A. D. Southam, U. Sommer, T. D. Williams, J. P. Bignell, M. R. Viant, J. K. Chipman, Disruption of DNA methylation via S-adenosylhomocysteine is a key process in high incidence liver carcinogenesis in fish. J. Proteome Research 12, 2895-2904 (2013).

J. A. Kirwan, D. I. Broadhurst, R. L. Davidson, M. R. Viant, Characterising and correcting batch variation in an automated direct infusion mass spectrometry (DIMS) metabolomics workflow. Anal. Bioanal. Chem405, 5147-5157 (2013).

W. B. Dunn, A. Erban, R. J. M. Weber, D. J. Creek, M. Brown, R. Breitling, T. Hankemeier, R. Goodacre, S. Neumann, J. Kopka, M. R. Viant, Mass appeal: metabolite identification in mass spectrometry-focused untargeted metabolomics. Metabolomics 9, S44-66 (2013).

M. R. Viant, and U. Sommer, Mass spectrometry based environmental metabolomics: A primer and review. Metabolomics 9, S144-158 (2013).

R. J. M. Weber, E. Li, J. Bruty, S. He, M. R. Viant, MaConDa: a publicly accessible Mass spectrometry Contaminants Database. Bioinformatics 28, 2856-2857 (2012).

C. Ludwig, J. M. Easton, A. Lodi, S. Tiziani, S. Manzoor, A. D. Southam, J. J. Byrne, L. M. Bishop, S. He, T. N. Arvanitis, U. L. Günther, M. R. Viant, Birmingham Metabolite Library: A publicly accessible database of 1-D 1H and 2-D 1H J-resolved NMR spectra of authentic metabolite standards (BML-NMR). Metabolomics 8, 8-18 (2012).

O. Hrydziuszko, M. R. Viant, Missing values in mass spectrometry based metabolomics: an undervalued step in the data processing pipeline. Metabolomics 8, 161-174 (2012).

T. D. Williams, N. Turan, A. M. Diab, H. Wu, C. Mackenzie, K. L. Bartie, O. Hrydziuszko, B. P. Lyons, G. D. Stentiford, M. J. Herbert, K. J. Abraham, I. Katsiadaki, M. J. Leaver, J. B. Taggart, S. G. George, M. R. Viant, J. K. Chipman, F. Falciani, Towards a System Level Understanding of Non-Model Organisms Sampled from the Environment: A Network Biology Approach. PLoS Comp. Biol. 7, e1002126 (2011).

I. Römer, T. A. White, M. Baalousha, J. K. Chipman, M. R. Viant, J. R. Lead, Aggregation and dispersion of silver nanoparticles in exposure media for aquatic toxicity tests. J. Chromatogr. A 1218, 4226-4233 (2011).

R. J. M. Weber, A. D. Southam, U. Sommer, M. R. Viant, Characterization of isotopic abundance measurements in high resolution FT-ICR and Orbitrap mass spectra for improved confidence of metabolite identification. Anal. Chem. 83, 3737-3743 (2011).

A. D. Southam, A. Lange, A. Hines, E. M. Hill, Y. Katsu, T. Iguchi, C. R. Tyler, M. R. Viant, Metabolomics reveals target and off-target toxicities of a model organophosphate pesticide to roach (Rutilus rutilus): Implications for biomonitoring. Environ. Sci. Technol. 45, 3759-3767 (2011).

H. C. Poynton, N. S. Taylor, J. Hicks, K. Colson, S. Chan, C. Clark, L. Scanlan, A. V. Loguinov, C. Vulpe, M. R. Viant, Metabolomics of Microliter Hemolymph Samples Enables an Improved Understanding of the Combined Metabolic and Transcriptional Responses of Daphnia magna. Environ. Sci. Technol. 45, 3710-3717 (2011).

N. S. Taylor, R. J. M. Weber, T. A. White, M. R. Viant, Discriminating between different acute chemical toxicities via changes in the daphnid metabolome. Toxicol. Sci. 118, 307–317 (2010).

R. J. M. Weber, M. R. Viant, MI-Pack: Increased confidence of metabolite identification in mass spectra by integrating accurate masses and metabolic pathways. Chemometrics and Intelligent Laboratory Systems 104, 75-82 (2010).

A. Hines, F. J. Staff, J. Widdows, R. Compton, F. Falciani, M. R. Viant, Discovery and validation of metabolic signatures for predicting whole organism toxicology. Toxicol. Sci. 115, 369-378 (2010) – selected as Highlight Article for this Issue.

E. M. Santos, J. S. Ball, T. D. Williams, H. Wu, F. Ortega, R. van Aerle, I. Katsiadaki, F. Falciani, M. R. Viant, J. K. Chipman, C. R. Tyler, Identifying health impacts of exposure to copper using transcriptomics and metabolomics in a fish model. Environ. Sci. Technol. 44, 820-826 (2010).

C. Ludwig, M. R. Viant, Two-dimensional J-resolved NMR spectroscopy: Review of a key methodology in the metabolomics toolbox. Phytochemical Analysis 21, 22-32 (2010).

T. G. Payne, A. D. Southam, T. N. Arvanitis, M. R. Viant, A signal filtering method for improved quantification and noise discrimination in Fourier transform ion cyclotron resonance mass spectrometry-based metabolomics data. J. Amer. Soc. Mass Spectrom. 20, 1087-1095 (2009).

N. S. Taylor, R. J. M. Weber, A. D. Southam, T. G. Payne, O. Hrydziuszko, T. N. Arvanitis, M. R. Viant, A new approach to toxicity testing in Daphnia magna: Application of high throughput FT-ICR mass spectrometry metabolomics. Metabolomics 5, 44-58 (2009).

J. G. Bundy, M. P. Davey, M. R. Viant, Environmental metabolomics: A critical review and future perspectives. Metabolomics 5, 3-21 (2009).

M. R. Viant, D. W. Bearden, J. G. Bundy, I. W. Burton, T. W. Collette, D. R. Ekman, V. Ezernieks, T. K. Karakach, C. Y. Lin, S. Rochfort, J. S. de Ropp, Q. Teng, R. S. Tjeerdema, J. A. Walter, H. Wu, International NMR-based Environmental Metabolomics Intercomparison Exercise. Environ. Sci. Technol. 43, 219-225 (2009).

A. D. Southam, J. M. Easton, G. D. Stentiford, C. Ludwig, T. N. Arvanitis, M. R. Viant, Metabolic changes in flatfish hepatic tumours revealed by NMR-based metabolomics and metabolic correlation networks. J. Proteome Res. 7, 5277-5285 (2008).

L. W. Sumner, A. Amberg, D. Barrett, M. H. Beale, R. Beger, C. A. Daykin, T. W. M. Fan, O. Fiehn, R. Goodacre, J. L. Griffin, T. Hankemeier, N. Hardy, J. Harnly, R. Higashi, J. Kopka, A. N. Lane, J. C. Lindon, P. Marriott, A. W. Nicholls, M. D. Raeily, J. J. Thaden, M. R. Viant, Proposed minimum reporting standards for chemical analysis Chemical Analysis Working Group (CAWG) Metabolomics Standards Initiative (MSI), Metabolomics 3(3), 211-221 (2007)

A. D. Southam, T. G. Payne, H. J. Cooper, T. N. Arvanitis, M. R. Viant, Dynamic range and mass accuracy of wide-scan direct infusion nanoelectrospray Fourier transform ion cyclotron resonance mass spectrometry-based metabolomics increased by the spectral stitching method. Anal. Chem. 79, 4595-4602 (2007).

A. Hines, G. S. Oladiran, J. P. Bignell, G. D. Stentiford and M. R. Viant, Direct Sampling of Organisms from the Field and Knowledge of their Phenotype: Key Recommendations for Environmental Metabolomics. Env. Sci. Technol. 41, 3375-3381 (2007).

M. R. Viant, E. S. Rosenblum and R. S. Tjeerdema, NMR-Based Metabolomics: A Powerful Approach for Characterizing the Effects of Environmental Stressors on Organism Health, Env. Sci. Technol. 37, 4982-4989 (2003).

M. R. Viant, Improved Methods for the Acquisition and Interpretation of NMR Metabolomic Data, Biochem. Biophys. Res. Comm. 310, 943-948 (2003).

Expertise

Using molecular techniques (specifically the ‘omics’ technique called metabolomics) to study the responses of animals living in the environment to stress, particularly environmental pollutants.