Richard Orton
Dr Richard Orton
314 Graham Kerr Building
Institute of Biodiversity, Animal Health and Comparative Medicine
University of Glasgow
Glasgow
G12 8QQ
E: Richard.Orton@glasgow.ac.uk
T: 0141 330 6638
W: www.richardorton.co.uk
About Me
I am a postdoctoral Research Associate at the Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow. I am currently employed on a BBSRC project entitled “Beyond the consensus - dissecting viral sequence diversity within samples” where I am using Next Generation Sequencing to analyse the sequence diversity of the Foot-and-Mouth disease virus within and between hosts. My research all centres around the field of computational biology and can be split into three different areas - Bioinformatics, Systems Biology, and Epidemiology.
Bioinformatics
I am interested in the visualisation and integration of biological data from different omic strategies (sequence, expression, interaction, pathways, models etc) and the development of software tools to aid in their analysis. I am currently working on the integration of computational models with the underlying biological data, and the application of Next Generation Sequencing technologies to the study of viral populations to further our understanding of genetic diversity and bottlenecks at various scales.
Systems Biology
I am interested in the computational modelling of biological pathways with my main research relating to the MAPK/ERK pathway, its role in cell signalling from different growth factor receptors, and how it is deregulated to cause cancer. I am particularly interested in the role negative feedback loops play in signalling and the drug resistance properties they can give a cancerous system. I am also interested in the development of computational tools for the simulation of pathways, and the development and management of models.
Epidemiology
I am interested in the computation modelling of infectious diseases with my main research focusing on the modelling of various livestock disease in GB such as bovine tuberculosis (bTB), bluetongue virus and Foot-and-Mouth disease (FMD) using both stochastic and probabilistic approaches to model the spatial spread of diseases via movements and local spread via vectors and wildlife reservoirs.
Background
2012 - Present: Research Associate (Dan Haydon), University of Glasgow
Bioinformatics - Next Generation Sequence analysis of FMD disease within and between hosts - diversity and genetic bottlenecks at different scales - software development of viral NGS analysis pipeline.
2009 - 2012: Scientific Programmer (Rowland Kao), University of Glasgow
Epidemiology - Stochastic and probabilistic modelling of the dynamics and spatial spread of FMD, bTB and Bluetongue diseases in British livestock - software development of modelling framework - C++, MySQL and GIS.
2008 - 2009: Software Developer, JPMorgan
Software developer working on Kapital (interest rate derivates) for the Securitized Products Group, New York - Smalltalk and Gemstone.
2003 - 2008: Research Associate (David Gilbert), University of Glasgow
Systems Biology - Computational modelling of cell signalling and cancer pathways, negative feedback loops and drug resistance - software development of model simulation and management tools - Java, PHP, MySQL and ODEs.
2000 - 2003: PhD Student (Dietlind Gerloff), University of Edinburgh
Bioinformatics - Visualisation, integration and analysis of genomic and functional genomic data sets for yeast - Java, Perl and MySQL.
1999 - 2000: Genotyper, Oxagen Ltd
Bioinformatics - QC and analysis of genotype data (variable repeat markers) to associate chromosomal regions from within diseased families to diseases such as diabetes.
1996 -1999: Undergraduate Student, University of Birmingham
BSc (Hons) Biochemistry with Biotechnology.
Publications
The Mammalian MAPK/ERK Pathway Exhibits Properties of a Negative Feedback Amplifier
Sturm OE, Orton RJ, Grindlay J, Birtwistle M, Vyshemirsky V, Gilbert D, Calder M, Pitt A, Kholodenko B, Kolch W
Science Signalling 3 (2010), ra90
Computational modelling of kinase signalling cascades
Gilbert DR, Heiner M, Breitling R, Orton R
Methods in molecular biology (2010) 661:369-84
Cell fate decisions specified by the dynamic ERK interactome
von Kriegsheim A, Baiocchi D, Birtwistle M, Sumpton D, Bienvenut W, Morrice N, Yamada K, Lamond A, Kalna G, Orton R, Gilbert D, Kolch W
Nature Cell Biology (2009), 11: 1458-1464
Computational modelling of cancerous mutations in the EGFR/ERK signalling pathway
Orton RJ, Adriaens ME, Gormand A, Sturm OE, Kolch W, Gilbert DR
BMC Systems Biology (2009), Vol 3 Article 100
Version control of pathway models using XML patches
Saffrey P, Orton R
BMC Systems Biology (2009), Vol 3, Article 34
Computational modelling reveals feedback redundancy within the EGFR/ERK signalling pathway
Orton RJ, Sturm O, Gormand A, Kolch W and Gilbert D
IET Systems Biology, Vol 2 Issue 4, 173-183, July 2008
A structured approach for the engineering of biochemical network models, illustrated for signalling pathways
Breitling R, Gilbert D, Heiner M, Orton R (2008).
Briefings in Bioinformatics, June 23, 2008.
Computational methodologies for modelling, analysis and simulation of signalling networks
Gilbert D, Fuss H, Gu X, Orton RJ, Robinson S, Vyshemirsky V, Kurth MJ, Downes CS, and Dubitzky W
Briefings in Bioinformatics 2006 7: 339-353
Analysis of Signalling Pathways using Continuous Time Markov Chains
Calder M, Vyshemirsky V, Gilbert D, and Orton RJ
Transactions on Computational Systems Biology VI, vol. 4220, pp. 44-67, Springer, 2006
Computational modelling of the receptor tyrosine kinase activated MAPK pathway
Orton RJ, Sturm OE, Vyshemirsky V, Calder M, Gilbert DR, Kolch W
Biochemical Journal: Vol 392 (2) 249-261, 01/12/2005
Analysis of Signalling Pathways using the Prism Model Checker
Calder M, Vyshemirsky V, Gilbert D, Orton RJ
Proceedings of Computational Methods in Systems Biology (CMSB) 2005
YETI: Yeast Exploration Tool Integrator
Orton RJ, Sellers WI, Gerloff DL
Bioinformatics: January 22nd 2004: 20(2): 284-5
Computer-Aided Visualisation of Archaeological Caves
Sellers WI, Orton R, Chamberlain AT
CAPRA: November 2001 (3)
Also Acknowledged In -
A unifying framework for modelling and analysing biochemical pathways using Petri Nets
Gilbert D, Heiner M, Lehrack S
Proceedings of Computational Methods in Systems Biology (CMSB) 2007
Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA
Calder M, Gilmore S and Hillston J
Transactions on Computational Systems Biology VII, vol. 4230, pp. 1-23, Springer, 2006
Stronger computational modelling of signalling pathways using both continuous and discrete-space methods
Calder M, Duguid A, Gilmore S, and Hillston J
Proceedings of Computational Methods in Systems Biology (CMSB) 2006
Reasoning about the ERK signal transduction pathway using BioSigNet-RR
Shankland C, Tran N, Baral C, and Kolch W
Proceedings of Computational Methods in Systems Biology (CMSB) 2005
Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA
Calder M, Gilmore S and Hillston J
Proceedings of Bio-CONCUR 2004
Links
Computational Modelling of the MAPK pathway
Supplementary information on the computational models analysed in the Biochemical Journal paper including links to SBML files, original papers and model pictures.
Slides from modelling lecture as part of the Computational Methods in Systems Biology MSc module.
Mitogen Activated Protein Kinase (MAPK) Model Database (password required)
