My research group is based in the Mathematical Institute, University of Oxford. We work on the development, analysis and application of mathematical and computational methods to biological systems. Some projects are also concerned with other areas of applied mathematics (industrial mathematics, environmental applications). Mathematical and computational approaches include differential equations (PDEs, ODEs, asymptotic analysis, numerical methods), stochastic simulations (algorithms and their analysis), networks (network inference, dynamics on networks) and data analysis (clustering, image analysis). My publications and preprints can be found here.

Group leader: Prof. Radek Erban - info about me can be found here

Current postdoctoral research assistants:

• Dr. Ulrich Dobramysl - stochastic and multiscale modelling in biology
• Dr. Martin Robinson - software development for reaction-diffusion modelling
• Dr. Marc Sturrock - stochastic modelling of reaction-diffusion processes

Past postdoctoral research assistants:

• Dr. Maria Bruna - modelling excluded volumes and macromolecular crowding (2012)
• Dr. Simon Cotter - multiscale modelling of biochemical systems (2010-2012)
• Dr. Wan Chen - mathematical modelling of ion channels (co-mentored with Prof. Chapman, 2010-2012)
• Dr. Andrew Duncan - stochastic and multiscale modelling in biology (2013-2014)
• Dr. Mark Flegg - stochastic modelling of reaction-diffusion processes (2010-2013)
• Dr. Chong Luo - multiscale modelling in liquid crystal science (co-mentored with Dr. Majumdar, 2010-2012)

Current doctoral students (Ph.D. students, Ph.D. is called DPhil in Oxford):

• Benjamin Franz - collective behaviour of systems of interacting particles
• Shuohao Liao - bifurcation analysis of stochastic biochemical systems
• Jochen Kursawe - modelling of tissue size control and apoptosis (co-supervised with Dr Baker and Prof. Maini)
• Tomislav Plesa - multiscale modelling in biology

Past doctoral students:

• Ornella Cominetti - cancer systems biology and data clustering (co-supervised with Prof. Maini)
• Patrick Dixon - network inference: application in Arabidopsis (co-supervised with Prof. Maini)
• Guido Klingbeil - reverse-engineering of biochemical networks (co-supervised with Prof. Maini and Prof. Novak)
• Margarita Schlackow - gene transcription: investigation of interactions between DNA, cohesin complex and mRNA polymerase (co-supervised with Dr. Gullerova)
• Jean-Charles Seguis - fictitious domain numerical method and its applications (co-supervised with Prof. Burrage, Dr. Kay)
• Tamas Szekely - multiscale modelling in biology (co-supervised with Prof. Burrage)
• Christian Yates - modelling domain growth and somitogenesis (co-supervised with Dr. Baker and Prof. Maini)

Shorter projects - MSc dissertations, Doctoral Training Centre (DTC) student projects, undegraduate research students:

• Christian Yates - MSc dissertation: "On the dynamics and evolution of self-propelled particle models", 2007 (co-supervised with Dr. Escudero and Dr. Sumpter)
• Aidan Twomey - MSc dissertation: "On the stochastic modelling of reaction-diffusion processes", 2007
• Ornella Cominetti - DTC project: "Multiscale modelling: application to solid tumour growth", 2008 (co-supervised with Dr. Kulasiri and Prof. Maini)
• Bubacarr Bah - MSc dissertation: "Diffusion maps: analysis and applications", 2008
• Christian Yates - DTC project: "A comparison of stochastic and analytical models for cell migration during early embryo somitogenesis", 2008 (co-supervised with Dr. Baker)
• Ornella Cominetti - DTC project: "Development of correlation map networks of differentially expressed genes in breast cancer from gene expression data: Invasive Ductal Carcinoma (IDC) and Invasive Lobular Carcinoma (ILC)", 2008 (co-supervised with Dr. Kulasiri, Prof. Maini and Dr. Samarasinghe)
• Jamie Hill - MPhys dissertation: "The physics of crowding, packing and adsorbing", 2009 (co-supervised with Dr. Jones and Dr. Porter)
• Hana Moore - MSc dissertation: "Mathematical modelling of water purification", 2009 (co-supervised with Dr. Majumdar and Dr. Peppin)
• Owen Jackson - MSc dissertation: "Growth of ice: fractals and glaciers", 2009 (co-supervised with Dr. Majumdar and Dr. Peppin)
• James Dean - MSc dissertation: "Mathematical modelling of liquid crystals", 2009 (co-supervised with Dr. Majumdar and Dr. Peppin)
• Jana Lipkova - OCCAM summer internship project: "Reversible reactions in reaction-diffusion stochastic simulation algorithms", 2009 (co-supervised with Dr. Zygalakis)
• Suruchi Bakshi - DTC project: "Stochastic oscillations in biological systems", 2009
• Tamas Szekely - DTC project: "Connecting models of individual and collective behaviour of cells", 2009
• Lorna Wilson - MMath project: "Analysis of stochastic models of biological systems", 2009-2010
• Patrick Raanes - MSc dissertation: "Crowding: using statics to understand the dynamics of densely packed hard spheres", 2010 (co-supervised with Dr. Jones and Dr. Porter)
• Margarita Schlackow - DTC project: "Mathematical modelling and experimental verification of interactions between the RNA polymerase and cohesin complex in transcription", 2010 (co-supervised with Dr. Gullerova)
• Krishna Kanhaiya - OCCAM summer internship project: "Mathematical modelling of ion channels: narrow escape problem", 2010 (co-supervised with Dr. Chen)
• Katie Leonard - DTC project: "Stochastic simulation of subdiffusion", 2010 (co-supervised with Dr. Baker and Dr MacNamara)
• Struan Murray - DTC project: "Comparative analysis of DNA sequences: an application to identification of polyA sites in Schizosaccharomyces pombe", 2010 (co-supervised with Dr. Gullerova)
• Matthew Phinney - MSc dissertation: "Multiscale methods for stochastic simulation of chemical reactions", 2011 (co-supervised with Dr. Cotter)
• William Berk - MPhys dissertation: "An investigation into transitions from disorder to order in driven systems of anisotropic particles", 2011 (co-supervised with Dr. Jones and Dr. Majumdar)
• Xiang Xue - MSc dissertation: "Chemical systems with fast and slow dynamics", 2012 (co-supervised with Dr. Cotter)
• Chin Pang Ho - MSc dissertation: "Multiscale reaction-diffusion simulations in biology", 2012 (co-supervised with Dr. Flegg)
• Mark Gilbert - MMath project: "Stochastic and deterministic models of chemical systems close to a bifurcation of the deterministic (ODE) model", 2011-2012
• Shuohao Liao - MSc dissertation: "Multiscale modelling of chemical systems: coupling differential equations models with stochastic algorithms", 2012 (co-supervised with Dr. Cotter)
• Robert Ross - DTC project: "Spatio-temporal modelling of the Min system in E.coli", 2013 (co-supervised with Dr. Flegg and Dr. Robinson)
• Jake Taylor-King - MSc dissertation: "Collective behaviour of interacting agents: from robot experiments to theory", 2013 (co-supervised with B. Franz and Dr. Yates)
• Tomislav Plesa - MSc dissertation: "Stochastic Hopf and homoclinic bifurcations", 2013 (co-supervised with Dr. Vejchodsky)
• Marcin Paczkowski - DTC project: "Stochastic modelling of intracellular calcium dynamics", 2013 (co-supervised with Dr. Flegg and Dr. Robinson)
• Dhruva Raman - DTC project: "Compartment-based stochastic reaction-diffusion models", 2013 (co-supervised with Dr. Yates)
• Andreas Harris - DTC project: "Multiscale modelling of actin dynamics in filopodia", 2013 (co-supervised with Dr. Flegg and Dr. Robinson)
• Tomislav Plesa - DTC project: "Complex chemical Langevin equation", 2014 (co-supervised with Dr. Vejchodsky)
• Rory Mills-Williams - MSc dissertation: "Brownian motion in rapidly fluctuating potentials", 2014 (co-supervised with Dr. Duncan)
• Juanjuan Sun - MSc dissertation: "Bimodality in stochastic gene regulatory network models", 2014 (co-supervised with Dr. Vejchodsky)
• David Kremer Garcia - MSc dissertation: "Swarm robotics", 2014 (co-supervised with Dr. Dobramysl)
• Fernando Gallego Bordallo - MSc dissertation: "Mathematical modelling of circadian rhythms", 2014 (co-supervised with Dr. Vejchodsky)
• Tomislav Plesa - DTC project: "Multiscale models of bacterial chemotaxis", 2014 (co-supervised with Dr. Duncan)

Back to my homepage