Postdoc opportunity – deadline approaching!

I’m looking for an excellent postdoc to work with Professor Michael Stumpf and I on an exciting collaborative project aimed at providing new approaches to connect models and quantitative data in the biosciences. A similar position is also available in Michael’s group at Imperial College. The aims of the project are to develop a complementary suite of approaches that will enable researchers in the modern life and biomedical sciences to (i) estimate model parameters and (ii) perform model selection for agent-based and multi-scale models of biological phenomena.

Adverts and further particulars (deadline 8th November)

Welcome to Rasa and Max!

Great to welcome two new members to the group! Rasa Giniunaite will focus on developing and applying new models of cell invasion to the problem of cranial neural crest invasion, in collaboration with Paul Kulesa at Stowers Institute for Medical Research. Maxandre Jacqueline (@MaxandreJacquel) will focus on developing models of three-dimensional culture systems for stem-cell-derived cardiomyocytes.

Congratulations to Chris!

Congratulations to D.Phil. student Chris Lester on being granted leave to supplicate! Chris’ thesis, supervised together with @Kit_Yates_Maths, focussed on developing efficient simulation methodologies for stochastic models of biochemical reaction networks. We wish Chris all the best in his postdoctoral position with @MagnusRattray in Manchester!

  • C. Lester, C. A. Yates and R. E. Baker (2017). Robustly simulating biochemical reaction kinetics using multi-level Monte Carlo approaches. arXiv
  • C. Lester, C. A. Yates and R. E. Baker (2017). Efficient parameter sensitivity computation for spatially-extended reaction networks. J. Chem. Phys. 146:044106. DOI arXiv
  • C. Lester, R. E. Baker, M. B. Giles and C. A. Yates (2016). Extending the multi-level method for the simulation of stochastic biological systems. Bull. Math. Biol. 78(8):1640-1677.  DOI arXiv
  • C. Lester, M. B. Giles, C. A. Yates and R. E. Baker (2015). An adaptive multi-level simulation algorithm for stochastic biological systems. J. Chem. Phys. 124:024113. DOI arXiv

QBIOX features on the MPLS website!

QBIOX – Quantitative Biology in Oxford is a network aimed at bringing together diverse groups of researchers to use interdisciplinary approaches to tackle key problems in the biosciences. We have a range of activities taking place, including regular colloquia and workshops, and small amounts of funding to help support interdisciplinary activities. If you’d like to find out more, see our article on the @mplsoxford website , or visit our website and follow us on Twitter as @qbiox_oxford

A ‘How To’ guide for producing hair

Recent work, carried out by Linus Schumacher (@LinusSchumacher) during his D.Phil. and EPSRC Doctoral Prize Fellowship in my group, has recently been published in Proc. Nat. Acac. Sci. USA (see PUbMed). The research looked at how the skin develops and produces hair follicles, and proceeded by dissociating the skin into individual cells and tracking the de novo skin formation process.

Summaries of the work can be found at

Congratulations to Jochen on passing his D.Phil. viva!

Congratulations to Jochen (@JochenKursawe) on passing his D.Phil. viva! Jochen’s thesis “Quantitative approaches to epithelial morphogenesis” makes a number of contributions, providing new mechanistic models for epithelial morphogenesis, methods for quantitative data analysis, and investigating how to interrogate mechanistic models using quantitative data. After finishing his EPSRC Postdoctoral Prize Fellowship in the group, Jochen is off to @PapalopuluLab for a postdoc – we look forward to hearing about what he gets up to!

  • J. Kursawe, R. E. Baker and A. G. Fletcher (2017). Impact of implementation choices on quantitative predictions of cell-based computational models. J. Comp. Phys. 345:752-767  DOI
  • J. Kursawe, R. Bardenet, J. J. Zartman, R. E. Baker and A. G. Fletcher (2016). Robust cell tracking in epithelial tissues through identification of maximum common subgraphs. J. Roy. Soc. Interface. 13(124):20160725. DOI bioRxiv
  • J. Kursawe, P. A. Brodskiy, J. J. Zartman, R. E. Baker and A. G. Fletcher (2015). Capabilities and limitations of tissue size control through passive mechanical forces. PLoS Comp. Biol. 11(12):e1004679. DOI

Welcome to Gergely Rost!

Delighted to welcome Gergely Rost ( from the University of Szeged, Hungary as a Marie Curie Individual Fellow in my group. Gergely will spend 18 months working with us, sharing his knowledge and expertise in delay differential equations and bifurcation theory, and learning about our research in quantitative cell and developmental biology.

Congratulations to Linus!

(Belated) congratulations to Linus (@LinusSchumacher) on being granted leave to supplicate for his D.Phil.!

Linus’ thesis explores the role of collective cell migration and self-organisation in the development of the embryo and in vitro tissue formation through mathematical and computational approaches. We consider how population heterogeneity, microenvironmental signals and cell-cell interactions facilitate cells to collectively organise and navigate, with the aim to work towards uncovering general rules and principles, rather than delving into the microscopic molecular details. To ensure the biological relevance of our results, we collaborate closely with experimental biologists working on two model systems.

Publications include:

  • R. McLennan, L. J. Schumacher, J. A. Morrison, J. M. Teddy, D. A. Ridenour, A. C. Box, C. L. Semerad, H. Li, W. McDowell, D. Kay, P. K. Maini, R. E. Baker and P. M. Kulesa (2015). Neural crest migration is driven by a few trailblazer cells with a unique molecular signature narrowly confined to the invasive front. Development 142:2014-2025. DOI
  • R. McLennan, L. J. Schumacher, J. A. Morrison, J. M. Teddy, D. A. Ridenour, A. C. Box, C. L. Semerad, H. Li, W. McDowell, D. Kay, P. K. Maini, R. E. Baker and P. M. Kulesa (2015). VEGF signals induce trailblazer cell identity that drives neural crest migration. Dev. Biol. 407(1):12-25. DOI

PhD studentship opportunity at the University of Bath

PhD studentship opportunity at the University of Bath.

Cross-disciplinary investigation of pattern formation in Zebrafish using spatially extended mathematical models with volume exclusion


Dr Christian Yates (Mathematical Sciences, University of Bath),
Professor Ruth Baker (Mathematics, University of Oxford),
Professor Robert Kelsh (Biology and Biochemistry, University of Bath).


Pigment pattern formation – the process generating functional and often beautiful distributions of pigment cells in the skin – represents a classic problem in pattern formation. Pigment pattern formation in adult zebrafish is now one of the best-studied examples. Three cell types are known to contribute to the striped pigment patterns of zebrafish; xanthophores, melanophores and iridophores. We have also recently identified Agouti Signalling Peptide (ASIP) as a further patterning component. Traditionally zebrafish pattern modelling has been conducted at the continuum level with Turing instability the proposed mechanism. However, the discrete nature of the agents (cells) involved suggests that individual-based models might be preferable, to allow inclusion of biological noise and to account for the finite volume of the cells.

Under the supervision of leading experts in stochastic mathematical modelling and developmental biology of pattern formation the student will generate a versatile framework to investigate the effects of stochasticity and finite cell size upon pattern formation models which include all cell-types and ASIP signalling. This model will be informed by the experimental data on zebrafish skin patterning. Biological predictions of the model will then be tested experimentally and the findings used to feedback into the model as part of an iterative model-development cycle.

In particular, the student will construct an on-lattice exclusion-process model in which cells interact with neighbours, and move to neighbouring lattice sites. A detailed investigation of the relationship between key length scales in the model, the system size and compartment size, and their impact on the patterns formed, will be carried out. Subsequently hypotheses on pigment cell interactions will be explicitly encoded into this framework to explore the potential of the model to replicate the patterns of both wild-type and mutant fish.

Guided by the modelling outputs, the student will generate data to test the models’ efficacy. Data will be obtained from the literature and targeted experimental studies. Experimental studies will include direct quantitative measurements of important properties of the pigment cell pattern, e.g. dynamic cell-cell distances and density; pair-correlation functions; and gene expression (e.g. using qRT-PCR) in skin samples at different stages.

The student selected for this project will develop invaluable skill sets in both mathematical modelling and experimental genetics and cell biology whilst also making a significant contribution to the
understanding of a canonical biological pattern formation system. These mixed skill sets will make the candidate a highly desirable recruitment prospect for future employers.

Reconciling transport models across scales

Our manuscript “Reconciling transport models across scales: the role of volume exclusion” with , and has just been accepted for publication as a Rapid Communication in Physical Review E! You can find a draft of our manuscript on the arXiv.

Adventures in the world of mathematical biology