Portrait of Sara-Jane Dunn

Sara-Jane Dunn

Scientist

I am a scientist based within the Biological Computation group at Microsoft Research Cambridge, and an affiliate researcher at the Wellcome Trust – Medical Research Council Stem Cell Institute, University of Cambridge. I am a mathematician, and received my doctoral degree from the Department of Computer Science, University of Oxford. I work at the interface between mathematics, computer science and biology.

Specifically, my research is centred on developing a theory of biology as computation, in which the biochemistry of the cell performs information processing in the service of decision-making. Towards this, I collaborate with researchers at MSR, and experimentalists at the Universities of Cambridge and Padova to investigate stem cell decision-making throughout Development. I seek to identify the necessary abstractions to develop predictive, explanatory models of biological behaviour. The goal of this research is ultimately to make cells programmable, which could fundamentally transform medicine, agriculture and even the ways we generate energy.

Collaborators

  • Prof Austin Smith, Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge
    • Dr Amy Li, Smith lab
  • Dr Graziano Martello, Department of Molecular Medicine, University of Padua
  • Prof Inke Nathke, School of Life Sciences, University of Dundee
  • Dr Brian Hendrich, Wellcome Trust-Medical Research Council Stem Cell Institute, University of Cambridge
    • Dr Nicola Reynolds, Hendrich lab
  • Dr James Osborne, School of Mathematics and Statistics, University of Melbourne

Press

 

Decision-Making in Stem Cells

Established: January 18, 2016

Development proceeds via a sequence of decisions that cells have to make about whether to divide, to differentiate, or to migrate. Differentiation is the process by which a cell changes from one type to another, which enables the expansion of the different lineages and growth of the different structures of the adult. Embryonic stem (ES) cells are uniquely naïve in this regard: these cells retain the ability to differentiate to any cell type of the adult body, as well as…

Reasoning Engine for Interaction Networks (RE:IN)

Established: January 1, 2012

This webpage is dedicated to the tool RE:IN, providing information on the latest version available, together with a tutorial, FAQ, and example files. About RE:IN The Reasoning Engine for Interaction Networks (RE:IN) is a tool that runs online in your web browser, which is designed for the synthesis and analysis of biological programs. Specifically, it encapsulates a methodology that uses automated reasoning to transform a set of critical components, possible interactions and regulation functions into a…

Z3-4Biology

Established: January 1, 2007

An SMT-based Framework for Analyzing Biological Computation The basic principles governing the development and function of living organisms remain only partially understood, despite significant progress in molecular and cellular biology and tremendous breakthroughs in experimental methods. The development of system-level, mechanistic, computational models has the potential to become a foundation for improving our understanding of natural biological systems, and for designing engineered biological systems with wide-ranging applications in nanomedicine, nanomaterials and computing. We…

2016

2015

2014

Ten Simple Rules for Effective Computational Research
James Osborne, Miguel Bernabeu, Maria Bruna, Ben Calderhead, Jonathan Cooper, Neil Dalchau, Sara-Jane Dunn, Alexander Fletcher, Derek Groen, Bernhard Knapp, Gary Mirams, Joe Pitt-Francis, Biswa Sengupta, David Wright, Christian Yates, David Gavaghan, Stephen Emmott, Charlotte Deane, PLoS Computational Biology (Public Library of Science Computational Biology),, March 1, 2014, View abstract, Download PDF

2013

2012

2011

2010

Biography

I studied Mathematics at the University of Oxford, graduating with an MMath in 2007. During the summer of 2006 I completed a NERC internship at the British Antarctic Survey, working with Dr. Andrew Edwards on the foraging behaviour of the wandering albatross.

I began my DPhil. in 2007, also at Oxford, as a student of the Life Science Interface Doctoral Training Centre (DTC). The first year of my doctoral studies was spent completing an intensive training course coordinated by the DTC in the application of mathematical, physical, computational and engineering science techniques to the biomedical and life sciences. At the end of this year, I joined the Computational Biology group to begin my DPhil. research project, supervised by Prof. David Gavaghan, Prof. Helen Byrne, Prof. Jon Chapman and Dr. James Osborne. The focus of this project was the development of a computational model of the intestinal crypt, to facilitate investigation of the initial stages of carcinogenesis which precede colorectal cancer. I completed my DPhil. in December 2010, just prior to joining Microsoft Research as a postdoctoral researcher. In June 2014 I became a permanent member of the Biological Computation group.

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