David S. Tourigny

David S. Tourigny

Research Scientist at Irving Institute for Cancer Dynamics
Columbia University, New York

I am a Research Scientist at the Irving Institute for Cancer Dynamics, Columbia University working with Simon Tavare and Ed Reznik. Prior to joining the IICD in September 2020, I held a Research Fellowship from the Simons Foundation and LSRF hosted by the Columbia University Irving Medical Centre. Before that, I was a Research Fellow in the Department of Applied Mathematics and Theoretical Physics, University of Cambridge where I also completed my PhD under the supervision of Venki Ramakrishnan and Garib Murshudov at the MRC Laboratory of Molecular Biology as a member of Trinity College.

Research

• Computational biology

My current research focus is on understanding the dynamic regulation of metabolism in space and time. I have used both experimental and theoretical approaches to study metabolism in a variety of contexts, ranging from microbial systems to neuronal networks. More recently, I have become interested in the way that stochasticity at the single-cell level and metabolic population heterogeneity contribute to phenomena such as microbial 'bet-hedging' or development of human diseases like cancer (see Publications and this video presentation for details on a current project). Having previously worked on the ribosome during my PhD, I have a longer-term ambition to explore the integration of metabolism with protein synthesis as one of the most energy-demanding processes inside the cell.

• Mathematics

Most of my work involves mathematical and computational modelling based on Applied Dynamical Systems Theory and Constrained Optimisation. In the past, I also have worked on these topics in their own right with relatively less application. Specifically, this involved some geometric properties of certain dynamical systems (see Publications).

• Scientific software

I am continually developing software tools for my own research purposes as well as the wider scientific community. See Software for more information.

Publications

Here is a short list of selected publications. A full list can be found via Google Scholar

Metabolism and protein synthesis

• Simulating single-cell metabolism using a stochastic flux-balance analysis algorithm (with AP Goldberg, JR Karr)
• Cooperative metabolic resource allocation in spatially-structured systems
• Dynamic metabolic resource allocation based on the maximum entropy principle
• Energetic substrate availability regulates synchronous activity in an excitatory neural network (with MKA Karim, R Echeveste, MRN Kotter, JS O'Neill)
• Elongation Factor G bound to the ribosome in an intermediate state of translocation (with IS Fernandez, AC Kelly, V Ramakrishnan)

Dynamical systems

• Networks of planar Hamiltonian systems
• Deformed Hamiltonian vector fields and Lagrangian fibrations

Software

I develop and maintain the Python/C++ package dfba (see also paper here) for dynamic flux-balance analysis (DFBA) simulations. This is joint work with Moritz E. Beber and Jorge Carrasco Muriel that forms part of the openCOBRA code base for constraint-based reconstruction and analysis of metabolic models.

Other software and scripts for data processing can be accessed via GitLab.

During my PhD I worked on a maximum likelihood-based algorithm for clustering and inferring diffraction data from macromolecular crystals (today, this would probably be called machine learning). Details can be found in the second section of my thesis.

Teaching

I have been involved in a small amount of teaching:

• Lecture on Mathematical Foundations of Constraint-Based Modelling at the M2S 2019 course and workshop organised by Felipe Scott and Raul Conejeros. Slides from the lecture are available here
• Supervisions for the course Mathematics for Natural Sciences at the University of Cambridge

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