
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
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
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