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.
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)
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.
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