(2dm) Decoding and Expanding Genome Functions for Living Technologies

Genomes define the entirety of functions that a cell can carry out in a modular and “exchangeable” fashion. While we have harnessed the ability to identify relevant gene functions for a cellular task and predict the structure and function of a protein from its sequence, we do not know yet how to predict cellular phenotypes from genome sequences with nucleotide resolution, or vice versa. In my graduate career, I developed mathematical formulations that link cellular processes to underlying phenotypes, identify nutritional requirements in terms of molecular structures, suggest missing biochemical annotations in genomes, and identify high order redundant sets of genes. I constructed the most comprehensive genome-scale metabolic models of at the time highly uncharacterized malaria parasites and achieved 80% accuracy in essentiality predictions as proven by experimental data. I also co-developed genome-scale models for the bacterium Pseudomonas veronii and the Apicomplexan parasite Toxoplasma gondii, both of which I helped curate against experimental data. Finally, I studied the mode of action of drugs and co-developed a pipeline for the large-scale analysis of drug metabolism and rational drug design.

As a postdoctoral fellow, I am continuing my multi-disciplinary journey by 1) co-developing a genomically recoded strain of Escherichia coli that lacks seven codons from its genome; 2) developing deep learning and mechanistic models connecting sequence-to-function relationships for genomes; and 3) analyzing the mode of action of antibiotics.

I would like to continue developing a cellular engineering toolbox involving computational and experimental technology to design and construct safe living technologies with therapeutic applications.

Teaching Interests:

Beside my research, I also have a passion for mentoring and teaching. Throughout my PhD and Postdoc, I have supervised 29 student projects including 18 semester, 7 master, and 4 PhD projects. All of these students have been excellent in their own way and have taught me to be a better scientist and mentor. It is until today that I remain in contact with them for career advice and support, and it makes me very happy and proud to see them grow and succeed.

During my undergraduate years, I organized study sessions with my classmates to help them with advanced calculus. Later during my Ph.D., I fostered my passion for teaching. I taught more than 1,000 hours in 5 years. This involved three undergraduate courses in which I was a project mentor or teaching assistant, three workshop courses in which I participated as a service teacher, and a graduate course at which I taught. The main course I taught for four year was “Introduction to Chemical Engineering” involving mass and energy balances. I introduced active learning techniques in my classes, for which I won the Excellence Teaching Award by the Chemistry and Chemical Engineering section at EPFL in 2016 and the appreciation of many students with whom I remain in contact. At Harvard and MIT, I have had the chance to teach two courses in the spring of 2022 involving more than 250 students. As a faculty, I would like to teach foundational courses of chemical engineering and courses on bioinformatics, molecular biology, and biochemistry. I would also enthusiastically introduce courses on computational biology, systems biology, or synthetic biology, among other options that could match the offered study programs.