My Research

I work at the interface of synthetic biology and computational biology,

decoding and expanding genome functions that introduce new chemistries in cells.

I will establish a leading research group focused on

developing computational and experimental cellular engineering tools

for the understanding and engineering of cellular functions with expanded codes.

We will employ fundamental synthetic biology, metabolic engineering, and machine learning approaches.

Discovered molecular processes involved in the evolution of an engineered genetic code using a 61-codon Escherichia coli strain, and developed technology for its bioisolation / biocontainment: Pre-print

Identified and troubleshooted cellular fitness issues arising from an E. coli 57-codon genome design, among other efforts toward the construction of the strain: Pre-print

Built deep learning models and mechanistic models to improve cellular fitness (in preparation)

Engineering cells with an engineered genetic code to encode non-standard amino acids (in preparation)

Collaboration with Prof. James J Collins (MIT) and Jonathan M Stokes (MIT, McMaster University):

Analyzed omics, sequencing, and structural data to understand protein-drug interactions and the mode of action of antibiotics discovered with artificial intelligence: E. coli and Acinetobacter baumannii

Collaboration with Prof. Stephanopoulos (MIT):

Identified metabolic constraints that allow modeling metabolism upon substrate co-feeding (in preparation)

Postdoctoral research

Led computational efforts of interdisciplinary and international MalarX project – involved collaborations with the University of Geneva and Bern (CH), Leiden (NL), and Sanger Institute (UK): publication

Established optimization-based computational tools for analysis of the cellular metabolic function in highly metabolically active (publications iPfa, iPbe) and dormant organisms (master thesis), understanding of the genotype-phenotype relationship (publication), annotation of missing biochemistry in metabolic reconstructions (publication), and analysis of labelled metabolic models (master thesis)

Worked on network analysis and reactive site identification to evaluate drug action mechanisms: publication

Image published in our press release