Modeling of Biological Systems

Modeling of Biological Systems

Predicting novel therapeutic targets against S. aureus

Using systems-level approaches to better predict and understand how alterations to steady state carbon and nitrogen metabolism affect S. aureus pathogenesis. Developing a ‘pangenome’ metabolic model and a kinetic model for S. aureus strains. Validating and refining the metabolic model using experimentally determined metabolite fluxes and protein concentrations. Predicting novel therapeutic targets against this human pathogen using genome scale essentiality and lethality analysis.  

Modeling microbiome-virome interaction in bovine rumen

To understand the interactions between the functional entities within the system, which dictates the community structure and functional dynamics and host physiology. To identify the unknown interactions between microbial species in the community and the role of viral auxiliary metabolic genes in relaxing the metabolic bottlenecks in the bacterial host and complementing the inter-species interactions. 

ME model of R. palustris

To develop a Genome scale Metabolic and Expression (ME) models, taking into account the synthesis of macromolecules (RNA, proteins, Transcription factors, etc.).  

Multi-tissue plant-scale modeling of Rice

To develop a multi-tissue genome scale metabolic model of rice by integrating the different tissue types (leaf, stalk, seed and root) and describing the metabolic interactions within these tissues. To study the interaction of the whole plant with the root rhizobiome.