Computational Biology

State and parameter estimation of ensemble pERK dynamics (TA only)

Guides: Ganesh Viswanathan and Sharad Bhartiya
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Proposing Faculty
Research Area
  • Computational Biology
  • Data Analysis
  • Identification
  • Modelling
  • Optimisation
  • Systems Biology

In vitro evolution to decipher the molecular mechanism of speciation in yeast

How does speciation take place? In this project, we aim to understand the mechanics and mechanisms of how does an ancestor diverge and give rise to two distinct species. This project involves working with yeast and theoretical modeling of evolutionary processes. [This project is in collaboration with Prof. PJ Bhat from BSBE, IITB]

Proposing Faculty
Research Area
  • Biochemical Engineering
  • Biomolecular Engineering
  • Computational Biology
  • Systems Biology

Modeling and simulations of anti-HIV protein SAMHD1






A human cellular
enzyme, SAMHD1 has recently generated immense interest in its activity and
regulation on account of its role in blocking HIV-1 infection in dendritic
cells. The enzyme has the potential to provide a solution to the pandemic that
has already taken an enormous human and economic toll. However, the functioning  read more »

Proposing Faculty
Research Area
  • Computational Biology

Theoretical models to understand evolutionary processes.

In the story of evolution from a single cell (LUCA: https://en.wikipedia.org/wiki/Last_universal_common_ancestor) to complex eukaryotes, there are several missing links. In this project, we aim to develop theoretical and computational models to analyze these missing aspects in our understanding of evolution of life on Earth.  read more »

Proposing Faculty
Research Area
  • Biochemical Engineering
  • Biomolecular Engineering
  • Computational Biology
  • Enzymology
  • Systems Biology
Swati Bhattacharya

Evolutionary dynamics of microbial populations.

Using experiments and/or theory, we want to uncover the "rules" of evolution for microbial populations. The project offers scope for experiments, theory, and computations.

Proposing Faculty
Research Area
  • Computational Biology
  • Systems Biology

Non-stationary 13C Metabolic Flux Analysis of photosynthetic microorganisms.



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Proposing Faculty
Research Area
  • Biochemical Engineering
  • Computational Biology

Reaction network of the nodes in the vertex cover of the Tumor Necrosis Factor alpha signaling network (TA/FA)

Tumor necrosis factor alpha (TNFa), a pleitrophic cytokine that can trigger both apoptosis and cell proliferation/survival, is recently being considered for combination drug therapies for cancer treatment. Success of such attempts hinges on the holistic understanding of the ability of cells triggered with TNFa to respond with the apoptosis phenotype or the programmed cell-death on all cells in a population. Recently, the group has put together a manually curated, comprehensive TNFa signalling network.  read more »

Proposing Faculty
Research Area
  • Biochemical Engineering
  • Biomolecular Engineering
  • Computational Biology
  • Enzymology
  • Heat and Mass Transfer
  • Reaction Engineering
  • Reactor Modelling
  • Systems Biology

Development of cofactor recycle system for Alcohol Dehydrogenase (ADH) enzyme mediated chiral synthesis (TA/FA)





A key challenge in the ADH
mediated chiral synthesis is the high cost of NADH or NADPH co-factor.  Several co-factor recycle systems using
coupled reactions or coupled enzymes are reported but they suffer from various
disadvantages.  The objective of the
current project is to design an efficient co-factor recycle system that will
offer a cofactor recycle ratio of > 1:1,000,000.  This will require an efficient coupled enzyme  read more »

Proposing Faculty
Research Area
  • Biomolecular Engineering
  • Computational Biology
  • Enzymology

Modeling and simulation of endoplasmic reticulum stress pathways (TA/FA)

Endoplasmic reticulum (ER) is responsible for many important cellular functions such as
folding of proteins, glycosylation and quality control etc. Many
environmental and genetic perturbations such as hypoxia, glucose deficiency, overload of unfolded protein can lead to ER stress. ER stress has been associated with pathogenesis of many diseases
such as diabetes, neurodegenarative diseases such as Alziemers and
Parkinsons. Further, industrial recombinant mammalian cell lines producting recombinant therapeutics are also subject to ER stress.  read more »

Proposing Faculty
Research Area
  • Biochemical Engineering
  • Biomolecular Engineering
  • Computational Biology
  • Systems Biology