Systems Biology

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

Guides: Ganesh Viswanathan and Sharad Bhartiya
 read more »

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

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

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

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

A new approach for cancer treatment: Apoptosis triggered by Tumor necrosis factor alpha (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
  • Systems Biology

Host engineering of cyanobacteria and micro-algae for biofuel applications (TA/FA/TAP)





One of the major challenges faced in implementing
cell based processes includes identification of a suitable host strain followed
by application of several orthogonal engineering strategies to optimize the
cell. Thus, host engineering
broadly refers to developing a host cell chassis for the production of a class
of molecules.  This project is on host
engineering of photosynthetic organisms. We argue that only the local  read more »

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

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

Genomic study of antibiotic resistance mechanisms (TA/FA)

Antibiotics have been critical for the dramatic rise of life expectancy and the fight against many diseases and infections in the past fifty years. However, over the past decade, antimicrobial resistance has emerged as a major public-health crisis. We are using Streptomyces coelicolor and Mycobacterium smegmatis as models to decipher the various mechanisms employed by bacteria to counter antibiotics. A transcriptomic study using whole-genome microarrays revealed a combination of mechanisms that Streptomyces uses to counter fluoroquinolones.  read more »

Proposing Faculty
Research Area
  • Biomolecular Engineering
  • Systems Biology

Analyzing whole body metabolism in Humans for characterizing dissease states

Whole body metabolism in various tissues is tightly regulated through several signalling networks. The project deals with analyzing the interconnections between the signaling pathway and the metabolism. Structural and parametric perturbations for various lifestyle conditions such as diet, exercise, infection will be studies to link the cause and effect for various lifestyle related diseases. An extensive model is already developed. Several what if situations and analysis using the model will be the scope.

Proposing Faculty
Research Area
  • Systems Biology