Guruprasad Raghavan

Computational and Experimental analysis of Organelle Networks at the Whole Cell scale I'm fascinated by the consistency of spatial organization of organelles exhibited by a eukaryotic cell across cell-types. Along with studying single organelle networks in isolation, the interaction amongst organelle networks interests me. To study these in more detail, I've worked on developing spatial statistics metrics to quantify spatial distribution of homotypic organelles and heterotypic organelle contact sites. I've also performed wet-lab experiments to actively control their spatial distribution in order to assess the existence of homotypic/heterotypic interactions.

Advisor: Dr. Ge Yang
Institution: Carnegie Mellon University, Pittsburgh
Relevant Reports: Masters Thesis

Evaluating the efficiency of a colonoscopy procedure I worked with a team on designing algorithms to detect the cecum (end of colon) from colonoscopy videos and tested the accuracy and robustness of algorithms developed to quantify distance traversed within a colon by manually snipping videos of pre-defined length (eg. 5cm, 10cm) traversed within the colon. The best segment of this practicum project was the opportunity to shadow Dr. Shyam Thakker (Endo/Colonoscopist) in most of his endoscopy and colonoscopy procedures performed at West Penn Hospital, Pittsburgh.

Advisor: Dr. Shyam Thakker, MD & Dr. Yang Cai, PhD
Institution: Allegheny General Hospital, Pittsburgh & Carnegie Mellon University, Pittsburgh
Relevant Reports: Practicum Report

Computational Modeling of Cellular Dynamics As a part of my Undergraduate Thesis, I developed an in-silico model to understand cell-population dynamics with & without the diffusional limitation of essential nutrients. This computational tissue set-up can be used as a model system to analyse the efficacy of specific drugs on the wound-healing process.

Advisor: Dr. Vignesh Muthuvijayan
Institution: Indian Institute of Technology, Madras
Relevant Reports: BTP Thesis

AFM observation of spatiotemporal control of Protein-DNA interaction I worked on Spatio-temporally controlling DNA-protein interactions at the nano-scale using visible light, and visualized the same using an Atomic Force Microscopy (AFM) and High-Speed AFM. Apart from experimentation, I computationally modelled the hybrid protein VVD-GAL4 to study the dynamics of DNA-protein complex formation.

Advisor: Dr. Masayuki Endo, Dr. Hiroshi Sugiyama
Institution: ICeMs, Kyoto University
Relevant Reports: Manuscript (in process)

Alteration of pH sensitive regime of DNA I-switch In order to study intracellular pH changes, "smart" nano-probes are required, that can simultaneously interface with the biological system (cell) as well as relay information. In order to do so, DNA-based pH sensors were developed at Dr. Yamuna's lab. As a summer intern, I worked on quantifying the dynamic range of modified LNA/DNA based pH sensors via FRET measurements. Apart from in-vitro work, I was trained to work with C.elegans; from learning how to pick them at different stages of growth (L1, L2, L3, L4 and Adult) to setting up crosses.

Advisor: Dr. Yamuna Krishnan
Institution: National Center for Biological Sciences, Bangalore
Relevant Reports: Internship Report

pH Mediated DNA Hopping As the leader of the undergraduate team representing IIT Madras at BIOMOD (Biomolecular Design Competition) conducted by Harvard University, we designed a Molecular Robot responsive to pH and verified the formation of the structure in-silico using NUPACK (online software) and Native PAGE (for DNA).

Advisor: Dr. N Manoj
Institution: Indian Institute of Technology, Madras
Relevant links: IIT Madras - BIOMOD Team