Om+Kulkarni

I am studying for a PhD in Bioinformatics at the Université Joseph Fourier, Grenoble. I am working with the Computational and Mathematical Biology Team at TIMC-IMAG Lab under the supervision of Michael Blum, in collaboration with Conrad Lichtenstein at Population Genetics Technologies Ltd in Cambridge, UK. I am particularly interested in using NGS and statistical techniques for understanding the evolutionary behavior of the Hepatitis C Virus (HCV), with a focus on augmenting current diagnostic protocols for HCV therapy.

Viruses are highly diverse in their genetic constitution, both within and between infected hosts. They adapt to the host’s environment with a high mutation rate and can make efficient treatment very difficult. Hepatitis C virus (HCV), which causes nearly 200 million chronic infections worldwide is curable with treatments which comprise immunoregulator and direct antiviral agents. Our analysis is a case study in which viral samples from 40 patients with chronic HCV are being sequenced using a 454 Roche GS Junior at different stages of treatment. Using variant callers, we obtain the frequency of the variants that are found in the viral population during the course of the treatment. We study the viral diversity during the treatment to assess whether the treatment actually decreases the viral diversity. Our main objective is to test if the viral diversity at the onset of the treatment is an important determinant of the treatment outcome. This would ultimately help in understanding the evolution of the virus and provide further insights into drug design and personalized treatment of HCV.

I have a background in computer science having done my undergrad, a B.E. in Computer Engineering from Mumbai University, India. I followed up with a MSc in Bioinformatics and Computational Systems Biology from Newcastle University, UK where my dissertation was a MATLAB-based ' //In silico// simulation of //Caenorhabditis elegans// neural network development using random axon outgrowth mechanism '.