Abhishek Mitra
I hold a B.Tech from Indian Institute of Information Technology. I also hold a MSCS and Ph.D.CSE from Dept. of CSE, UC Riverside. My Postdoc training was in the field of bioinformatics, in the Rowicka Lab, Univ. of Texas Med. Branch.

I develop algorithms and implement them as software tools that do statistical analysis for Molecular Biologists. The tools help them analyze data from experiments involving Next Generation Sequencing.

Some examples: a) mapping double stranded breaks in human genome (Breakome)[Published in Nature Methods 2013]

b) identifying transcription factors binding sites and binding motifs from protein-dna interaction (NF-kB cistrome)[Published in Nuc. Acids Research 2013, and JBC 2014]

c) identifying gene expression (NF-kB/RelA functional genes)[Published in Nuc. Acids Research 2013]

Our ideal computational objective for NGS data in a nutshell is: ``Analysis of Terabytes of raw data using Teraflop systems with Kilobytes of code and in a few Kilo seconds.''

Major areas that I am involved in include:

a) developing genomics / NGS data analysis software in C/C++

b) developing and tuning NGS data analaysis pipelines for ChIP-Seq, RNA-Seq, BLESS, etc.

b) string / regex matching, PCRE, awk, etc.

c) multi-threading: computing on multicore CPUs as well as GPUs

I use Linux, C, C++ with STL, boost libs, GSL, pthreads/OMP, R, Matlab and Wikipedia as tools.
Research

Most Recent Areas of Interest:

Bioinformatics and Statistical Methods

Next Generation Sequencing Data Analysis

Strings, Regex, Algorithms and Large Scale Data Processing

CPU, GPU, HPC, Cloud Computing and Linux

Prior areas of interest:

Reconfigurable Computing with FPGAs

Flash Memories and SSDs

Wireless and Sensors

Embedded Systems

Sample Research Statement from year 2008

Resume

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Publications

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Contact

Phone: +41 91 820 0392

Email: a m i t r a () cs <> ucr <> edu

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