Abhishek Sarkar

I graduated in May 2011 with a B.S. Computer Science from the University of North Carolina at Chapel Hill.

I am currently a graduate student at Massachusetts Institute of Technology. Refer to my CV for more detailed information.

Research

My main research interests are in bioinformatics and data mining. I am particularly interested in developing novel algorithms and software tools for biological analyses.

Undergraduate

I worked in the UNC Computational Genetics Research Group with Dr. Wei Wang.

The broad focus of this work is on genetic recombination. I collaborated on the implementation of haplotype and ancestry inference tools which infer alleles from genotypes and inheritance of contiguous regions of the genome. In particular, I worked on a dynamic programming–based tool and an HMM-based tool for ancestry inference.

Publications

  1. David L. Aylor, William Valdar, Wendy Foulds-Mathes, Ryan J. Buus, Ricardo A. Verdugo, Ralph S. Baric, Martin T. Ferris, Jeffrey A. Frelinger, Mark Heise, Matt B. Frieman, Lisa E. Gralinski, Timothy A. Bell, John P. Didion, Kunjie Hua, Derrick L. Nehrenberg, Christine L. Powell, Jill Steigerwalt, Yuying Xie, Samir N. P. Kelada, Francis S. Collins, Ivana V. Yang, David A. Schwartz, Lisa A. Branstetter, Elissa J. Chesler, Darla R. Miller, Jason Spence, Eric Yi Liu, Leonard McMillan, Abhishek Sarkar, Jeremy Wang, Wei Wang, Qi Zhang, Karl W. Broman, Ron Korstanje, Caroline Durrant, Richard Mott, Fuad A. Iraqi, Daniel Pomp, David Threadgill, Fernando Pardo-Manuel de Villena, and Gary A. Churchill. “Genetic Analysis of Complex Traits in the Emerging Collaborative Cross.” Genome Research. Accepted for publication.
  2. Qi Zhang, Eric Yi Liu, Abhishek Sarkar and Wei Wang. “Split-Order Distance for Clustering and Classification Hierarchies.” Proceedings of the 21st International Conference on Scientific and Statistical Database Management, New Orleans, LA, USA. Springer-Verlag, 2009. 517–534.

Other Interests

Classical music

I'm currently studying piano with Dr. Clara Yang and am especially interested in 20th Century and contemporary Western classical music. I have also studied with Dr. Mayron Tsong and John Herrmann. I'm also trying to make sense of Indian classical music using my background in Western music theory.

Recreational Programming

I have participated in the ACM ICPC each of the past three years and have had a lot of fun developing my problem solving and programming skills.

Free Open Source Software

I use open source tools, especially (Arch) Linux, the GNU toolchain, and Emacs for nearly all of my daily computing.