abhinav sarje

This page gives information about my present academic and research work.

Presently, I am a graduate student of computer engineering at the department of ECpE in Iowa State University. My studies are supported with a research assistantship under my advisor, Dr. Srinivas Aluru. In our research group, we work mostly on parallel and high-performance computing with applications to computational biology and scentific computing.

In the rest of this page, a brief overview of my research and course work is given.

select research projects

Parallel algorithms for sequence alignments on the Cell processor Two prominent parallel algorithms for sequence alignments exist. One uses the wavefront pattern, and the other is based on parallel-prefix. A comparison of these algorithms for performance on a cheap high-performance processor, the Cell BE, leads to a hybrid algorithm based on these two approaches. This scheme gives speedups of four on a Playstation 3 (six SPEs) compared to a Pentium 4 processor. Furthermore, it gives speedups of seven on a QS20 Cell blade (sixteen SPEs). These hold for the three varieties of alignments – global, spliced and syntenic.

select publications

Abhinav Sarje Srinivas Aluru Parallel Genomic Alignments on the Cell Broadband Engine to appear in IEEE Transactions on Parallel and Distributed Systems (TPDS) 2009

Abhinav Sarje Srinivas Aluru Parallel Biological Sequence Alignments on the Cell Broadband Engine 22nd IEEE International Parallel and Distributed Processing Symposium (IPDPS'08) pp. 1-11 2008

Abhinav Sarje Amit Chawre Shivashankar Nair Reinforcement Learning of Player Agents in RoboCup Soccer Simulation 4th IEEE International Conference on Hybrid Intelligent Systems (HIS'04) pp. 480-481 2004


fall '05

CPRE 548 Fundamental Algorithms in Computational Biology Dr. Srinivas Aluru
CPRE 594 Probabilistic Methods in Computer Engineering Dr. Srikanta Tirthapura

spring '06

COMS 518 Introduction to Computational Geometry Dr. Yan-Bin Jia
COMS 531 Theory of Computation Dr. Pavan Aduri

fall '06

CPRE 526 Parallel Algorithms and Programming Dr. Srikanta Tirthapura
COMS 562 Database Implementation Dr. Shashi Gadia

spring '07

CPRE 626 Parallel Algorithms for Scientific Applications Dr. Srinivas Aluru
CPRE 540 Principles of Compiling Dr. Hui-Hsien Chou

fall '07

CPRE 581 Computer Systems Architecture Dr. Zhao Zhang

spring '08

COMS 612 Distributed Algorithms Dr. Soma Chaudhuri

copyright © Abhinav Sarje 2008