Kianfar, Kiavash Adjunct Associate Professor

The research in Kianfar Lab is focused on theory, computation, and software design for bioinformatics data analysis (Thrust A), discrete and combinatorial optimization (Thrust B), and complex network systems (Thrust C).





Thrust A. Bioinformatics: Algorithms, Optimization, and Software

The research on bioinformatics is focused on developing and optimizing secondary bioinformatics analysis algorithms. In particular Kianfar Lab has introduced the first method to find optimal search schemes for approximate alignment of high-throughput sequencing reads using bidirectional FM-index resulting in an order of magnitude speed-up in approximate search in index compared to backtracking. Kianfar Lab has also developed Map2Peak, a ChIP-Seq peak calling software that performed read mapping and peak calling concurrently avoiding mapping of many redundant reads.



Thrust B. Integer Programming Theory and Computation

The research in this area is on development of new cutting plane theories with application in network capacity planning. This research has resulted in n-step mixed integer rounding theory and its extensions for mixed integer programming. The applications of this theory to cost-effective capacity planning involving differently sized capacity modules with focus on multi-module capacitated network design problems is another major part of this research.



Thrust C. Combinatorial Optimization Algorithms in Complex Network Systems

The research in this thrust is focused on developing optimization algorithm for problems arising in complex networks including reliability analysis of state estimators in large-scale sensor systems, planar maximum coverage location problem with partial coverage, and optimal deployment of emission reduction technologies in large fleets.