Research:
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Publications:
- An Ω(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem
Mukul S. Bansal, Oliver Eulenstein.
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB); In press.
Note: This is the full and expanded journal version of our WABI 2007 paper.
- The Multiple Gene Duplication Problem Revisited
Mukul S. Bansal, Oliver Eulenstein.
ISMB 2008; Bioinformatics, 24(13): i132-i138, 2008.
- DupTree: A program for large-scale phylogenetic analyses using gene tree parsimony
Andre Wehe, Mukul S. Bansal, J. G. Burleigh, Oliver Eulenstein.
Bioinformatics, 24(13): 1540-1541, 2008.
- The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches
Mukul S. Bansal, Oliver Eulenstein.
ISBRA 2008, LNCS/LNBI 4983: 14-25.
Invited to a special issue of IEEE/ACM TCBB (of selected papers from ISBRA 2008).
- Comparing and Aggregating Partially Resolved Trees
Mukul S. Bansal, Jianrong Dong, David Fernández-Baca.
LATIN 2008, LNCS 4957: 72-83.
- Locating Multiple Gene Duplications Through Reconciled Trees
J. G. Burleigh, Mukul S. Bansal, Andre Wehe, Oliver Eulenstein.
RECOMB 2008, LNCS/LNBI 4955: 273-284.
Invited to a special issue of JCB (of selected papers from RECOMB 2008).
- PhyloFinder: An intelligent search engine for phylogenetic tree databases
Duhong Chen, J.G. Burleigh, Mukul S. Bansal, David Fernández-Baca.
BMC Evolutionary Biology 2008, 8:90.
- An Ω(n2/ log n) speed-up of TBR heuristics for the gene-duplication problem
Mukul S. Bansal, Oliver Eulenstein.
WABI 2007, LNCS/LNBI 4645: 124-135.
Invited to a special issue of IEEE/ACM TCBB (of selected papers from WABI 2007).
(Note: Lemma 5 in the LNCS version of this paper is incorrectly stated. The linked paper contains the correctly stated version of this Lemma.)
- Heuristics for the gene-duplication problem: A Q(n) speed-up for the local search
Mukul S. Bansal, J.G. Burleigh, Oliver Eulenstein, Andre Wehe.
RECOMB 2007, LNCS/LNBI 4453: 238-252.
Invited to a special issue of JCB (of selected papers from RECOMB 2007).
- A Note on Finding a Maximum Clique in a Graph using BDDs
Mukul S. Bansal, V.Ch.Venkaiah.
Australasian Journal of Combinatorics, 32 (2005): 253-258.
Technical reports and other technical writings:
- Improved Fully Polynomial Time Approximation Scheme for the 0-1 Multiple-choice Knapsack Problem
Mukul S. Bansal, V.Ch.Venkaiah.
SIAM Conference on Discrete Mathematics, (2004).
Technical Report No. IIIT/TR/2004/3, International Institute of Information Technology, India.
(Note: We later discovered through a referee report that similar results had been independently obtained and described by Kellerer et al. in their book Knapsack Problems, also published in 2004.)
- Algorithms for minimum bipartite fill-in and the gene-duplication problem
Masters Thesis, Iowa State University, (2006).
Papers under submission:
- Computing Distances Between Partial Rankings
Mukul S. Bansal, David Fernández-Baca.
Submitted.
- Genome-scale phylogenetics: inferring the plant tree of life from 18,896 discordant gene trees
J. G. Burleigh, M. S. Bansal, O. Eulenstein, S. Hartmann, A. Wehe, and T. J. Vision.
Submitted.
- The Gene-Duplication Problem: Near-Linear Time Algorithms for NNI Based Local Searches
Mukul S. Bansal, Oliver Eulenstein, Andre Wehe.
This is the full and expanded journal version of the ISBRA 2008 paper, and includes detailed experimental analysis.
Submitted.
- Locating Large-Scale Gene Duplication Events Through Reconciled Trees: Implications For Identifying Ancient Polyploidy Events In Plants
J. G. Burleigh, Mukul S. Bansal, Andre Wehe, Oliver Eulenstein.
This is the full journal version of our RECOMB 2008 paper, and includes detailed biological analysis.
Submitted.
Research Software:
- DupTree (Formerly known as FastGeneDup): This is a tool box that allows the user to heuristically search for a species supertree that best reconciles the input gene trees under the gene duplication model. Joint work with Andre Wehe (with help from Oliver Eulenstein). This software can be downloaded from http://genome.cs.iastate.edu/CBL/DupTree/.
- ExactMGD: This is a program that can be used to infer (and identify) the smallest number of multiple gene duplication episodes that can reconcile the given gene trees with a given species tree. It is based on the multiple gene duplication model introduced by Guigo et al. in 1996. This software will be made available soon.
- PhyloFinder: This is an intelligent search engine for phylogenetic tree databases. Joint work with Duhong Chen, J.G. Burleigh and David Fernández-Baca. An implementation of PhyloFinder using TreeBASE data is available at http://pilin.cs.iastate.edu/phylofinder/.
Fun Software:
- Linchess: During my first year of undergraduate studies, just for fun, I wrote a chess program called Linchess (in joint work with Abhishek Sharma). Linchess featured a completely original chess playing algorithm. Of course, it probably won't be able to beat you if you are a better than average chess player, but hey, playing against Linchess is fun! Linchess was designed to work in console mode in Linux, which means you can even play it over ssh or telnet. Linchess can be downloaded here. A crude help file is available here.