Journals

1. J. Dutheil, G. Ganapathy, M. K. Uyenoyama, A. Hobolth, M. Schierup and T. Mailund. Speciation times and effective population sizes using an explicit model of the coalescent with recombination: Application to the Human-Chimp-Gorilla-Orangutan system. To appear in Genetics., 2009. doi:10.1534/genetics.109.103010. pdf

2. G. Ganapathy and M. K. Uyenoyama. Site frequency spectra from genomic SNP surveys. Theoretical Population Biology, 75(4), pages 346-354, 2009. pdf

3. G. Ganapathy, H. Le, B. Goodson, R. Jansen, V. Ramachandran, and T. Warnow. Pattern identification in biogeography. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), vol. 3, no. 4, pages 334–346, 2006. pdf

4. B. W. Sidlauskas, G. Ganapathy, S. Price, E. Hazkani-Covo, L. W. McCall, P. Spaeth, K. P. Jenkins, R. Scherle and H. Lapp, D. M. Kidd. Linking big: The continuing promise of evolutionary synthesis. Non-peer-reviewed commentary. To appear in Evolution, 2009.

Peer-reviewed international conferences

(In computer science, conference proceedings are the primary outlet for original work and are thus peer-reviewed with high rejection rates and considered the equivalent of a journal publication.)

5. G. Ganapathy, B. Goodson, R. Jansen, V. Ramachandran, and T. Warnow. Pattern identification in biogeography. In Proceedings of the Fifth International Workshop on Algorithms in Bioinformatics (WABI), pages 112–127, 2005. pdf ( Impact factor estimated to be in the top 25%)

6. G. Ganapathy, V. Ramachandran, and T. Warnow. On contract-and-refine-transformations between phylogenetic trees. In Proceedings of the Fifteenth ACM-SIAM Symposium on Discrete Algorithms1 (SODA), pages 893–902, 2004. pdf (estimated impact factor in top 9%: assessment 1. assessment 2)

7. G. Ganapathy, V. Ramachandran, and T. Warnow. Better hill-climbing searches for parsimony. In Proceedings of the Third International Workshop on Algorithms in Bioinformatics (WABI), pages 245–258, 2003. pdf. (estimated impact factor in the top 25%)

8. G. Ganapathy and T. Warnow. Approximating the complement of the maximum compatible subset of leaves of k trees. In Proceedings of the Fifth International Workshop on Approximation Algorithms for Combinatorial Optimization1, pages 122–134, 2002. pdf (estimated impact factor in the top 30%)

9. G. Ganapathy and T. Warnow. “Finding the maximum compatible tree for a bounded number of trees with bounded degree is solvable in polynomial time.” In Proceedings of the First International Workshop on Algorithms and Bioinformatics (WABI), pages 156–163, 2001. pdf (estimated impact factor in the top 25%)

Manuscripts in preparation

1. G. Ganapathy, A. Balaban, P. Zheng and M. Uyenoyama. A sample-based approach to estimating character-specific speciation and extinction rates.