Biblio
] , “The compatibility of binary characters on phylogenetic networks: Complexity and parameterized algorithms”, Algorithmica, vol. 51, pp. 99-128, 2008.
, “Efficient Inference of Bacterial Strain Trees From Genome-scale Multi-locus Data”, Bioinformatics, vol. 24, pp. i123-i131, 2008.
, “Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer”, in Proceedings of the Sixth RECOMB Comparative Genomics Satellite Workshop, 2008, vol. 5267, pp. 113-127.
, “PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships”, BMC Bioinformatics, vol. 9, p. 322, 2008.
, “Rapidly Exploring Structural and Dynamic Properties of Signaling Networks Using PathwayOracle”, BMC Systems Biology, vol. 2, p. 76, 2008.
, “Seeing the trees and their branches in the network is hard”, Theoretical Computer Science, vol. 401, pp. 153-164, 2008.
, “The Signaling Petri Net-based Simulator: A Non-parametric Strategy for Characterizing the Dynamics of Cell-specific Signaling Networks”, PLoS Computational Biology, vol. 4, p. e1000005, 2008.
, “SPR-based tree reconciliation: Non-binary trees and multiple solutions”, in Proceedings of the Sixth Asia Pacific Bioinformatics Conference (APBC), 2008, pp. 251-260.
, “Confounding Factors in {HGT} Detection: Statistical Error, Coalescent Effects, and Multiple Solutions”, Journal of Computational Biology, vol. 14, pp. 517-535, 2007.
, “De novo Signaling Pathway Predictions based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis”, in Proceedings of the RECOMB Satellite Workshop on Systems Biology and Proteomics, 2007, vol. 4205, pp. 108-118.
, “Inferring phylogenetic networks by the maximum parsimony criterion: a case study”, Molecular Biology and Evolution, vol. 24, pp. 324-337, 2007.
, “A New Linear-time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance”, in Proceedings of the International Symposium on Bioinformatics Research and Applications, 2007, vol. 4463, pp. 61-72.
, “Seeing the trees and their branches in the network is hard”, in Proceedings of the Tenth Italian Conference on Theoretical Computer Science (ICTCS), 2007, pp. 82-93.
, “Efficient parsimony-based methods for phylogenetic network reconstruction”, Bioinformatics, vol. 23, pp. e123-e128, 2006.
, “Graph-theoretic Hypothesis Generation in Biological Signaling Networks”, Journal of Computational Biology, vol. 13, pp. 1546-1557, 2006.
, “Identifiability issues in phylogeny-based detection of horizontal gene transfer”, in Proceedings of the Fourth RECOMB Comparative Genomics Satellite Workshop, 2006, vol. 4205, pp. 215-219.
, “Identification of Three Distinct Phylogenetic Groups of CAX Cation/Proton Antiporters”, Journal of Molecular Evolution, vol. 63, pp. 815-825, 2006.
, “Maximum likelihood of phylogenetic networks”, Bioinformatics, vol. 22, pp. 2604-2611, 2006.
, “PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction”, International Journal on Bioinformatics Research and Applications, vol. 2, pp. 407-419, 2006.
, “RECOMP: A Parsimony-based Method for Detecting Recombination”, in Proceedings of the Fourth Asia-Pacific Bioinformatics Conference, 2006, pp. 59-68.
, “Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms”, in Proceedings of the 12th Annual International Computing and Combinatorics Conference (COCOON 2006), 2006, vol. 4112, pp. 299-308.
, “Techniques for Assessing Phylogenetic Branch Support: A Performance Study”, in Proceedings of the Fourth Asia-Pacific Bioinformatics Conference, 2006, pp. 187-196.
, “A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset”, Transactions of the Philological Society, vol. 3, pp. 171-192, 2005.
, “Parallel divide-and-conquer phylogeny reconstruction by maximum likelihood”, in Proceedings of the 2005 International Conference on High Performance Computing and Communications, 2005, vol. 2, pp. 346-350.
, “Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages”, LANGUAGE, Journal of the Linguistic Society of America, vol. 81, pp. 382-420, 2005.