Biblio
] , “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.
, “Phylogenetic Networks: Properties and Relationship to Trees and Clusters”, LNCS Transactions on Computational Systems Biology, II, vol. 3680, pp. 82-99, 2005.
, “Phylogenetic networks, trees, and clusters”, in Proceedings of the 2005 International Workshop on Bioinformatics Research and Applications (IWBRA 05), 2005, vol. 3515, pp. 919-926.
, “PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction”, in Proceedigns of the First IEEE Workshop on High Performance Computing in Medicine and Biology, 2005, vol. 2, pp. 346-350.
, “Recombination and phylogeny: effects and detection”, International Journal on Bioinformatics Research and Applications, vol. 1, pp. 202-212, 2005.
, “Reconstructing phylogenetic networks using maximum parsimony”, in Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005), 2005, pp. 93-102.
, “Reconstructing reticulate evolution in species–theory and practice”, in Journal of Computational Biology, 2005, vol. 12(6-7), pp. 796-811.
, “RIATA-HGT: A Fast and accurate heuristic for reconstrucing horizontal gene transfer”, in Proceedings of the Eleventh International Computing and Combinatorics Conference (COCOON 05), 2005, vol. 3595, pp. 84-93.
, “Network (reticulate) evolution: biology, models, and algorithms”, in The Ninth Pacific Symposium on Biocomputing (PSB), 2004.
, “Phylogenetic networks: modeling, reconstructibility, and accuracy”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, pp. 13–23, 2004.
, “Reconstructing reticulate evolution in species–theory and practice”, in Proc.\ 8th Ann.İnt’l Conf.\ Comput.\ Mol.\ Biol.\ ({RECOMB04}), 2004, pp. 337–346.