Biblio

2006
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., “Maximum likelihood of phylogenetic networks”, Bioinformatics, vol. 22, pp. 2604-2611, 2006.
Y. Dotsenko, Coarfa, C., Nakhleh, L., Mellor-Crummey, J., and Roshan, U., “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.
D. Ruths and Nakhleh, L., “RECOMP: A Parsimony-based Method for Detecting Recombination”, in Proceedings of the Fourth Asia-Pacific Bioinformatics Conference, 2006, pp. 59-68.
I. Kanj, Nakhleh, L., and Xia, G., “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.
D. Ruths and Nakhleh, L., “Techniques for Assessing Phylogenetic Branch Support: A Performance Study”, in Proceedings of the Fourth Asia-Pacific Bioinformatics Conference, 2006, pp. 187-196.
2007
C. Than, Ruths, D., Innan, H., and Nakhleh, L., “Confounding Factors in {HGT} Detection: Statistical Error, Coalescent Effects, and Multiple Solutions”, Journal of Computational Biology, vol. 14, pp. 517-535, 2007.
D. Ruths, Tseng, J. T., Nakhleh, L., and Ram, P. T., “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.
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., “Inferring phylogenetic networks by the maximum parsimony criterion: a case study”, Molecular Biology and Evolution, vol. 24, pp. 324-337, 2007.
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., “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.
I. A. Kanj, Nakhleh, L., Than, C., and Xia, G., “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.
2008
I. A. Kanj, Nakhleh, L., and Xia, G., “The compatibility of binary characters on phylogenetic networks: Complexity and parameterized algorithms”, Algorithmica, vol. 51, pp. 99-128, 2008.
C. Than, Sugino, R., Innan, H., and Nakhleh, L., “Efficient Inference of Bacterial Strain Trees From Genome-scale Multi-locus Data”, Bioinformatics, vol. 24, pp. i123-i131, 2008.
G. Jin, Nakhleh, L., and Than, C., “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.
C. Than, Ruths, D., and Nakhleh, L., “PhyloNet: A Software Package for Analyzing and Reconstructing Reticulate Evolutionary Relationships”, BMC Bioinformatics, vol. 9, p. 322, 2008.
D. Ruths, Nakhleh, L., and Ram, P. T., “Rapidly Exploring Structural and Dynamic Properties of Signaling Networks Using PathwayOracle”, BMC Systems Biology, vol. 2, p. 76, 2008.
I. A. Kanj, Nakhleh, L., Than, C., and Xia, G., “Seeing the trees and their branches in the network is hard”, Theoretical Computer Science, vol. 401, pp. 153-164, 2008.
D. Ruths, Muller, M., Tseng, J. T., Nakhleh, L., and Ram, P. T., “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.
C. Than and Nakhleh, L., “SPR-based tree reconciliation: Non-binary trees and multiple solutions”, in Proceedings of the Sixth Asia Pacific Bioinformatics Conference (APBC), 2008, pp. 251-260.
2009
L. Nakhleh, Ruths, D., and Innan, H., “Gene trees, species trees, and species networks”, in Meta-analysis and Combining Information in Genetics, R. Guerra and Goldstein, D., Eds. Chapman & Hall, CRC Press, 2009, pp. 275-293.
T. Ruths, Ruths, D., and Nakhleh, L., “GS2: An efficiently computable measure of GO-based similarity of gene sets”, Bioinformatics, vol. 25, pp. 1178-1184, 2009.
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., “Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-time Heuristic”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 6, pp. 495-505, 2009.
C. Than and Nakhleh, L., “Species tree inference by minimizing deep coalescences”, PLoS Computational Biology, vol. 5, p. e1000501, 2009.
2010
H. J. Park, Jin, G., and Nakhleh, L., “Algorithmic strategies for estimating the amount of reticulation from a collection of gene trees”, Proceedings of the 9th Annual International Conference on Computational Systems Biology. pp. 114-123, 2010.PDF icon ParkEtAl-CSB2010.pdf (946.56 KB)
H. J. Park, Jin, G., and Nakhleh, L., “Bootstrap-based support of HGT inferred by maximum parsimony”, BMC Evolutionary Biology, vol. 10, p. 131, 2010.PDF icon BMCEvolBiol2010.pdf (1.18 MB)
D. Ruths and Nakhleh, L., “Deriving predictive models of signaling network dynamics from qualitative experimental data”, in Proceedings of the 9th Annual International Conference on Computational Systems Biology, 2010.PDF icon RuthsNakhleh-CSB2010.pdf (548.82 KB)

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