Biblio

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2010
L. Nakhleh, “A metric on the space of reduced phylogenetic networks”, IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 7, pp. 218-222, 2010.PDF icon tcbb-Metric.pdf (287.01 KB)
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.
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.
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.
2006
G. Jin, Nakhleh, L., Snir, S., and Tuller, T., “Efficient parsimony-based methods for phylogenetic network reconstruction”, Bioinformatics, vol. 23, pp. e123-e128, 2006.
D. Ruths, Nakhleh, L., Iyengar, M. S., Reddy, S. A. G., and Ram, P. T., “Graph-theoretic Hypothesis Generation in Biological Signaling Networks”, Journal of Computational Biology, vol. 13, pp. 1546-1557, 2006.
C. Than, Ruths, D., Innan, H., and Nakhleh, L., “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.
T. Shigaki, Rees, I., Nakhleh, L., and Hirschi, K., “Identification of Three Distinct Phylogenetic Groups of CAX Cation/Proton Antiporters”, Journal of Molecular Evolution, vol. 63, pp. 815-825, 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.

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