Biblio

Export 108 results:
Author Keyword Title Type [ Year(Asc)]
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)
L. Nakhleh, Evolutionary phylogenetic networks: models and issues, in The Problem Solving Handbook for Computational Biology and Bioinformatics, L. Heath and Ramakrishnan, N. Springer, 2010, pp. 125-158.PDF icon HeathRamakrishnanBookChapter.pdf (381.74 KB)
C. Than and Nakhleh, L., Inference of parsimonious species phylogenies from multi-locus data by minimizing deep coalescences, in Estimating Species Trees: Practical and Theoretical Aspects, L. L. Knowles and Kubatko, L. S. Wiley-VCH, 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. 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.

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