Biblio

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Conference Paper
L. Nakhleh, Jin, G., Zhao, F., and Mellor-Crummey, J., Reconstructing phylogenetic networks using maximum parsimony, in Proceedings of the 2005 IEEE Computational Systems Bioinformatics Conference (CSB2005), 2005, pp. 93-102.
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., RECOMP: A Parsimony-based Method for Detecting Recombination, in Proceedings of the Fourth Asia-Pacific Bioinformatics Conference, 2006, pp. 59-68.
C. Coarfa, Dotsenko, Y., Mellor-Crummey, J., Nakhleh, L., and Roshan, U., 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.
L. Nakhleh and Wang, L. S., 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.
L. Nakhleh, Roshan, U., John, S. K., Sun, J., and Warnow, T., The Performance of Phylogenetic Methods on Trees of Bounded Diameter, in First International Workshop on Algorithms in Bioinformatics (WABI 01), 2001, vol. Lecture Notes in Computer Science 2149, pp. 214–226.
Z. Du, Stamatakis, A., Lin, F., Roshan, U., and Nakhleh, L., 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.
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.
C. R. Linder, Moret, B. M. E., Nakhleh, L., and Warnow, T., Network (reticulate) evolution: biology, models, and algorithms, in The Ninth Pacific Symposium on Biocomputing (PSB), 2004.
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., 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.
L. Nakhleh, Roshan, U., Vawter, L., and Warnow, T., Estimating the Deviation from a Molecular Clock, in Proceedings of the Second International Workshop on Algorithms in Bioinformatics (WABI 02), Rome, Italy, 2002, vol. 2452, pp. 287-299.
Z. Cao, Zhu, J., and Nakhleh, L., Empirical performance of tree-based inference of phylogenetic networks, in Workshop on Algorithms in Bioinformatics (WABI), 2019.PDF icon CaoEtAl-WABI19.pdf (1.2 MB)
X. Fan, Xu, J., and Nakhleh, L., Detecting large indels using optical map data, in RECOMB Comparative Genomics, 2018.PDF icon FanEtAl18.pdf (2.94 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)
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.
M. Edrisi, Zafar, H., and Nakhleh, L., A Combinatorial Approach for Single-cell Vairant Detection via Phylogenetic Inference, in Workshop on Algorithms in Bioinformatics (WABI), 2019.PDF icon EdrisiEtAl-WABI19.pdf (2.03 MB)
L. Nakhleh, Moret, B. M. E., Roshan, U., John, S. K., Sun, J., and Warnow, T., The Accuracy of Phylogenetic Methods for Large Datasets, in Proc.\ 7th Pacific Symp. on Biocomputing ({PSB02}), 2002, vol. 7, pp. 211-222.

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