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Biblio
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L. Nakhleh
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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.
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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.
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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.
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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.
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C. Than
and
Nakhleh, L.
,
“
Species tree inference by minimizing deep coalescences
”
,
PLoS Computational Biology
, vol. 5, p. e1000501, 2009.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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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.
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G. Jin
,
Nakhleh, L.
,
Snir, S.
, and
Tuller, T.
,
“
Maximum likelihood of phylogenetic networks
”
,
Bioinformatics
, vol. 22, pp. 2604-2611, 2006.
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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.
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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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