Luay Nakhleh

Hyun Jung Park, Luay Nakhleh: Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria. BMC Bioinformatics 13(S-19): S12 (2012)

Natalie Berestovsky, Riya Fukui, Luay Nakhleh: On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks. CIBCB 2012: 184-191

Hyun Jung Park, Luay Nakhleh: MURPAR: A Fast Heuristic for Inferring Parsimonious Phylogenetic Networks from Multiple Gene Trees. ISBRA 2012: 213-224

Yun Zhu, Luay Nakhleh: Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models. WABI 2012: 57-68

Yun Yu, Luay Nakhleh: Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting. CoRR abs/1212.1909 (2012)

Wanding Zhou, Luay Nakhleh: The strength of chemical linkage as a criterion for pruning metabolic graphs. Bioinformatics 27(14): 1957-1963 (2011)

Wanding Zhou, Luay Nakhleh: Properties of Metabolic Graphs: Biological Organization or Representation Artifacts? BMC Bioinformatics 12: 132 (2011)

Yun Yu, Tandy Warnow, Luay Nakhleh: Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles. Journal of Computational Biology 18(11): 1543-1559 (2011)

Yun Yu, Tandy Warnow, Luay Nakhleh: Algorithms for MDC-Based Multi-locus Phylogeny Inference. RECOMB 2011: 531-545

Luay Nakhleh: A Metric on the Space of Reduced Phylogenetic Networks. IEEE/ACM Trans. Comput. Biology Bioinform. 7(2): 218-222 (2010)

Troy A. Ruths, Derek A. Ruths, Luay Nakhleh: GS²: an efficiently computable measure of GO-based similarity of gene sets. Bioinformatics 25(9): 1178-1184 (2009)

Cuong Than, Luay Nakhleh: Species Tree Inference by Minimizing Deep Coalescences. PLoS Computational Biology 5(9) (2009)

Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic. IEEE/ACM Trans. Comput. Biology Bioinform. 6(3): 495-505 (2009)

Iyad A. Kanj, Luay Nakhleh, Ge Xia: The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms. Algorithmica 51(2): 99-128 (2008)

Cuong Than, Derek A. Ruths, Luay Nakhleh: PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinformatics 9 (2008)

Derek A. Ruths, Melissa Muller, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram: The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks. PLoS Computational Biology 4(2) (2008)

Iyad A. Kanj, Luay Nakhleh, Cuong Than, Ge Xia: Seeing the trees and their branches in the network is hard. Theor. Comput. Sci. 401(1-3): 153-164 (2008)

Cuong Than, Luay Nakhleh: SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. APBC 2008: 251-260

Cuong Than, R. Sugino, Hideki Innan, Luay Nakhleh: Efficient inference of bacterial strain trees from genome-scale multilocus data. ISMB 2008: 123-131

Cuong Than, Guohua Jin, Luay Nakhleh: Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. RECOMB-CG 2008: 113-127

Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinformatics 23(2): 123-128 (2007)

Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: Maximum likelihood of phylogenetic networks. Bioinformatics 23(8): 1046-1047 (2007)

Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh: Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. Journal of Computational Biology 14(4): 517-535 (2007)

Iyad A. Kanj, Luay Nakhleh, Cuong Than, Ge Xia: Seeing the Trees and Their Branches in the Forest is Hard. ICTCS 2007: 82-93

Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. ISBRA 2007: 61-72

Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller: Maximum likelihood of phylogenetic networks. Bioinformatics 22(21): 2604-2611 (2006)

Yuri Dotsenko, Cristian Coarfa, Luay Nakhleh, John M. Mellor-Crummey, Usman Roshan: PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction. IJBRA 2(4): 407-419 (2006)

Derek A. Ruths, Luay Nakhleh, M. Sriram Iyengar, Shrikanth A. G. Reddy, Prahlad T. Ram: Hypothesis Generation in Signaling Networks. Journal of Computational Biology 13(9): 1546-1557 (2006)

Derek A. Ruths, Luay Nakhleh: RECOMP: A Parsimony-Based Method for Detecting Recombination. APBC 2006: 59-68

Derek A. Ruths, Luay Nakhleh: Techniques for Assessing Phylogenetic Branch Support: A Performance Study. APBC 2006: 187-196

Iyad A. Kanj, Luay Nakhleh, Ge Xia: Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms. COCOON 2006: 299-308

Derek A. Ruths, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram: De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis. Systems Biology and Computational Proteomics 2006: 108-118

Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh: Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. Comparative Genomics 2006: 215-229

Derek A. Ruths, Luay Nakhleh: Recombination and phylogeny: effects and detection. IJBRA 1(2): 202-212 (2005)

Luay Nakhleh, Tandy Warnow, C. Randal Linder, Katherine St. John: Reconstructing Reticulate Evolution in SpeciesTheory and Practice. Journal of Computational Biology 12(6): 796-811 (2005)

Luay Nakhleh, Li-San Wang: Phylogenetic Networks: Properties and Relationship to Trees and Clusters. T. Comp. Sys. Biology 2: 82-99 (2005)

Luay Nakhleh, Derek A. Ruths, Li-San Wang: RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. COCOON 2005: 84-93

Luay Nakhleh, Guohua Jin, Fengmei Zhao, John M. Mellor-Crummey: Reconstructing Phylogenetic Networks Using Maximum Parsimony. CSB 2005: 93-102

Z. Du, Alexandros Stamatakis, F. Lin, Usman Roshan, Luay Nakhleh: Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood. HPCC 2005: 776-785

Luay Nakhleh, Li-San Wang: Phylogenetic Networks, Trees, and Clusters. International Conference on Computational Science (2) 2005: 919-926

Cristian Coarfa, Yuri Dotsenko, John M. Mellor-Crummey, Luay Nakhleh, Usman Roshan: PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction. ICPADS (2) 2005: 346-350

Bernard M. E. Moret, Luay Nakhleh, Tandy Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun, Ruth E. Timme: Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. IEEE/ACM Trans. Comput. Biology Bioinform. 1(1): 13-23 (2004)

Luay Nakhleh, Tandy Warnow, C. Randal Linder: Reconstructing reticulate evolution in species: theory and practice. RECOMB 2004: 337-346

Luay Nakhleh, Daniel P. Miranker, François Barbançon, William H. Piel, Michael J. Donoghue: Requirements of Phylogenetic Databases. BIBE 2003: 141-148

Esra Erdem, Vladimir Lifschitz, Luay Nakhleh, Donald Ringe: Reconstructing the Evolutionary History of Indo-European Languages Using Answer Set Programming. PADL 2003: 160-176

Luay Nakhleh, Jerry Sun, Tandy Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse: Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. Pacific Symposium on Biocomputing 2003: 315-326

Luay Nakhleh, Bernard M. E. Moret, Usman Roshan, Katherine St. John, Jerry Sun, Tandy Warnow: The Accuracy of Fast Phylogenetic Methods for Large Datasets. Pacific Symposium on Biocomputing 2002: 211-222

Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy Warnow: Estimating the Deviation from a Molecular Clock. WABI 2002: 287-299

Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy Warnow: Designing fast converging phylogenetic methods. ISMB (Supplement of Bioinformatics) 2001: 190-198

Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy Warnow: The Performance of Phylogenetic Methods on Trees of Bounded Diameter. WABI 2001: 214-226