Designing fast converging phylogenetic methods. - Luay Nakhleh; Usman Roshan; Katherine St. John; Jerry Sun 001; Tandy J. Warnow (ISMB (Supplement of Bioinformatics), 2001)

The Performance of Phylogenetic Methods on Trees of Bounded Diameter. - Luay Nakhleh; Usman Roshan; Katherine St. John; Jerry Sun 001; Tandy J. Warnow (WABI, 2001)

The Accuracy of Fast Phylogenetic Methods for Large Datasets. - Luay Nakhleh; Bernard M. E. Moret; Usman Roshan; Katherine St. John; Jerry Sun 001; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2002)

Estimating the Deviation from a Molecular Clock. - Luay Nakhleh; Usman Roshan; Lisa Vawter; Tandy J. Warnow (WABI, 2002)

Requirements of Phylogenetic Databases. - Luay Nakhleh; Daniel P. Miranker; François Barbançon; William H. Piel; Michael J. Donoghue (BIBE, 2003)

Reconstructing the Evolutionary History of Indo-European Languages Using Answer Set Programming. - Esra Erdem 001; Vladimir Lifschitz; Luay Nakhleh; Donald Ringe (PADL, 2003)

Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. - Luay Nakhleh; Jerry Sun 001; Tandy J. Warnow; C. Randal Linder; Bernard M. E. Moret; Anna Tholse (Pacific Symposium on Biocomputing, 2003)

Reconstructing reticulate evolution in species: theory and practice. - Luay Nakhleh; Tandy J. Warnow; C. Randal Linder (RECOMB, 2004)

Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. - Bernard M. E. Moret; Luay Nakhleh; Tandy J. Warnow; C. Randal Linder; Anna Tholse; Anneke Padolina; Jerry Sun 001; Ruth E. Timme (IEEE ACM Trans. Comput. Biol. Bioinform., 2004)

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

Reconstructing Phylogenetic Networks Using Maximum Parsimony. - Luay Nakhleh; Guohua Jin; Fengmei Zhao; John M. Mellor-Crummey (CSB, 2005)

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

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

Recombination and phylogeny: effects and detection. - Derek A. Ruths; Luay Nakhleh (Int. J. Bioinform. Res. Appl., 2005)

Reconstructing Reticulate Evolution in SpeciesTheory and Practice. - Luay Nakhleh; Tandy J. Warnow; C. Randal Linder; Katherine St. John (J. Comput. Biol., 2005)

Phylogenetic Networks: Properties and Relationship to Trees and Clusters. - Luay Nakhleh; Li-San Wang (Trans. Comp. Sys. Biology, 2005)

RECOMP: A Parsimony-Based Method for Detecting Recombination. - Derek A. Ruths; Luay Nakhleh (APBC, 2006)

Techniques for Assessing Phylogenetic Branch Support: A Performance Study. - Derek A. Ruths; Luay Nakhleh (APBC, 2006)

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

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

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

Maximum likelihood of phylogenetic networks. - Guohua Jin; Luay Nakhleh; Sagi Snir; Tamir Tuller (Bioinform., 2006)

PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction. - Yuri Dotsenko; Cristian Coarfa; Luay Nakhleh; John M. Mellor-Crummey; Usman Roshan (Int. J. Bioinform. Res. Appl., 2006)

Hypothesis Generation in Signaling Networks. - Derek A. Ruths; Luay Nakhleh; M. Sriram Iyengar; Shrikanth A. G. Reddy; Prahlad T. Ram (J. Comput. Biol., 2006)

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

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

Efficient parsimony-based methods for phylogenetic network reconstruction. - Guohua Jin; Luay Nakhleh; Sagi Snir; Tamir Tuller (Bioinform., 2007)

Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. - Cuong Than; Derek A. Ruths; Hideki Innan; Luay Nakhleh (J. Comput. Biol., 2007)

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

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

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

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

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

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle. - Derek A. Ruths; Luay Nakhleh; Prahlad T. Ram (BMC Syst. Biol., 2008)

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

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

GS2: an efficiently computable measure of GO-based similarity of gene sets. - Troy A. Ruths; Derek A. Ruths; Luay Nakhleh (Bioinform., 2009)

Species Tree Inference by Minimizing Deep Coalescences. - Cuong Than; Luay Nakhleh (PLoS Comput. Biol., 2009)

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

A Metric on the Space of Reduced Phylogenetic Networks. - Luay Nakhleh (IEEE ACM Trans. Comput. Biol. Bioinform., 2010)

Algorithms for MDC-Based Multi-locus Phylogeny Inference. - Yun Yu; Tandy J. Warnow; Luay Nakhleh (RECOMB, 2011)

The strength of chemical linkage as a criterion for pruning metabolic graphs. - Wanding Zhou; Luay Nakhleh (Bioinform., 2011)

Properties of Metabolic Graphs: Biological Organization or Representation Artifacts? - Wanding Zhou; Luay Nakhleh (BMC Bioinform., 2011)

Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles. - Yun Yu; Tandy J. Warnow; Luay Nakhleh (J. Comput. Biol., 2011)

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

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

Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models. - Yun Zhu; Luay Nakhleh (WABI, 2012)

Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria. - Hyun Jung Park; Luay Nakhleh (BMC Bioinform., 2012)

Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting - Yun Yu; Luay Nakhleh (CoRR, 2012)

Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways. - Wanding Zhou; Luay Nakhleh (J. Chem. Inf. Model., 2012)

Integrated genotyping of structural variation. - Xian Fan; Luay Nakhleh; Ken Chen 001 (GlobalSIP, 2013)

Session introduction. - Luay Nakhleh; Noah A. Rosenberg; Tandy J. Warnow (Pacific Symposium on Biocomputing, 2013)

Boosting forward-time population genetic simulators through genotype compression. - Troy A. Ruths; Luay Nakhleh (BMC Bioinform., 2013)

Fast algorithms and heuristics for phylogenomics under ILS and hybridization. - Yun Yu; Nikola Ristic; Luay Nakhleh (BMC Bioinform., 2013)

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks. - Natalie Berestovsky; Wanding Zhou; Deepak Nagrath; Luay Nakhleh (PLoS Comput. Biol., 2013)

Towards accurate characterization of clonal heterogeneity based on structural variation. - Xian Fan; Wanding Zhou; Zechen Chong; Luay Nakhleh; Ken Chen 001 (BMC Bioinform., 2014)

An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes. - Kevin J. Liu; Jingxuan Dai; Kathy Truong; Ying Song; Michael H. Kohn; Luay Nakhleh (PLoS Comput. Biol., 2014)

A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. - Yun Yu; Luay Nakhleh (ISBRA, 2015)

In the light of deep coalescence: revisiting trees within networks. - Jiafan Zhu; Yun Yu; Luay Nakhleh (BMC Bioinform., 2016)

Inferring Local Genealogies on Closely Related Genomes. - Ryan A. Leo Elworth; Luay Nakhleh (RECOMB-CG, 2017)

Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence Model. - Peng Du; Luay Nakhleh (BCB, 2018)

Detecting Large Indels Using Optical Map Data. - Xian Fan; Jie Xu; Luay Nakhleh (RECOMB-CG, 2018)

DGEN: A Test Statistic for Detection of General Introgression Scenarios. - Ryan A. Leo Elworth; Chabrielle Allen; Travis Benedict; Peter Dulworth; Luay Nakhleh (WABI, 2018)

ALPHA: a toolkit for Automated Local PHylogenomic Analyses. - Ryan A. Leo Elworth; Chabrielle Allen; Travis Benedict; Peter Dulworth; Luay Nakhleh (Bioinform., 2018)

Towards an accurate and efficient heuristic for species/gene tree co-estimation. - Yaxuan Wang; Luay Nakhleh (Bioinform., 2018)

Inference of species phylogenies from bi-allelic markers using pseudo-likelihood. - Jiafan Zhu; Luay Nakhleh (Bioinform., 2018)

Bayesian inference of phylogenetic networks from bi-allelic genetic markers. - Jiafan Zhu; Dingqiao Wen; Yun Yu; Heidi M. Meudt; Luay Nakhleh (PLoS Comput. Biol., 2018)

Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks. - Peng Du; Huw A. Ogilvie; Luay Nakhleh (ISBRA, 2019)

Empirical Performance of Tree-Based Inference of Phylogenetic Networks. - Zhen Cao; Jiafan Zhu; Luay Nakhleh (WABI, 2019)

A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference. - Mohammad Amin Edrisi; Hamim Zafar; Luay Nakhleh (WABI, 2019)

A divide-and-conquer method for scalable phylogenetic network inference from multilocus data. - Jiafan Zhu; Xinhao Liu 004; Huw A. Ogilvie; Luay Nakhleh (Bioinform., 2019)

Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data. - Xian F. Mallory; Mohammad Amin Edrisi; Nicholas Navin; Luay Nakhleh (PLoS Comput. Biol., 2020)

Phylogenetic Network Dissimilarity Measures that Take Branch Lengths into Account. - Berk A. Yakici; Huw A. Ogilvie; Luay Nakhleh (RECOMB-CG, 2022)

Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data. - Mohammad Amin Edrisi; Monica V. Valecha; Sunkara B. V. Chowdary; Sergio Robledo; Huw A. Ogilvie; David Posada; Hamim Zafar; Luay Nakhleh (Bioinform., 2022)

SimSCSnTree: a simulator of single-cell DNA sequencing data. - Xian F. Mallory; Luay Nakhleh (Bioinform., 2022)

Annotation-free delineation of prokaryotic homology groups. - Yongze Yin; Huw A. Ogilvie; Luay Nakhleh (PLoS Comput. Biol., 2022)

MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural Networks. - Mohammad Amin Edrisi; Huw A. Ogilvie; Meng Li 002; Luay Nakhleh (RECOMB-CG, 2023)

Polyphest: fast polyploid phylogeny estimation. - Zhi Yan 008; Zhen Cao; Luay Nakhleh (Bioinform., 2024)

NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model. - Yushu Liu; Mohammad Amin Edrisi; Zhi Yan 008; Huw A. Ogilvie; Luay Nakhleh (Algorithms Mol. Biol., 2024)

Inferring Phylogenetic Trees of Cancer Evolution from Longitudinal Single-Cell Copy Number Profiles. - Yushu Liu; Luay Nakhleh (RECOMB-CG, 2025)

tMHG-Finder: Tree-Guided Maximal Homologous Group Finder for Bacterial Genomes. - Yongze Yin; Bryce Kille; Huw A. Ogilvie; Todd J. Treangen; Luay Nakhleh (RECOMB-CG, 2025)