Luay Nakhleh

According to our database, Luay Nakhleh authored at least 77 papers between 2001 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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, Huw A. Ogilvie, Luay Nakhleh

Algorithms Mol. Biol., December, 2024

2023

MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural Networks.

Mohammad Amin Edrisi, Huw A. Ogilvie, Meng Li, Luay Nakhleh

Proceedings of the Comparative Genomics - 20th International Conference, 2023

2022

Annotation-free delineation of prokaryotic homology groups.

Yongze Yin, Huw A. Ogilvie, Luay Nakhleh

PLoS Comput. Biol., 2022

SimSCSnTree: a simulator of single-cell DNA sequencing data.

Xian F. Mallory, Luay Nakhleh

Bioinform., 2022

Phylogenetic Network Dissimilarity Measures that Take Branch Lengths into Account.

Berk A. Yakici, Huw A. Ogilvie, Luay Nakhleh

Proceedings of the Comparative Genomics - 19th International Conference, 2022

2020

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

2019

A divide-and-conquer method for scalable phylogenetic network inference from multilocus data.

Jiafan Zhu, Xinhao Liu, Huw A. Ogilvie, Luay Nakhleh

Bioinform., 2019

A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference.

Mohammad Amin Edrisi, Hamim Zafar, Luay Nakhleh

Proceedings of the 19th International Workshop on Algorithms in Bioinformatics, 2019

Empirical Performance of Tree-Based Inference of Phylogenetic Networks.

Zhen Cao, Jiafan Zhu, Luay Nakhleh

Proceedings of the 19th International Workshop on Algorithms in Bioinformatics, 2019

Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks.

Peng Du, Huw A. Ogilvie, Luay Nakhleh

Proceedings of the Bioinformatics Research and Applications - 15th International Symposium, 2019

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

Inference of species phylogenies from bi-allelic markers using pseudo-likelihood.

Jiafan Zhu, Luay Nakhleh

Bioinform., 2018

Towards an accurate and efficient heuristic for species/gene tree co-estimation.

Yaxuan Wang, Luay Nakhleh

Bioinform., 2018

ALPHA: a toolkit for Automated Local PHylogenomic Analyses.

Ryan A. Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, Luay Nakhleh

Bioinform., 2018

DGEN: A Test Statistic for Detection of General Introgression Scenarios.

Ryan A. Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, Luay Nakhleh

Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

Detecting Large Indels Using Optical Map Data.

Xian Fan, Jie Xu, Luay Nakhleh

Proceedings of the Comparative Genomics - 16th International Conference, 2018

Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence Model.

Peng Du, Luay Nakhleh

Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017

Inferring Local Genealogies on Closely Related Genomes.

Ryan A. Leo Elworth, Luay Nakhleh

Proceedings of the Comparative Genomics - 15th International Workshop, 2017

2016

In the light of deep coalescence: revisiting trees within networks.

Jiafan Zhu, Yun Yu, Luay Nakhleh

BMC Bioinform., 2016

2015

A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting.

Yun Yu, Luay Nakhleh

Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

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

Towards accurate characterization of clonal heterogeneity based on structural variation.

Xian Fan, Wanding Zhou, Zechen Chong, Luay Nakhleh, Ken Chen

BMC Bioinform., 2014

2013

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks.

Natalie Berestovsky, Wanding Zhou, Deepak Nagrath, Luay Nakhleh

PLoS Comput. Biol., 2013

Fast algorithms and heuristics for phylogenomics under ILS and hybridization.

Yun Yu, Nikola Ristic, Luay Nakhleh

BMC Bioinform., 2013

Boosting forward-time population genetic simulators through genotype compression.

Troy A. Ruths, Luay Nakhleh

BMC Bioinform., 2013

Session introduction.

Luay Nakhleh, Noah A. Rosenberg, Tandy J. Warnow

Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Integrated genotyping of structural variation.

Xian Fan, Luay Nakhleh, Ken Chen

Proceedings of the IEEE Global Conference on Signal and Information Processing, 2013

2012

Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways.

Wanding Zhou, Luay Nakhleh

J. Chem. Inf. Model., 2012

Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting

Yun Yu, Luay Nakhleh

CoRR, 2012

Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria.

Hyun Jung Park, Luay Nakhleh

BMC Bioinform., 2012

Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models.

Yun Zhu, Luay Nakhleh

Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

MURPAR: A Fast Heuristic for Inferring Parsimonious Phylogenetic Networks from Multiple Gene Trees.

Hyun Jung Park, Luay Nakhleh

Proceedings of the Bioinformatics Research and Applications - 8th International Symposium, 2012

On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks.

Natalie Berestovsky, Riya Fukui, Luay Nakhleh

Proceedings of the 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology, 2012

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

Properties of Metabolic Graphs: Biological Organization or Representation Artifacts?

Wanding Zhou, Luay Nakhleh

BMC Bioinform., 2011

The strength of chemical linkage as a criterion for pruning metabolic graphs.

Wanding Zhou, Luay Nakhleh

Bioinform., 2011

Algorithms for MDC-Based Multi-locus Phylogeny Inference.

Yun Yu, Tandy J. Warnow, Luay Nakhleh

Proceedings of the Research in Computational Molecular Biology, 2011

2010

A Metric on the Space of Reduced Phylogenetic Networks.

Luay Nakhleh

IEEE ACM Trans. Comput. Biol. Bioinform., 2010

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

Species Tree Inference by Minimizing Deep Coalescences.

Cuong Than, Luay Nakhleh

PLoS Comput. Biol., 2009

GS²: an efficiently computable measure of GO-based similarity of gene sets.

Troy A. Ruths, Derek A. Ruths, Luay Nakhleh

Bioinform., 2009

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

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

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle.

Derek A. Ruths, Luay Nakhleh, Prahlad T. Ram

BMC Syst. Biol., 2008

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships.

Cuong Than, Derek A. Ruths, Luay Nakhleh

BMC Bioinform., 2008

The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms.

Iyad A. Kanj, Luay Nakhleh, Ge Xia

Algorithmica, 2008

Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer.

Cuong Than, Guohua Jin, Luay Nakhleh

Proceedings of the Comparative Genomics, International Workshop, 2008

Efficient inference of bacterial strain trees from genome-scale multilocus data.

Cuong Than, R. Sugino, Hideki Innan, Luay Nakhleh

Proceedings of the Proceedings 16th International Conference on Intelligent Systems for Molecular Biology (ISMB), 2008

SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions.

Cuong Than, Luay Nakhleh

Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

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

Efficient parsimony-based methods for phylogenetic network reconstruction.

Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller

Bioinform., 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

Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007

Seeing the Trees and Their Branches in the Forest is Hard.

Iyad A. Kanj, Luay Nakhleh, Cuong Than, Ge Xia

Proceedings of the Theoretical Computer Science, 10th Italian Conference, 2007

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

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

Maximum likelihood of phylogenetic networks.

Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller

Bioinform., 2006

Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer.

Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh

Proceedings of the Comparative Genomics, 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

Proceedings of the Systems Biology and Computational Proteomics, 2006

Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms.

Iyad A. Kanj, Luay Nakhleh, Ge Xia

Proceedings of the Computing and Combinatorics, 12th Annual International Conference, 2006

Techniques for Assessing Phylogenetic Branch Support: A Performance Study.

Derek A. Ruths, Luay Nakhleh

Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, 2006

RECOMP: A Parsimony-Based Method for Detecting Recombination.

Derek A. Ruths, Luay Nakhleh

Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, 2006

2005

Phylogenetic Networks: Properties and Relationship to Trees and Clusters.

Luay Nakhleh, Li-San Wang

Trans. Comp. Sys. Biology, 2005

Reconstructing Reticulate Evolution in SpeciesTheory and Practice.

Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Katherine St. John

J. Comput. Biol., 2005

Recombination and phylogeny: effects and detection.

Derek A. Ruths, Luay Nakhleh

Int. J. Bioinform. Res. Appl., 2005

Phylogenetic Networks, Trees, and Clusters.

Luay Nakhleh, Li-San Wang

Proceedings of the Computational Science, 2005

Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood.

Z. Du, Alexandros Stamatakis, F. Lin, Usman Roshan, Luay Nakhleh

Proceedings of the High Performance Computing and Communications, 2005

Reconstructing Phylogenetic Networks Using Maximum Parsimony.

Luay Nakhleh, Guohua Jin, Fengmei Zhao, John M. Mellor-Crummey

Proceedings of the Fourth International IEEE Computer Society Computational Systems Bioinformatics Conference, 2005

RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer.

Luay Nakhleh, Derek A. Ruths, Li-San Wang

Proceedings of the Computing and Combinatorics, 11th Annual International Conference, 2005

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, Ruth E. Timme

IEEE ACM Trans. Comput. Biol. Bioinform., 2004

Reconstructing reticulate evolution in species: theory and practice.

Luay Nakhleh, Tandy J. Warnow, C. Randal Linder

Proceedings of the Eighth Annual International Conference on Computational Molecular Biology, 2004

2003

Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods.

Luay Nakhleh, Jerry Sun, Tandy J. Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse

Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Reconstructing the Evolutionary History of Indo-European Languages Using Answer Set Programming.

Esra Erdem, Vladimir Lifschitz, Luay Nakhleh, Donald Ringe

Proceedings of the Practical Aspects of Declarative Languages, 5th International Symposium, 2003

Requirements of Phylogenetic Databases.

Luay Nakhleh, Daniel P. Miranker, François Barbançon, William H. Piel, Michael J. Donoghue

Proceedings of the 3rd IEEE International Symposium on BioInformatics and BioEngineering (BIBE 2003), 2003

2002

Estimating the Deviation from a Molecular Clock.

Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy J. Warnow

Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

The Accuracy of Fast Phylogenetic Methods for Large Datasets.

Luay Nakhleh, Bernard M. E. Moret, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow

Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2001

The Performance of Phylogenetic Methods on Trees of Bounded Diameter.

Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow

Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001

Designing fast converging phylogenetic methods.

Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow

Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001