Luay Nakhleh

Orcid: 0000-0003-3288-6769

Affiliations:
  • Rice University, Houston, TX, USA


According to our database1, Luay Nakhleh authored at least 77 papers between 2001 and 2024.

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Bibliography

2024
NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model.
Algorithms Mol. Biol., December, 2024

2023
MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural Networks.
Proceedings of the Comparative Genomics - 20th International Conference, 2023

2022
Annotation-free delineation of prokaryotic homology groups.
PLoS Comput. Biol., 2022

SimSCSnTree: a simulator of single-cell DNA sequencing data.
Bioinform., 2022

Phylogenetic Network Dissimilarity Measures that Take Branch Lengths into Account.
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.
PLoS Comput. Biol., 2020

2019
A divide-and-conquer method for scalable phylogenetic network inference from multilocus data.
Bioinform., 2019

A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference.
Proceedings of the 19th International Workshop on Algorithms in Bioinformatics, 2019

Empirical Performance of Tree-Based Inference of Phylogenetic Networks.
Proceedings of the 19th International Workshop on Algorithms in Bioinformatics, 2019

Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks.
Proceedings of the Bioinformatics Research and Applications - 15th International Symposium, 2019

2018
Bayesian inference of phylogenetic networks from bi-allelic genetic markers.
PLoS Comput. Biol., 2018

Inference of species phylogenies from bi-allelic markers using pseudo-likelihood.
Bioinform., 2018

Towards an accurate and efficient heuristic for species/gene tree co-estimation.
Bioinform., 2018

ALPHA: a toolkit for Automated Local PHylogenomic Analyses.
Bioinform., 2018

DGEN: A Test Statistic for Detection of General Introgression Scenarios.
Proceedings of the 18th International Workshop on Algorithms in Bioinformatics, 2018

Detecting Large Indels Using Optical Map Data.
Proceedings of the Comparative Genomics - 16th International Conference, 2018

Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence Model.
Proceedings of the 2018 ACM International Conference on Bioinformatics, 2018

2017
Inferring Local Genealogies on Closely Related Genomes.
Proceedings of the Comparative Genomics - 15th International Workshop, 2017

2016
In the light of deep coalescence: revisiting trees within networks.
BMC Bioinform., 2016

2015
A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting.
Proceedings of the Bioinformatics Research and Applications - 11th International Symposium, 2015

2014
An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes.
PLoS Comput. Biol., 2014

Towards accurate characterization of clonal heterogeneity based on structural variation.
BMC Bioinform., 2014

2013
Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks.
PLoS Comput. Biol., 2013

Fast algorithms and heuristics for phylogenomics under ILS and hybridization.
BMC Bioinform., 2013

Boosting forward-time population genetic simulators through genotype compression.
BMC Bioinform., 2013

Session introduction.
Proceedings of the Biocomputing 2013: Proceedings of the Pacific Symposium, 2013

Integrated genotyping of structural variation.
Proceedings of the IEEE Global Conference on Signal and Information Processing, 2013

2012
Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways.
J. Chem. Inf. Model., 2012

Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting
CoRR, 2012

Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria.
BMC Bioinform., 2012

Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models.
Proceedings of the Algorithms in Bioinformatics - 12th International Workshop, 2012

MURPAR: A Fast Heuristic for Inferring Parsimonious Phylogenetic Networks from Multiple Gene Trees.
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.
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.
J. Comput. Biol., 2011

Properties of Metabolic Graphs: Biological Organization or Representation Artifacts?
BMC Bioinform., 2011

The strength of chemical linkage as a criterion for pruning metabolic graphs.
Bioinform., 2011

Algorithms for MDC-Based Multi-locus Phylogeny Inference.
Proceedings of the Research in Computational Molecular Biology, 2011

2010
A Metric on the Space of Reduced Phylogenetic Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2010

2009
Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic.
IEEE ACM Trans. Comput. Biol. Bioinform., 2009

Species Tree Inference by Minimizing Deep Coalescences.
PLoS Comput. Biol., 2009

GS<sup>2</sup>: an efficiently computable measure of GO-based similarity of gene sets.
Bioinform., 2009

2008
Seeing the trees and their branches in the network is hard.
Theor. Comput. Sci., 2008

The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks.
PLoS Comput. Biol., 2008

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle.
BMC Syst. Biol., 2008

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships.
BMC Bioinform., 2008

The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms.
Algorithmica, 2008

Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer.
Proceedings of the Comparative Genomics, International Workshop, 2008

Efficient inference of bacterial strain trees from genome-scale multilocus data.
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.
Proceedings of the 6th Asia-Pacific Bioinformatics Conference, 2008

2007
Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions.
J. Comput. Biol., 2007

Efficient parsimony-based methods for phylogenetic network reconstruction.
Bioinform., 2007

A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance.
Proceedings of the Bioinformatics Research and Applications, Third International Symposium, 2007

Seeing the Trees and Their Branches in the Forest is Hard.
Proceedings of the Theoretical Computer Science, 10th Italian Conference, 2007

2006
Hypothesis Generation in Signaling Networks.
J. Comput. Biol., 2006

PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction.
Int. J. Bioinform. Res. Appl., 2006

Maximum likelihood of phylogenetic networks.
Bioinform., 2006

Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer.
Proceedings of the Comparative Genomics, 2006

De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis.
Proceedings of the Systems Biology and Computational Proteomics, 2006

Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms.
Proceedings of the Computing and Combinatorics, 12th Annual International Conference, 2006

Techniques for Assessing Phylogenetic Branch Support: A Performance Study.
Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, 2006

RECOMP: A Parsimony-Based Method for Detecting Recombination.
Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February 2006, 2006

2005
Phylogenetic Networks: Properties and Relationship to Trees and Clusters.
Trans. Comp. Sys. Biology, 2005

Reconstructing Reticulate Evolution in SpeciesTheory and Practice.
J. Comput. Biol., 2005

Recombination and phylogeny: effects and detection.
Int. J. Bioinform. Res. Appl., 2005

Phylogenetic Networks, Trees, and Clusters.
Proceedings of the Computational Science, 2005

Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood.
Proceedings of the High Performance Computing and Communications, 2005

Reconstructing Phylogenetic Networks Using Maximum Parsimony.
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.
Proceedings of the Computing and Combinatorics, 11th Annual International Conference, 2005

2004
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy.
IEEE ACM Trans. Comput. Biol. Bioinform., 2004

Reconstructing reticulate evolution in species: theory and practice.
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.
Proceedings of the 8th Pacific Symposium on Biocomputing, 2003

Reconstructing the Evolutionary History of Indo-European Languages Using Answer Set Programming.
Proceedings of the Practical Aspects of Declarative Languages, 5th International Symposium, 2003

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

2002
Estimating the Deviation from a Molecular Clock.
Proceedings of the Algorithms in Bioinformatics, Second International Workshop, 2002

The Accuracy of Fast Phylogenetic Methods for Large Datasets.
Proceedings of the 7th Pacific Symposium on Biocomputing, 2002

2001
The Performance of Phylogenetic Methods on Trees of Bounded Diameter.
Proceedings of the Algorithms in Bioinformatics, First International Workshop, 2001

Designing fast converging phylogenetic methods.
Proceedings of the Ninth International Conference on Intelligent Systems for Molecular Biology, 2001


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