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List of works by Luay Nakhleh

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

scientific article published on 01 July 2019

A maximum pseudo-likelihood approach for phylogenetic networks

scientific article published on 2 October 2015

A metric on the space of reduced phylogenetic networks

scientific article

ALPHA: a toolkit for Automated Local PHylogenomic Analyses

scientific article published on 01 August 2018

Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles ⬇️

scientific article published on October 28, 2011

An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data

scientific article

An HMM-based comparative genomic framework for detecting introgression in eukaryotes

scientific article

Annotation-free delineation of prokaryotic homology groups

scientific article published on 08 June 2022

Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data

scientific article published on 13 July 2020

Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

scientific article published on 4 May 2016

Bayesian inference of phylogenetic networks from bi-allelic genetic markers

scientific article published on 10 January 2018

Boosting forward-time population genetic simulators through genotype compression

scientific article

Bootstrap-based support of HGT inferred by maximum parsimony

scientific article

Co-estimating Reticulate Phylogenies and Gene Trees from Multi-locus Sequence Data

scientific article published on 27 October 2017

Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting ⬇️

scientific article published on January 19, 2011

Comments on the model parameters in "SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models"

scientific article published on 16 May 2019

Complexity of avian evolution revealed by family-level genomes

scientific article published in April 2024

Computational approaches to species phylogeny inference and gene tree reconciliation

scientific article

Confounding factors in HGT detection: statistical error, coalescent effects, and multiple solutions

scientific article

Convergent evolution of modularity in metabolic networks through different community structures ⬇️

scientific article published on September 14, 2012

Correction: Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

scientific article published on 8 February 2017

Designing fast converging phylogenetic methods

scientific article published on 01 January 2001

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

scientific article

Efficient parsimony-based methods for phylogenetic network reconstruction

scientific article published in January 2007

Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics

scientific article published on 14 February 2019

Evolution after whole-genome duplication: a network perspective

scientific article

Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks

scientific article

Fast algorithms and heuristics for phylogenomics under ILS and hybridization

scientific article

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

scientific article published on 16 March 2009

Gene Duplicability-Connectivity-Complexity across Organisms and a Neutral Evolutionary Explanation ⬇️

scientific article published on September 11, 2012

HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies

scientific article published on 19 January 2017

Hypothesis generation in signaling networks

scientific article published in November 2006

Identification of three distinct phylogenetic groups of CAX cation/proton antiporters.

scientific article

In the light of deep coalescence: revisiting trees within networks

scientific article

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

scientific article published on December 19, 2012

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

scientific article published in July 2018

Inferring Local Genealogies on Closely Related Genomes

scientific article published on 15 September 2017

Inferring Phylogenetic Networks Using PhyloNet

scientific article published on 01 July 2018

Inferring phylogenetic networks by the maximum parsimony criterion: a case study

scientific article published on 26 October 2006

Integrated likelihood for phylogenomics under a no-common-mechanism model

scientific article published on 16 April 2020

Interspecific introgressive origin of genomic diversity in the house mouse

scientific article

Irrational exuberance for resolved species trees

scientific article published on 7 December 2015

Mapping network motif tunability and robustness in the design of synthetic signaling circuits

scientific article

Matrilysin/MMP-7 Cleavage of Perlecan/HSPG2 Complexed with Semaphorin 3A Supports FAK-Mediated Stromal Invasion by Prostate Cancer Cells.

scientific article

Maximum likelihood inference of reticulate evolutionary histories

scientific article

Maximum likelihood of phylogenetic networks

scientific article

Methods for copy number aberration detection from single-cell DNA-sequencing data

scientific article published on 17 August 2020

Modeling integrated cellular machinery using hybrid Petri-Boolean networks

scientific article (publication date: 2013)

Monovar: single-nucleotide variant detection in single cells

scientific article published on 18 April 2016

Mutations in global regulators lead to metabolic selection during adaptation to complex environments

scientific article

Networks: expanding evolutionary thinking

scientific article published on 11 June 2013

Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology

scientific article published on 22 April 2013

PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction

scientific article published in January 2006

Parsimonious inference of hybridization in the presence of incomplete lineage sorting

scientific article published on 04 June 2013

Parsimony score of phylogenetic networks: hardness results and a linear-time heuristic

scientific article published in July 2009

Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages

scholarly article by Luay Nakhleh et al published 2005 in Language

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

scientific article

Phylogenetic networks: modeling, reconstructibility, and accuracy

scientific article published in January 2004

Phylogenomic assessment of the role of hybridization and introgression in trait evolution

scientific article published in 2021

Population Genomics in Bacteria: A Case Study of Staphylococcus aureus ⬇️

scientific article published on October 17, 2011

Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees

scientific article published on 20 February 2020

Properties of metabolic graphs: biological organization or representation artifacts? ⬇️

scientific article published on May 4, 2011

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

scientific article published on September 28, 2012

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle

scientific article

Recombination and phylogeny: effects and detection

scientific article published on 01 January 2005

Reconstructing phylogenetic networks using maximum parsimony.

scientific article published in January 2005

Reconstructing reticulate evolution in species-theory and practice

scientific article published in July 2005

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

scientific article published on 25 January 2016

SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data

scientific article published on 18 October 2019

SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models

scientific article published on 19 September 2017

Species tree inference by minimizing deep coalescences

scientific article

Stranger in a strange land: the experiences of immigrant researchers

scientific article published on 15 December 2017

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection ⬇️

scientific article published on April 19, 2012

The accuracy of fast phylogenetic methods for large datasets

scientific article published on 01 January 2002

The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks

scientific article

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

scientific article published on May 5, 2011

Towards accurate characterization of clonal heterogeneity based on structural variation

scientific article

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

scientific article published on 01 September 2018

Towards the development of computational tools for evaluating phylogenetic network reconstruction methods.

scientific article published in January 2003

ncDNA and drift drive binding site accumulation ⬇️

scientific article published on August 30, 2012

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