L. Nakhleh

发表

Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood

Alexandros Stamatakis, Luay Nakhleh, F. Lin, 2005, HPCC.

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

T. Warnow, L. Nakhleh, D. Ringe, 2005 .

Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling

Luay Nakhleh, Yiling Lu, Kakajan Komurov, 2011, Oncogene.

Monovar: single nucleotide variant detection in single cells

Ken Chen, Luay Nakhleh, Nicholas Navin, 2016, Nature Methods.

Computational approaches for inferring tumor evolution from single-cell genomic data

Ken Chen, Luay Nakhleh, Nicholas Navin, 2018 .

ncDNA and drift drive binding site

L. Nakhleh, 2012 .

Maximum likelihood inference of reticulate evolutionary histories

Kevin J. Liu, L. Nakhleh, Jianrong Dong, 2014, Proceedings of the National Academy of Sciences.

A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset

T. Warnow, S. Evans, L. Nakhleh, 2004 .

SiFit: A Method for Inferring Tumor Trees from Single-Cell Sequencing Data under Finite-site Models

N. Navin, L. Nakhleh, Ken Chen, 2016, bioRxiv.

Evolutionary Phylogenetic Networks: Models and Issues

L. Nakhleh, 2010 .

Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting.

Luay Nakhleh, Cuong Than, Yun Yu, 2011, Systematic biology.

Inferring Phylogenetic Networks Using PhyloNet

Luay Nakhleh, David Posada, Yun Yu, 2017, bioRxiv.

Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

Luay Nakhleh, Yun Yu, Dingqiao Wen, 2016, PLoS genetics.

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

Luay Nakhleh, Matthew W. Hahn, Yun Yu, 2016, Molecular ecology.

Interspecific introgressive origin of genomic diversity in the house mouse

Kevin J. Liu, L. Nakhleh, E. Steinberg, 2013, Proceedings of the National Academy of Sciences.

ALGORITHMIC STRATEGIES FOR ESTIMATING THE AMOUNT OF RETICULATION FROM A COLLECTION OF GENE TREES

L. Nakhleh, L. Nakhleh, H. J. Park, 2010 .

Inference of parsimonious species phylogenies from multi-locus data

Luay Nakhleh, Cuong Than, L. Nakhleh, 2010 .

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

Luay Nakhleh, James H. Degnan, Yun Yu, 2012, PLoS genetics.

Parsimonious inference of hybridization in the presence of incomplete lineage sorting.

Luay Nakhleh, Yun Yu, L. Nakhleh, 2013, Systematic biology.

Gene Trees, Species Trees, and Species Networks

Luay Nakhleh, Hideki Innan, Derek A. Ruths, 2005 .

CHAPTER 1 Gene Trees , Species Trees , and Species Networks

Derek A. Ruths, L. Nakhleh, 2005 .

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

N. Navin, L. Nakhleh, Xian F. Mallory, 2020, Genome Biology.

Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks

Luay Nakhleh, Huw A. Ogilvie, Peng Du, 2019, bioRxiv.

Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes

L. Nakhleh, H. Ogilvie, Zhi Yan, 2021, Systematic biology.

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

L. Nakhleh, Yun Zhu, Peng Du, 2012, PloS one.

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

Ken Chen, Luay Nakhleh, Nicholas Navin, 2018, Genome Research.

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

L. Nakhleh, T. Ruths, 2013, Proceedings of the National Academy of Sciences.

“Correcting” gene trees to be more like species trees increases topological error when incomplete lineage sorting is high

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, bioRxiv.

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

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, bioRxiv.

MaCroDNA: Accurate integration of single-cell DNA and RNA 1 data for a deeper understanding of tumor heterogeneity

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022 .

Mutations in Global Regulators Lead to Metabolic Selection during Adaptation to Complex Environments

Y. Shamoo, L. Nakhleh, E. Merkley, 2014, PLoS genetics.

Comparing Inference under the MSC versus the MSC-with-Recombination

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, bioRxiv.

Annotation-free delineation of prokaryotic homology groups

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, PLoS Comput. Biol..

The Impact of Model Misspecification on Phylogenetic Network Inference

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, bioRxiv.

In the light of deep coalescence: revisiting trees within networks

L. Nakhleh, Yun Yu, Jiafan Zhu, 2016, BMC Bioinformatics.

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

L. Nakhleh, H. Park, 2012, BMC Bioinformatics.

Deriving executable models of biochemical network dynamics from qualitative data

Derek Ruths, Luay Nakhleh, Derek A. Ruths, 2009 .

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle

Luay Nakhleh, Prahlad T. Ram, Derek A. Ruths, 2008, BMC Systems Biology.

The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks

Luay Nakhleh, Melissa Muller, Prahlad T. Ram, 2008, PLoS Comput. Biol..

Identification of Three Distinct Phylogenetic Groups of CAX Cation/Proton Antiporters

L. Nakhleh, K. Hirschi, I. Rees, 2006, Journal of Molecular Evolution.

Recombination and phylogeny: effects and detection

Luay Nakhleh, Derek A. Ruths, L. Nakhleh, 2005, Int. J. Bioinform. Res. Appl..

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

L. Nakhleh, L. Chung, D. Harrington, 2018, Scientific Reports.

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

Luay Nakhleh, Derek A. Ruths, Troy A. Ruths, 2009, Bioinform..

MaCroDNA: Accurate integration of single-cell DNA and RNA data for a deeper understanding of tumor heterogeneity

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2023, bioRxiv.

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

Luay Nakhleh, Huw A. Ogilvie, Yaxuan Wang, 2019, bioRxiv.

DGEN: A Test Statistic for Detection of General Introgression Scenarios

Luay Nakhleh, Ryan A. Leo Elworth, Chabrielle Allen, 2018, bioRxiv.

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

Luay Nakhleh, Dingqiao Wen, L. Nakhleh, 2017, bioRxiv.

Inferring Local Genealogies on Closely Related Genomes

Luay Nakhleh, Ryan A. Leo Elworth, L. Nakhleh, 2017, RECOMB-CG.

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

Luay Nakhleh, Dingqiao Wen, L. Nakhleh, 2017 .

An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes

Ying Song, Luay Nakhleh, Kevin J. Liu, 2013, PLoS Comput. Biol..

Evolution After Whole-Genome Duplication: A Network Perspective

Luay Nakhleh, L. Nakhleh, Zhenguo Lin, 2013, G3: Genes, Genomes, Genetics.

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

Yun Zhu, Luay Nakhleh, L. Nakhleh, 2012, WABI.

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

Tandy J. Warnow, Yun Yu, Luay Nakhleh, 2011, J. Comput. Biol..

Algorithms for MDC-Based Multi-locus Phylogeny Inference

Tandy J. Warnow, Yun Yu, Luay Nakhleh, 2011, RECOMB.

Phylovar: Towards scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data

Huw A. Ogilvie, L. Nakhleh, D. Posada, 2022, bioRxiv.

Current progress and open challenges for applying deep learning across the biosciences

Cameron R. Wolfe, Michael G. Nute, Richard Baraniuk, 2022, Nature Communications.

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

Luay Nakhleh, Xian Fan, Mohammadamin Edrisi, 2019, Genome Biology.

A comparison of phylogenetic reconstruction methods on an Indo‐European dataset

Luay Nakhleh, Tandy Warnow, Steven N. Evans, 2005 .

Towards accurate characterization of clonal heterogeneity based on structural variation

Ken Chen, Luay Nakhleh, Zechen Chong, 2014, BMC Bioinformatics.

Population genomics in bacteria: a case study of Staphylococcus aureus.

Luay Nakhleh, Hideki Innan, L. Nakhleh, 2012, Molecular biology and evolution.

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

Luay Nakhleh, Hamim Zafar, Mohammadamin Edrisi, 2019, bioRxiv.

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

Ken Chen, Nicholas Navin, Hamim Zafar, 2017, Genome Biology.

De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis

Luay Nakhleh, Prahlad T. Ram, Derek A. Ruths, 2006, Systems Biology and Computational Proteomics.

Hypothesis Generation in Signaling Networks

Luay Nakhleh, M. Sriram Iyengar, Prahlad T. Ram, 2006, J. Comput. Biol..

Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs

L. Nakhleh, Megan L. Smith, Peng Du, 2021, Systematic biology.

Species Tree Inference under the Multispecies Coalescent on Data with Paralogs is Accurate

Luay Nakhleh, L. Nakhleh, Peng Du, 2018, bioRxiv.

A maximum pseudo-likelihood approach for phylogenetic networks

Yun Yu, L. Nakhleh, L. Nakhleh, 2015, BMC Genomics.

Species Tree Inference by Minimizing Deep Coalescences

Luay Nakhleh, Cuong Than, L. Nakhleh, 2009, PLoS Comput. Biol..

Detecting Large Indels Using Optical Map Data

Jie Xu, Luay Nakhleh, Xian Fan, 2018, bioRxiv.

Comparing Inference under the Multispecies Coalescent with and without Recombination.

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2023, Molecular phylogenetics and evolution.

Supporting per-locus substitution rates improves the accuracy of species networks and avoids spurious reticulations

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, bioRxiv.

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

Luay Nakhleh, Derek A. Ruths, Cuong Than, 2008, BMC Bioinformatics.

NestedBD: Bayesian Inference of Phylogenetic Trees From Single-Cell DNA Copy Number Profile Data Under a Birth-Death Model

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2022, bioRxiv.

Phylogenetic Network Dissimilarity Measures That Take Branch Lengths Into Account

L. Nakhleh, H. Ogilvie, Berk A. Yakici, 2022, bioRxiv.

Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting pdf

Yun Yu, Luay Nakhleh, Y. Yu, 2012, ArXiv.

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

Luay Nakhleh, Li-San Wang, Derek A. Ruths, 2005, COCOON.

Fast algorithms and heuristics for phylogenomics under ILS and hybridization

Yun Yu, Luay Nakhleh, Nikola Ristic, 2013, BMC Bioinformatics.

Seeing the trees and their branches in the network is hard

Ge Xia, Luay Nakhleh, Iyad A. Kanj, 2007, Theor. Comput. Sci..

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

Ken Chen, Luay Nakhleh, Xian Fan, 2016, bioRxiv.

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

Luay Nakhleh, Xian Fan, Mark J. P. Chaisson, 2016 .

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

Luay Nakhleh, Hideki Innan, R. Sugino, 2008, ISMB.

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

Luay Nakhleh, Mohammadamin Edrisi, Nicholas Navin, 2020, PLoS Comput. Biol..

A STOCHASTIC MODEL OF LANGUAGE EVOLUTION THAT INCORPORATES HOMOPLASY AND BORROWING

T. Warnow, S. Evans, L. Nakhleh, 2005 .

Integrated genotyping of structural variation

Ken Chen, Luay Nakhleh, Xian Fan, 2013, 2013 IEEE Global Conference on Signal and Information Processing.

Boosting forward-time population genetic simulators through genotype compression

Luay Nakhleh, Troy A. Ruths, L. Nakhleh, 2013, BMC Bioinformatics.

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

Luay Nakhleh, Yaxuan Wang, L. Nakhleh, 2018, Bioinform..

SimSCSnTree: a simulator of single-cell DNA sequencing data

L. Nakhleh, X. Mallory, 2022, Bioinform..

Reconstructing phylogenetic networks using maximum parsimony

John M. Mellor-Crummey, Luay Nakhleh, Guohua Jin, 2005, 2005 IEEE Computational Systems Bioinformatics Conference (CSB'05).

Multispecies Coalescent: Theory and Applications in Phylogenetics

Luay Nakhleh, Tandy Warnow, Siavash Mirarab, 2021, Annual Review of Ecology, Evolution, and Systematics.

PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction

John M. Mellor-Crummey, Luay Nakhleh, Cristian Coarfa, 2005, 11th International Conference on Parallel and Distributed Systems (ICPADS'05).

Bayesian inference of phylogenetic networks from bi-allelic genetic markers

Yun Yu, Jiafan Zhu, Luay Nakhleh, 2017, bioRxiv.

Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions

Luay Nakhleh, Hideki Innan, Derek A. Ruths, 2007, J. Comput. Biol..

Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization

Huw A. Ogilvie, R.A.L. Elworth, H. A. Ogilvie, 2018, Bioinformatics and Phylogenetics.

In the light of deep coalescence: revisiting trees within networks

Yun Yu, Jiafan Zhu, Luay Nakhleh, 2016, BMC Bioinformatics.

Techniques for Assessing Phylogenetic Branch Support: A Performance Study

Luay Nakhleh, Derek A. Ruths, L. Nakhleh, 2005, APBC.

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

L. Nakhleh, Yun Yu, James H. Degnan, 2012, PLoS Genetics.

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

L. Nakhleh, L. Nakhleh, H. Tidwell, 2018, BMC Genomics.

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

Jiafan Zhu, Luay Nakhleh, L. Nakhleh, 2018, bioRxiv.

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

L. Nakhleh, Dingqiao Wen, Yun-Xia Yu, 2017, PLoS genetics.

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

Yun Yu, Luay Nakhleh, L. Nakhleh, 2015, ISBRA.

RECOMP: A Parsimony-Based Method for Detecting Recombination

Luay Nakhleh, Derek A. Ruths, L. Nakhleh, 2005, APBC.

Bootstrap-based Support of HGT Inferred by Maximum Parsimony

Hyun Jung Park, L. Nakhleh, G. Jin, 2010, BMC Evolutionary Biology.

Bootstrap-based Support of HGT Inferred by Maximum Parsimony

Guohua Jin, Hyun Jung Park, L. Nakhleh, 2010, BMC Evolutionary Biology.

Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer

Luay Nakhleh, Hideki Innan, Derek A. Ruths, 2006, Comparative Genomics.

“Correcting” Gene Trees to be More Like Species Trees Frequently Increases Topological Error

Huw A. Ogilvie, L. Nakhleh, Zhi Yan, 2023, Genome biology and evolution.

Population genomics in bacteria: a case study of Staphylococcus aureus.

L. Nakhleh, H. Innan, R. Sugino, 2012, Molecular biology and evolution.

Maximum likelihood inference of reticulate evolutionary histories

L. Nakhleh, Jianrong Dong, Yun Yu, 2014, Proceedings of the National Academy of Sciences.

Phylogenetic Network Dissimilarity Measures That Take Branch Lengths Into Account

Huw A. Ogilvie, L. Nakhleh, Berk A. Yakici, 2022, bioRxiv.

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

Luay Nakhleh, Hyun Jung Park, L. Nakhleh, 2012, BMC Bioinformatics.

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

N. Navin, L. Nakhleh, Ken Chen, 2019, Genome Biology.

Accurate integration of single-cell DNA and RNA for analyzing intratumor heterogeneity using MaCroDNA

Huw A. Ogilvie, L. Nakhleh, M. Edrisi, 2023, Nature communications.

Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data

Huw A. Ogilvie, L. Nakhleh, M. Edrisi, 2022, Bioinformatics.