Luay K. Nakhleh

发表

ncDNA and drift drive binding site accumulation

T. Ruths, L. Nakhleh, Luay K. Nakhleh, 2012, BMC Evolutionary Biology.

Properties of metabolic graphs: biological organization or representation artifacts?

Luay Nakhleh, Wanding Zhou, Wanding Zhou, 2011, BMC Bioinformatics.

Reconstructing reticulate evolution in species: theory and practice

Tandy J. Warnow, Luay Nakhleh, C. Randal Linder, 2004, RECOMB.

Designing fast converging phylogenetic methods

Tandy J. Warnow, Luay Nakhleh, Katherine St. John, 2001, ISMB.

Network ( Reticulate ) Evolution : Biology , Models , and Algorithms

Bernard M. E. Moret, C. Randal Linder, T. Warnow, 2004 .

Network (Reticulated) Evolution: Biology, Models, and Algorithms

Bernard M. E. Moret, Tandy Warnow, T. Warnow, 2004 .

The Performance of Phylogenetic Methods on Trees of Bounded Diameter

Tandy J. Warnow, Luay Nakhleh, Katherine St. John, 2001, WABI.

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

Alexandre Antonelli, John Wiedenhoeft, Bengt Oxelman, 2019, PeerJ.

Irrational exuberance for resolved species trees

Matthew W. Hahn, Matthew W Hahn, L. Nakhleh, 2016, Evolution; international journal of organic evolution.

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

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2020, bioRxiv.

Practical Aspects of Phylogenetic Network Analysis Using PhyloNet

Xinhao Liu, Zhi Yan, Zhen Cao, 2019, bioRxiv.

Empirical Performance of Tree-based Inference of Phylogenetic Networks

Luay Nakhleh, Zhen Cao, Jiafan Zhu, 2019, bioRxiv.

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

Xinhao Liu, Jiafan Zhu, Huw A. Ogilvie, 2019, bioRxiv.

Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks

Yun Yu, Christopher Jermaine, Luay K. Nakhleh, 2016, BMC Genomics.

A maximum pseudo-likelihood approach for phylogenetic networks

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

Computational approaches to species phylogeny inference and gene tree reconciliation.

L. Nakhleh, Luay Nakhleh, Luay K. Nakhleh, 2013, Trends in ecology & evolution.

Networks: expanding evolutionary thinking.

Steven Kelk, Leen Stougie, Mike Steel, 2013, Trends in genetics : TIG.

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

Natalie Berestovsky, L. Nakhleh, Luay Nakhleh, 2013, PloS one.

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

T. Tuller, S. Snir, L. Nakhleh, 2006, Molecular biology and evolution.

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks

Luay Nakhleh, Natalie Berestovsky, Deepak Nagrath, 2013, PLoS Comput. Biol..

The Accuracy of Fast Phylogenetic Methods for Large Datasets

Bernard M. E. Moret, T. Warnow, Usman Roshan, 2001, Pacific Symposium on Biocomputing.

Maximum likelihood of phylogenetic networks

Sagi Snir, Luay Nakhleh, Guohua Jin, 2006, Bioinform..

Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways

Luay Nakhleh, Wanding Zhou, Wanding Zhou, 2012, J. Chem. Inf. Model..

Requirements of phylogenetic databases

Daniel P. Miranker, Luay Nakhleh, François Barbançon, 2003, Third IEEE Symposium on Bioinformatics and Bioengineering, 2003. Proceedings..

Species Tree Inference on Data with Paralogs is Accurate Using Methods Intended to Deal with Incomplete Lineage Sorting

L. Nakhleh, Megan L. Smith, Peng Du, 2018 .

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

Huw A. Ogilvie, L. Nakhleh, H. Ogilvie, 2020, bioRxiv.

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

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

Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks

Yun Yu, Christopher Jermaine, L. Nakhleh, 2016, BMC Genomics.

Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic

Sagi Snir, Guohua Jin, Tamir Tuller, 2009, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance

Sagi Snir, Luay Nakhleh, Guohua Jin, 2007, ISBRA.

Efficient parsimony-based methods for phylogenetic network reconstruction

Sagi Snir, Luay Nakhleh, Guohua Jin, 2007, Bioinform..

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

Tandy J. Warnow, Bernard M. E. Moret, Luay Nakhleh, 2002, Pacific Symposium on Biocomputing.

Estimating the Deviation from a Molecular Clock

Tandy J. Warnow, Luay Nakhleh, Usman Roshan, 2002, WABI.

The Accuracy of Fast Phylogenetic Methods for Large Datasets

Bernard M. E. Moret, T. Warnow, Jerry Sun, 2001, Pacific Symposium on Biocomputing.

Convergent evolution of modularity in metabolic networks through different community structures

Wanding Zhou, Wanding Zhou, L. Nakhleh, 2012, BMC Evolutionary Biology.

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

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

Variational inference using approximate likelihood under the coalescent with recombination

Xinhao Liu, Luay Nakhleh, Huw A. Ogilvie, 2020, bioRxiv.