Luay Nakhleh

Publication Activity (10 Years)

Years Active: 2001-2024
Publications (10 Years): 19

Top Topics

Gene Duplication

Bayesian Inference

Similarity Measure

Top Venues

PLoS Comput. Biol.

Publications

Yushu Liu, Mohammad Amin Edrisi, Zhi Yan, Huw A. Ogilvie, Luay Nakhleh
NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model. Algorithms Mol. Biol. 19 (1) (2024)
Mohammad Amin Edrisi, Huw A. Ogilvie, Meng Li, Luay Nakhleh
MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural Networks. RECOMB-CG (2023)
Yongze Yin, Huw A. Ogilvie, Luay Nakhleh
Annotation-free delineation of prokaryotic homology groups. PLoS Comput. Biol. 18 (6) (2022)
Berk A. Yakici, Huw A. Ogilvie, Luay Nakhleh
Phylogenetic Network Dissimilarity Measures that Take Branch Lengths into Account. RECOMB-CG (2022)
Xian F. Mallory, Luay Nakhleh
SimSCSnTree: a simulator of single-cell DNA sequencing data. Bioinform. 38 (10) (2022)
Xian F. Mallory, Mohammad Amin Edrisi, Nicholas Navin, Luay Nakhleh
Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data. PLoS Comput. Biol. 16 (7) (2020)
Jiafan Zhu, Xinhao Liu, Huw A. Ogilvie, Luay Nakhleh
A divide-and-conquer method for scalable phylogenetic network inference from multilocus data. Bioinform. 35 (14) (2019)
Peng Du, Huw A. Ogilvie, Luay Nakhleh
Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks. ISBRA (2019)
Mohammad Amin Edrisi, Hamim Zafar, Luay Nakhleh
A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference. WABI (2019)
Zhen Cao, Jiafan Zhu, Luay Nakhleh
Empirical Performance of Tree-Based Inference of Phylogenetic Networks. WABI (2019)
Ryan A. Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, Luay Nakhleh
ALPHA: a toolkit for Automated Local PHylogenomic Analyses. Bioinform. 34 (16) (2018)
Peng Du, Luay Nakhleh
Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence Model. BCB (2018)
Jiafan Zhu, Luay Nakhleh
Inference of species phylogenies from bi-allelic markers using pseudo-likelihood. Bioinform. 34 (13) (2018)
Yaxuan Wang, Luay Nakhleh
Towards an accurate and efficient heuristic for species/gene tree co-estimation. Bioinform. 34 (17) (2018)
Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M. Meudt, Luay Nakhleh
Bayesian inference of phylogenetic networks from bi-allelic genetic markers. PLoS Comput. Biol. 14 (1) (2018)
Xian Fan, Jie Xu, Luay Nakhleh
Detecting Large Indels Using Optical Map Data. RECOMB-CG (2018)
Ryan A. Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, Luay Nakhleh
DGEN: A Test Statistic for Detection of General Introgression Scenarios. WABI (2018)
Ryan A. Leo Elworth, Luay Nakhleh
Inferring Local Genealogies on Closely Related Genomes. RECOMB-CG (2017)
Jiafan Zhu, Yun Yu, Luay Nakhleh
In the light of deep coalescence: revisiting trees within networks. BMC Bioinform. 17 (S-14) (2016)
Yun Yu, Luay Nakhleh
A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. ISBRA (2015)
Kevin J. Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H. Kohn, Luay Nakhleh
An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes. PLoS Comput. Biol. 10 (6) (2014)
Xian Fan, Wanding Zhou, Zechen Chong, Luay Nakhleh, Ken Chen
Towards accurate characterization of clonal heterogeneity based on structural variation. BMC Bioinform. 15 (2014)
Xian Fan, Luay Nakhleh, Ken Chen
Integrated genotyping of structural variation. GlobalSIP (2013)
Troy A. Ruths, Luay Nakhleh
Boosting forward-time population genetic simulators through genotype compression. BMC Bioinform. 14 (2013)
Luay Nakhleh, Noah A. Rosenberg, Tandy J. Warnow
Session introduction. Pacific Symposium on Biocomputing (2013)
Natalie Berestovsky, Wanding Zhou, Deepak Nagrath, Luay Nakhleh
Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks. PLoS Comput. Biol. 9 (11) (2013)
Yun Yu, Nikola Ristic, Luay Nakhleh
Fast algorithms and heuristics for phylogenomics under ILS and hybridization. BMC Bioinform. 14 (S-15) (2013)
Hyun Jung Park, Luay Nakhleh
Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria. BMC Bioinform. 13 (S-19) (2012)
Natalie Berestovsky, Riya Fukui, Luay Nakhleh
On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks. CIBCB (2012)
Yun Yu, Luay Nakhleh
Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting CoRR (2012)
Hyun Jung Park, Luay Nakhleh
MURPAR: A Fast Heuristic for Inferring Parsimonious Phylogenetic Networks from Multiple Gene Trees. ISBRA (2012)
Wanding Zhou, Luay Nakhleh
Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways. J. Chem. Inf. Model. 52 (10) (2012)
Yun Zhu, Luay Nakhleh
Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models. WABI (2012)
Wanding Zhou, Luay Nakhleh
The strength of chemical linkage as a criterion for pruning metabolic graphs. Bioinform. 27 (14) (2011)
Yun Yu, Tandy J. Warnow, Luay Nakhleh
Algorithms for MDC-Based Multi-locus Phylogeny Inference. RECOMB (2011)
Wanding Zhou, Luay Nakhleh
Properties of Metabolic Graphs: Biological Organization or Representation Artifacts? BMC Bioinform. 12 (2011)
Yun Yu, Tandy J. Warnow, Luay Nakhleh
Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles. J. Comput. Biol. 18 (11) (2011)
Luay Nakhleh
A Metric on the Space of Reduced Phylogenetic Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 7 (2) (2010)
Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic. IEEE ACM Trans. Comput. Biol. Bioinform. 6 (3) (2009)
Troy A. Ruths, Derek A. Ruths, Luay Nakhleh
: an efficiently computable measure of GO-based similarity of gene sets. Bioinform. 25 (9) (2009)
Cuong Than, Luay Nakhleh
Species Tree Inference by Minimizing Deep Coalescences. PLoS Comput. Biol. 5 (9) (2009)
Derek A. Ruths, Luay Nakhleh, Prahlad T. Ram
Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle. BMC Syst. Biol. 2 (2008)
Iyad A. Kanj, Luay Nakhleh, Cuong Than, Ge Xia
Seeing the trees and their branches in the network is hard. Theor. Comput. Sci. 401 (1-3) (2008)
Iyad A. Kanj, Luay Nakhleh, Ge Xia
The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms. Algorithmica 51 (2) (2008)
Cuong Than, Luay Nakhleh
SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. APBC (2008)
Cuong Than, Derek A. Ruths, Luay Nakhleh
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinform. 9 (2008)
Cuong Than, Guohua Jin, Luay Nakhleh
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. RECOMB-CG (2008)
Cuong Than, R. Sugino, Hideki Innan, Luay Nakhleh
Efficient inference of bacterial strain trees from genome-scale multilocus data. ISMB (2008)
Derek A. Ruths, Melissa Muller, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram
The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks. PLoS Comput. Biol. 4 (2) (2008)
Iyad A. Kanj, Luay Nakhleh, Cuong Than, Ge Xia
Seeing the Trees and Their Branches in the Forest is Hard. ICTCS (2007)
Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh
Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. J. Comput. Biol. 14 (4) (2007)
Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinform. 23 (2) (2007)
Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
Maximum likelihood of phylogenetic networks. Bioinform. 23 (8) (2007)
Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. ISBRA (2007)
Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh
Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. Comparative Genomics (2006)
Iyad A. Kanj, Luay Nakhleh, Ge Xia
Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms. COCOON (2006)
Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
Maximum likelihood of phylogenetic networks. Bioinform. 22 (21) (2006)
Derek A. Ruths, Luay Nakhleh, M. Sriram Iyengar, Shrikanth A. G. Reddy, Prahlad T. Ram
Hypothesis Generation in Signaling Networks. J. Comput. Biol. 13 (9) (2006)
Derek A. Ruths, Luay Nakhleh
RECOMP: A Parsimony-Based Method for Detecting Recombination. APBC (2006)
Yuri Dotsenko, Cristian Coarfa, Luay Nakhleh, John M. Mellor-Crummey, Usman Roshan
PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction. Int. J. Bioinform. Res. Appl. 2 (4) (2006)
Derek A. Ruths, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram
De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis. Systems Biology and Computational Proteomics (2006)
Derek A. Ruths, Luay Nakhleh
Techniques for Assessing Phylogenetic Branch Support: A Performance Study. APBC (2006)
Luay Nakhleh, Li-San Wang
Phylogenetic Networks, Trees, and Clusters. International Conference on Computational Science (2) (2005)
Derek A. Ruths, Luay Nakhleh
Recombination and phylogeny: effects and detection. Int. J. Bioinform. Res. Appl. 1 (2) (2005)
Luay Nakhleh, Li-San Wang
Phylogenetic Networks: Properties and Relationship to Trees and Clusters. Trans. Comp. Sys. Biology 2 (2005)
Cristian Coarfa, Yuri Dotsenko, John M. Mellor-Crummey, Luay Nakhleh, Usman Roshan
PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction. ICPADS (2) (2005)
Luay Nakhleh, Derek A. Ruths, Li-San Wang
RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. COCOON (2005)
Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Katherine St. John
Reconstructing Reticulate Evolution in SpeciesTheory and Practice. J. Comput. Biol. 12 (6) (2005)
Z. Du, Alexandros Stamatakis, F. Lin, Usman Roshan, Luay Nakhleh
Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood. HPCC (2005)
Luay Nakhleh, Guohua Jin, Fengmei Zhao, John M. Mellor-Crummey
Reconstructing Phylogenetic Networks Using Maximum Parsimony. CSB (2005)
Luay Nakhleh, Tandy J. Warnow, C. Randal Linder
Reconstructing reticulate evolution in species: theory and practice. RECOMB (2004)
Bernard M. E. Moret, Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun, Ruth E. Timme
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. IEEE ACM Trans. Comput. Biol. Bioinform. 1 (1) (2004)
Esra Erdem, Vladimir Lifschitz, Luay Nakhleh, Donald Ringe
Reconstructing the Evolutionary History of Indo-European Languages Using Answer Set Programming. PADL (2003)
Luay Nakhleh, Jerry Sun, Tandy J. Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse
Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. Pacific Symposium on Biocomputing (2003)
Luay Nakhleh, Daniel P. Miranker, François Barbançon, William H. Piel, Michael J. Donoghue
Requirements of Phylogenetic Databases. BIBE (2003)
Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy J. Warnow
Estimating the Deviation from a Molecular Clock. WABI (2002)
Luay Nakhleh, Bernard M. E. Moret, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow
The Accuracy of Fast Phylogenetic Methods for Large Datasets. Pacific Symposium on Biocomputing (2002)
Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow
Designing fast converging phylogenetic methods. ISMB (Supplement of Bioinformatics) (2001)
Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow
The Performance of Phylogenetic Methods on Trees of Bounded Diameter. WABI (2001)