Luay Nakhleh - RankMe

84 papers A 1B 5C 10Misc 6Journal 42Unranked 19

Year	Rank	Type	Title / Venue / Authors
2025	—	`conf`	Inferring Phylogenetic Trees of Cancer Evolution from Longitudinal Single-Cell Copy Number Profiles. RECOMB-CG Yushu Liu, Luay Nakhleh
2025	—	`conf`	tMHG-Finder: Tree-Guided Maximal Homologous Group Finder for Bacterial Genomes. RECOMB-CG Yongze Yin, Bryce Kille, Huw A. Ogilvie, Todd J. Treangen, Luay Nakhleh
2024	J	`jnl`	NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model. Algorithms Mol. Biol. Yushu Liu, Mohammad Amin Edrisi, Zhi Yan, Huw A. Ogilvie, Luay Nakhleh
2024	J	`jnl`	Polyphest: fast polyploid phylogeny estimation. Bioinform. Zhi Yan, Zhen Cao, Luay Nakhleh
2023	—	`conf`	MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural Networks. RECOMB-CG Mohammad Amin Edrisi, Huw A. Ogilvie, Meng Li, Luay Nakhleh
2022	J	`jnl`	Annotation-free delineation of prokaryotic homology groups. PLoS Comput. Biol. Yongze Yin, Huw A. Ogilvie, Luay Nakhleh
2022	—	`conf`	Phylogenetic Network Dissimilarity Measures that Take Branch Lengths into Account. RECOMB-CG Berk A. Yakici, Huw A. Ogilvie, Luay Nakhleh
2022	J	`jnl`	Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data. Bioinform. Mohammad Amin Edrisi, Monica V. Valecha, Sunkara B. V. Chowdary, Sergio Robledo, Huw A. Ogilvie, David Posada, Hamim Zafar, Luay Nakhleh
2022	J	`jnl`	SimSCSnTree: a simulator of single-cell DNA sequencing data. Bioinform. Xian F. Mallory, Luay Nakhleh
2020	J	`jnl`	Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data. PLoS Comput. Biol. Xian F. Mallory, Mohammad Amin Edrisi, Nicholas Navin, Luay Nakhleh
2019	C	`conf`	A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference. WABI Mohammad Amin Edrisi, Hamim Zafar, Luay Nakhleh
2019	J	`jnl`	A divide-and-conquer method for scalable phylogenetic network inference from multilocus data. Bioinform. Jiafan Zhu, Xinhao Liu, Huw A. Ogilvie, Luay Nakhleh
2019	C	`conf`	Empirical Performance of Tree-Based Inference of Phylogenetic Networks. WABI Zhen Cao, Jiafan Zhu, Luay Nakhleh
2019	—	`conf`	Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks. ISBRA Peng Du, Huw A. Ogilvie, Luay Nakhleh
2018	J	`jnl`	ALPHA: a toolkit for Automated Local PHylogenomic Analyses. Bioinform. Ryan A. Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, Luay Nakhleh
2018	J	`jnl`	Bayesian inference of phylogenetic networks from bi-allelic genetic markers. PLoS Comput. Biol. Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M. Meudt, Luay Nakhleh
2018	C	`conf`	DGEN: A Test Statistic for Detection of General Introgression Scenarios. WABI Ryan A. Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, Luay Nakhleh
2018	—	`conf`	Detecting Large Indels Using Optical Map Data. RECOMB-CG Xian Fan, Jie Xu, Luay Nakhleh
2018	J	`jnl`	Inference of species phylogenies from bi-allelic markers using pseudo-likelihood. Bioinform. Jiafan Zhu, Luay Nakhleh
2018	—	`conf`	Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence Model. BCB Peng Du, Luay Nakhleh
2018	J	`jnl`	Towards an accurate and efficient heuristic for species/gene tree co-estimation. Bioinform. Yaxuan Wang, Luay Nakhleh
2017	—	`ed.`	Comparative Genomics - 15th International Workshop, RECOMB CG 2017, Barcelona, Spain, October 4-6, 2017, Proceedings RECOMB-CG Joao Meidanis, Luay Nakhleh
2017	—	`conf`	Inferring Local Genealogies on Closely Related Genomes. RECOMB-CG Ryan A. Leo Elworth, Luay Nakhleh
2016	J	`jnl`	In the light of deep coalescence: revisiting trees within networks. BMC Bioinform. Jiafan Zhu, Yun Yu, Luay Nakhleh
2015	—	`conf`	A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. ISBRA Yun Yu, Luay Nakhleh
2014	J	`jnl`	An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes. PLoS Comput. Biol. Kevin J. Liu, Jingxuan Dai, Kathy Truong, Ying Song, Michael H. Kohn, Luay Nakhleh
2014	J	`jnl`	Towards accurate characterization of clonal heterogeneity based on structural variation. BMC Bioinform. Xian Fan, Wanding Zhou, Zechen Chong, Luay Nakhleh, Ken Chen
2013	J	`jnl`	Boosting forward-time population genetic simulators through genotype compression. BMC Bioinform. Troy A. Ruths, Luay Nakhleh
2013	J	`jnl`	Fast algorithms and heuristics for phylogenomics under ILS and hybridization. BMC Bioinform. Yun Yu, Nikola Ristic, Luay Nakhleh
2013	—	`conf`	Integrated genotyping of structural variation. GlobalSIP Xian Fan, Luay Nakhleh, Ken Chen
2013	J	`jnl`	Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks. PLoS Comput. Biol. Natalie Berestovsky, Wanding Zhou, Deepak Nagrath, Luay Nakhleh
2013	Misc	`conf`	Session introduction. Pacific Symposium on Biocomputing Luay Nakhleh, Noah A. Rosenberg, Tandy J. Warnow
2012	J	`jnl`	Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting CoRR Yun Yu, Luay Nakhleh
2012	J	`jnl`	Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria. BMC Bioinform. Hyun Jung Park, Luay Nakhleh
2012	—	`conf`	MURPAR: A Fast Heuristic for Inferring Parsimonious Phylogenetic Networks from Multiple Gene Trees. ISBRA Hyun Jung Park, Luay Nakhleh
2012	C	`conf`	On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks. CIBCB Natalie Berestovsky, Riya Fukui, Luay Nakhleh
2012	J	`jnl`	Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways. J. Chem. Inf. Model. Wanding Zhou, Luay Nakhleh
2012	C	`conf`	Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models. WABI Yun Zhu, Luay Nakhleh
2011	J	`jnl`	Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles. J. Comput. Biol. Yun Yu, Tandy J. Warnow, Luay Nakhleh
2011	B	`conf`	Algorithms for MDC-Based Multi-locus Phylogeny Inference. RECOMB Yun Yu, Tandy J. Warnow, Luay Nakhleh
2011	J	`jnl`	Properties of Metabolic Graphs: Biological Organization or Representation Artifacts? BMC Bioinform. Wanding Zhou, Luay Nakhleh
2011	J	`jnl`	The strength of chemical linkage as a criterion for pruning metabolic graphs. Bioinform. Wanding Zhou, Luay Nakhleh
2010	J	`jnl`	A Metric on the Space of Reduced Phylogenetic Networks. IEEE ACM Trans. Comput. Biol. Bioinform. Luay Nakhleh
2009	J	`jnl`	GS Bioinform. Troy A. Ruths, Derek A. Ruths, Luay Nakhleh
2009	J	`jnl`	Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic. IEEE ACM Trans. Comput. Biol. Bioinform. Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
2009	J	`jnl`	Species Tree Inference by Minimizing Deep Coalescences. PLoS Comput. Biol. Cuong Than, Luay Nakhleh
2008	A	`conf`	Efficient inference of bacterial strain trees from genome-scale multilocus data. ISMB Cuong Than, R. Sugino, Hideki Innan, Luay Nakhleh
2008	—	`conf`	Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. RECOMB-CG Cuong Than, Guohua Jin, Luay Nakhleh
2008	J	`jnl`	PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinform. Cuong Than, Derek A. Ruths, Luay Nakhleh
2008	J	`jnl`	Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle. BMC Syst. Biol. Derek A. Ruths, Luay Nakhleh, Prahlad T. Ram
2008	B	`conf`	SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. APBC Cuong Than, Luay Nakhleh
2008	J	`jnl`	Seeing the trees and their branches in the network is hard. Theor. Comput. Sci. Iyad A. Kanj, Luay Nakhleh, Cuong Than, Ge Xia
2008	J	`jnl`	The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms. Algorithmica Iyad A. Kanj, Luay Nakhleh, Ge Xia
2008	J	`jnl`	The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks. PLoS Comput. Biol. Derek A. Ruths, Melissa Muller, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram
2007	—	`conf`	A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance. ISBRA Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
2007	J	`jnl`	Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. J. Comput. Biol. Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh
2007	J	`jnl`	Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinform. Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
2007	J	`jnl`	Maximum likelihood of phylogenetic networks. Bioinform. Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
2007	—	`conf`	Seeing the Trees and Their Branches in the Forest is Hard. ICTCS Iyad A. Kanj, Luay Nakhleh, Cuong Than, Ge Xia
2006	—	`conf`	De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis. Systems Biology and Computational Proteomics Derek A. Ruths, Jen-Te Tseng, Luay Nakhleh, Prahlad T. Ram
2006	J	`jnl`	Hypothesis Generation in Signaling Networks. J. Comput. Biol. Derek A. Ruths, Luay Nakhleh, M. Sriram Iyengar, Shrikanth A. G. Reddy, Prahlad T. Ram
2006	—	`conf`	Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. Comparative Genomics Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh
2006	J	`jnl`	Maximum likelihood of phylogenetic networks. Bioinform. Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
2006	J	`jnl`	PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction. Int. J. Bioinform. Res. Appl. Yuri Dotsenko, Cristian Coarfa, Luay Nakhleh, John M. Mellor-Crummey, Usman Roshan
2006	B	`conf`	RECOMP: A Parsimony-Based Method for Detecting Recombination. APBC Derek A. Ruths, Luay Nakhleh
2006	Misc	`conf`	Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms. COCOON Iyad A. Kanj, Luay Nakhleh, Ge Xia
2006	B	`conf`	Techniques for Assessing Phylogenetic Branch Support: A Performance Study. APBC Derek A. Ruths, Luay Nakhleh
2005	—	`conf`	PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction. ICPADS (2) Cristian Coarfa, Yuri Dotsenko, John M. Mellor-Crummey, Luay Nakhleh, Usman Roshan
2005	C	`conf`	Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood. HPCC Z. Du, Alexandros Stamatakis, F. Lin, Usman Roshan, Luay Nakhleh
2005	Misc	`conf`	Phylogenetic Networks, Trees, and Clusters. International Conference on Computational Science (2) Luay Nakhleh, Li-San Wang
2005	J	`jnl`	Phylogenetic Networks: Properties and Relationship to Trees and Clusters. Trans. Comp. Sys. Biology Luay Nakhleh, Li-San Wang
2005	Misc	`conf`	RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. COCOON Luay Nakhleh, Derek A. Ruths, Li-San Wang
2005	J	`jnl`	Recombination and phylogeny: effects and detection. Int. J. Bioinform. Res. Appl. Derek A. Ruths, Luay Nakhleh
2005	—	`conf`	Reconstructing Phylogenetic Networks Using Maximum Parsimony. CSB Luay Nakhleh, Guohua Jin, Fengmei Zhao, John M. Mellor-Crummey
2005	J	`jnl`	Reconstructing Reticulate Evolution in SpeciesTheory and Practice. J. Comput. Biol. Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Katherine St. John
2004	J	`jnl`	Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. IEEE ACM Trans. Comput. Biol. Bioinform. Bernard M. E. Moret, Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Anna Tholse, Anneke Padolina, Jerry Sun, Ruth E. Timme
2004	B	`conf`	Reconstructing reticulate evolution in species: theory and practice. RECOMB Luay Nakhleh, Tandy J. Warnow, C. Randal Linder
2003	C	`conf`	Reconstructing the Evolutionary History of Indo-European Languages Using Answer Set Programming. PADL Esra Erdem, Vladimir Lifschitz, Luay Nakhleh, Donald Ringe
2003	C	`conf`	Requirements of Phylogenetic Databases. BIBE Luay Nakhleh, Daniel P. Miranker, François Barbançon, William H. Piel, Michael J. Donoghue
2003	Misc	`conf`	Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods. Pacific Symposium on Biocomputing Luay Nakhleh, Jerry Sun, Tandy J. Warnow, C. Randal Linder, Bernard M. E. Moret, Anna Tholse
2002	C	`conf`	Estimating the Deviation from a Molecular Clock. WABI Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy J. Warnow
2002	Misc	`conf`	The Accuracy of Fast Phylogenetic Methods for Large Datasets. Pacific Symposium on Biocomputing Luay Nakhleh, Bernard M. E. Moret, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow
2001	—	`conf`	Designing fast converging phylogenetic methods. ISMB (Supplement of Bioinformatics) Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow
2001	C	`conf`	The Performance of Phylogenetic Methods on Trees of Bounded Diameter. WABI Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow