Luay Nakhleh
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Computer Science
Luay Nakhleh's Degrees
- PhD Computer Science Stanford University
- Masters Computer Science Stanford University
- Bachelors Computer Science Stanford University
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Why Is Luay Nakhleh Influential?
(Suggest an Edit or Addition)According to Wikipedia, Luay K. Nakhleh : لؤي نخله; born May 8, 1974 Biography Nakhleh was born on May 8, 1974, to a Christian, Palestinian family in Israel. He currently lives with his Japanese wife and two children in Texas, and holds both U.S. and Israeli citizenship.
Luay Nakhleh's Published Works
Number of citations in a given year to any of this author's works
Total number of citations to an author for the works they published in a given year. This highlights publication of the most important work(s) by the author
Published Works
- PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships (2008) (369)
- Maximum likelihood inference of reticulate evolutionary histories (2014) (218)
- Species Tree Inference by Minimizing Deep Coalescences (2009) (199)
- Phylogenetic networks (2004) (198)
- Networks: expanding evolutionary thinking. (2013) (192)
- Computational approaches to species phylogeny inference and gene tree reconciliation. (2013) (188)
- Phylogenetic networks: modeling, reconstructibility, and accuracy (2004) (186)
- Coalescent histories on phylogenetic networks and detection of hybridization despite incomplete lineage sorting. (2011) (186)
- The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection (2012) (185)
- Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages (2005) (178)
- Identification of Three Distinct Phylogenetic Groups of CAX Cation/Proton Antiporters (2006) (175)
- Inferring Phylogenetic Networks Using PhyloNet (2017) (174)
- Reconstructing reticulate evolution in species: theory and practice (2004) (171)
- Irrational exuberance for resolved species trees (2016) (153)
- A maximum pseudo-likelihood approach for phylogenetic networks (2015) (149)
- Maximum likelihood of phylogenetic networks (2006) (129)
- Monovar: single nucleotide variant detection in single cells (2016) (127)
- Evolutionary Phylogenetic Networks: Models and Issues (2010) (120)
- SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models (2017) (118)
- Parsimonious inference of hybridization in the presence of incomplete lineage sorting. (2013) (111)
- The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks (2008) (107)
- Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data (2018) (98)
- Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis (2016) (94)
- Embracing heterogeneity: coalescing the Tree of Life and the future of phylogenomics (2019) (92)
- Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent (2016) (90)
- Inferring phylogenetic networks by the maximum parsimony criterion: a case study. (2006) (88)
- RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer (2005) (88)
- Seeing the trees and their branches in the network is hard (2007) (87)
- Interspecific introgressive origin of genomic diversity in the house mouse (2013) (86)
- Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions (2007) (84)
- Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles (2011) (78)
- SiCloneFit: Bayesian inference of population structure, genotype, and phylogeny of tumor clones from single-cell genome sequencing data (2018) (75)
- A comparison of phylogenetic reconstruction methods on an Indo‐European dataset (2005) (74)
- Towards the Development of Computational Tools for Evaluating Phylogenetic Network Reconstruction Methods (2002) (74)
- Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling (2011) (70)
- Reconstructing phylogenetic networks using maximum parsimony (2005) (68)
- Designing fast converging phylogenetic methods (2001) (67)
- Efficient parsimony-based methods for phylogenetic network reconstruction (2007) (58)
- Advances in Computational Methods for Phylogenetic Networks in the Presence of Hybridization (2018) (56)
- An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes (2013) (55)
- An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data (2013) (54)
- Reconstructing Reticulate Evolution in SpeciesTheory and Practice (2005) (54)
- An experimental study comparing linguistic phylogenetic reconstruction methods (2013) (54)
- GS2: an efficiently computable measure of GO-based similarity of gene sets (2009) (49)
- A Metric on the Space of Reduced Phylogenetic Networks (2010) (48)
- Mutations in Global Regulators Lead to Metabolic Selection during Adaptation to Complex Environments (2014) (47)
- Bayesian inference of phylogenetic networks from bi-allelic genetic markers (2017) (45)
- Fast algorithms and heuristics for phylogenomics under ILS and hybridization (2013) (43)
- The Accuracy of Fast Phylogenetic Methods for Large Datasets (2001) (42)
- In the light of deep coalescence: revisiting trees within networks (2016) (41)
- Properties of metabolic graphs: biological organization or representation artifacts? (2011) (40)
- Methods for copy number aberration detection from single-cell DNA-sequencing data (2019) (40)
- A STOCHASTIC MODEL OF LANGUAGE EVOLUTION THAT INCORPORATES HOMOPLASY AND BORROWING (2005) (40)
- Population genomics in bacteria: a case study of Staphylococcus aureus. (2012) (39)
- Reconstructing the Evolutionary History of Indo-European Languages Using Answer Set Programming (2003) (36)
- Network (Reticulated) Evolution: Biology, Models, and Algorithms (2004) (32)
- HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies. (2017) (31)
- Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time Heuristic (2009) (31)
- Hypothesis Generation in Signaling Networks (2006) (30)
- Requirements of phylogenetic databases (2003) (29)
- Algorithms for MDC-Based Multi-locus Phylogeny Inference (2011) (28)
- Computational approaches for inferring tumor evolution from single-cell genomic data (2018) (28)
- Recombination and phylogeny: effects and detection (2005) (28)
- Methods for copy number aberration detection from single-cell DNA-sequencing data (2020) (28)
- Inference of species phylogenies from bi-allelic markers using pseudo-likelihood (2018) (27)
- Species Tree Inference under the Multispecies Coalescent on Data with Paralogs is Accurate (2018) (27)
- Co-estimating Reticulate Phylogenies and Gene Trees from Multi-locus Sequence Data (2017) (23)
- Practical Aspects of Phylogenetic Network Analysis Using PhyloNet (2019) (23)
- Current progress and open challenges for applying deep learning across the biosciences (2022) (22)
- Species Tree Inference on Data with Paralogs is Accurate Using Methods Intended to Deal with Incomplete Lineage Sorting (2018) (22)
- A Comparison of Phylogenetic Reconstruction Methods on an IE Dataset (2004) (22)
- Efficient inference of bacterial strain trees from genome-scale multilocus data (2008) (20)
- Convergent evolution of modularity in metabolic networks through different community structures (2012) (20)
- The Performance of Phylogenetic Methods on Trees of Bounded Diameter (2001) (20)
- Matrilysin/MMP-7 Cleavage of Perlecan/HSPG2 Complexed with Semaphorin 3A Supports FAK-Mediated Stromal Invasion by Prostate Cancer Cells (2018) (20)
- Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data (2020) (19)
- Bootstrap-based Support of HGT Inferred by Maximum Parsimony (2010) (18)
- DGEN: A Test Statistic for Detection of General Introgression Scenarios (2018) (18)
- Gene Trees, Species Trees, and Species Networks (2005) (18)
- Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle (2008) (16)
- SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions (2007) (16)
- Evolution After Whole-Genome Duplication: A Network Perspective (2013) (16)
- Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks (2013) (16)
- Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria (2012) (15)
- Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology (2013) (15)
- Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood (2005) (14)
- A divide-and-conquer method for scalable phylogenetic network inference from multilocus data (2019) (14)
- Species Tree Inference Methods Intended to Deal with Incomplete Lineage Sorting Are Robust to the Presence of Paralogs (2021) (13)
- A New Linear-Time Heuristic Algorithm for Computing the Parsimony Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance (2007) (13)
- Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks (2019) (13)
- Towards accurate characterization of clonal heterogeneity based on structural variation (2014) (12)
- Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence Model (2018) (12)
- Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer (2006) (12)
- Efficient parsimony-based methods for phylogenetic network (2006) (11)
- Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer (2008) (11)
- Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways (2012) (11)
- PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction (2005) (10)
- A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting (2015) (10)
- A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference (2019) (9)
- Inference of parsimonious species phylogenies from multi-locus data (2010) (9)
- ncDNA and drift drive binding site accumulation (2012) (9)
- Multispecies Coalescent: Theory and Applications in Phylogenetics (2021) (9)
- ALGORITHMIC STRATEGIES FOR ESTIMATING THE AMOUNT OF RETICULATION FROM A COLLECTION OF GENE TREES (2010) (9)
- Markov chains and hidden Markov models (2002) (9)
- RECOMP: A Parsimony-Based Method for Detecting Recombination (2005) (8)
- MURPAR: A Fast Heuristic for Inferring Parsimonious Phylogenetic Networks from Multiple Gene Trees (2012) (8)
- De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction, Targeted Therapy and Protein Microarray Analysis (2006) (8)
- Phylogenetic Networks: Properties and Relationship to Trees and Clusters (2005) (8)
- Phylogenomic assessment of the role of hybridization and introgression in trait evolution (2020) (7)
- Mapping Network Motif Tunability and Robustness in the Design of Synthetic Signaling Circuits (2014) (7)
- Towards an accurate and efficient heuristic for species/gene tree co‐estimation (2018) (7)
- Phylogenetic Networks, Trees, and Clusters (2005) (6)
- Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting (2012) (6)
- SiFit: A Method for Inferring Tumor Trees from Single-Cell Sequencing Data under Finite-site Models (2016) (6)
- Boosting forward-time population genetic simulators through genotype compression (2013) (6)
- Empirical Performance of Tree-based Inference of Phylogenetic Networks (2019) (5)
- Estimating the Deviation from a Molecular Clock (2002) (5)
- The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms (2008) (5)
- Correction: Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent (2017) (5)
- Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms (2006) (4)
- Techniques for Assessing Phylogenetic Branch Support: A Performance Study (2005) (4)
- Variational inference using approximate likelihood under the coalescent with recombination (2020) (4)
- The strength of chemical linkage as a criterion for pruning metabolic graphs (2011) (4)
- Detecting Large Indels Using Optical Map Data (2018) (4)
- Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models (2012) (3)
- NestedBD: Bayesian Inference of Phylogenetic Trees From Single-Cell DNA Copy Number Profile Data Under a Birth-Death Model (2022) (3)
- Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes (2020) (3)
- Gene Duplicability-Connectivity-Complexity across Organisms and a Neutral Evolutionary Explanation (2012) (3)
- SimSCSnTree: a simulator of single-cell DNA sequencing data (2022) (3)
- Practical Speedup of Bayesian Inference of Species Phylogenies by Restricting the Space of Gene Trees (2019) (2)
- ALPHA: a toolkit for Automated Local PHylogenomic Analyses (2018) (2)
- A Divide-and-Conquer Method for Scalable Phylogenetic Network Inference from Multi-locus Data (2019) (2)
- Phylovar: toward scalable phylogeny-aware inference of single-nucleotide variations from single-cell DNA sequencing data (2022) (2)
- Deriving executable models of biochemical network dynamics from qualitative data (2009) (2)
- Comments on the model parameters in “SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models” (2019) (1)
- A maximum pseudo-likelihood approach for phylogenetic networks (2015) (1)
- Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks (2016) (1)
- HySA: A Hybrid Structural variant Assembly approach using next generation and single-molecule sequencing technologies (2016) (1)
- Data from: Co-estimating reticulate phylogenies and gene trees from multi-locus sequence data (2017) (1)
- Seeing the Trees and Their Branches in the Forest is Hard (2007) (1)
- Fast algorithms and heuristics for phylogenomics under ILS and hybridization (2013) (1)
- Integrated likelihood for phylogenomics under a no-common-mechanism model (2018) (1)
- Supporting per-locus substitution rates improves the accuracy of species networks and avoids spurious reticulations (2022) (1)
- Boosting forward-time population genetic simulators through genotype compression (2013) (1)
- Inferring Local Genealogies on Closely Related Genomes (2017) (1)
- ncDNA and drift drive binding site accumulation (2012) (1)
- Towards accurate characterization of clonal heterogeneity based on structural variation (2014) (1)
- Accurate Inference of Phylogenetic Relationships from Multi-locus Data (2010) (0)
- Phylogenomics and population genomics: Moddels, algorithms, and analytical tools (2012) (0)
- Comments on the model parameters in “SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models” (2019) (0)
- Problems Turing Machines and ( Un ) (0)
- MaCroDNA: Accurate integration of single-cell DNA and RNA data for a deeper understanding of tumor heterogeneity (2023) (0)
- On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks (2012) (0)
- 226. Next-Generation Sleeping Beauty Integration Profiles of T-Cell Adoptive Immunotherapy (2015) (0)
- 3 . 2 Example : Graph Traversal Time (2019) (0)
- Reconstructing Domain Compositions of Ancestral Multi-domain Proteins Behshad Behzadi and Martin Vingron Domain Architecture in Homolog Identification (2006) (0)
- Comparing Inference under the Multispecies Coalescent with and without Recombination. (2023) (0)
- Phylogenetic Network Dissimilarity Measures That Take Branch Lengths Into Account (2022) (0)
- Annotation-free delineation of prokaryotic homology groups (2022) (0)
- In the light of deep coalescence: revisiting trees within networks (2016) (0)
- Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks (2016) (0)
- Motifs in cellular networks : case studies (2013) (0)
- Efficient sampling in networks (2015) (0)
- “Correcting” gene trees to be more like species trees increases topological error when incomplete lineage sorting is high (2022) (0)
- Matrilysin/MMP-7 Cleavage of Perlecan/HSPG2 Complexed with Semaphorin 3A Supports FAK-Mediated Stromal Invasion by Prostate Cancer Cells (2018) (0)
- Supplementary-Material for the work Maximum Likelihood of Phylogenetic Networks (2006) (0)
- SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models (2017) (0)
- Convergent evolution of modularity in metabolic networks through different community structures (2012) (0)
- Stranger in a strange land: the experiences of immigrant researchers (2017) (0)
- Generating Metabolic-Signaling Network Hypotheses Using ODE and Petri Net Simulations (2007) (0)
- MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural Networks (2022) (0)
- Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria (2012) (0)
- Towards accurate reconstruction of phylogenetic networks (2012) (0)
- Algorithmic Thinking Prim and Dijkstra : Efficiency and Correctness (2018) (0)
- Integrated genotyping of structural variation (2013) (0)
- CHAPTER 1 Gene Trees , Species Trees , and Species Networks (2005) (0)
- COMP 182 : Algorithmic Thinking Markov Chains and Hidden Markov Models (2018) (0)
- The Multispecies Network Coalescent and Phylogenetic Network Inference (2016) (0)
- The Impact of Model Misspecification on Phylogenetic Network Inference (2022) (0)
- Abstract 1563: Interplay between perlecan/HSPG2 and matrilysin/MMP-7 in the prostate cancer tumor microenvironment directs metastatic programming through focal adhesion kinase and FoxM1 (2016) (0)
- Stranger in a strange land: the experiences of immigrant researchers (2017) (0)
- Sequence Alignment : Scoring Schemes COMP 571-Spring 2016 (2016) (0)
- Comparing Inference under the MSC versus the MSC-with-Recombination (2022) (0)
- Integration of functional proteomics with discrete non-parametric token-based modeling to identify combinational therapies targeting EGFR homeostatic loops in breast cancer cells (2007) (0)
- COMP 182 : Algorithmic Thinking Dynamic Programming (2016) (0)
- ncDNA and drift drive binding site (2012) (0)
- Tools for Accurate and Efficient Analysis of Complex Evolutionary Mechanisms in Microbial Genomes. Final Report (2014) (0)
- SimSCSnTree: a simulator of single-cell DNA sequencing data. (2022) (0)
- 212. Of States and Fates: Predicting T-Cell Immunity By the Numbers (2015) (0)
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