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Luay Nakhleh
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- affiliation: Rice University, Houston, TX, USA
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2020 – today
- 2024
- [j39]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): 18 (2024) - 2023
- [c39]Mohammad Amin Edrisi
, Huw A. Ogilvie
MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive Neural Networks. RECOMB-CG 2023: 232-247 - 2022
- [j38]Xian F. Mallory
SimSCSnTree: a simulator of single-cell DNA sequencing data. Bioinform. 38(10): 2912-2914 (2022) - [j37]Yongze Yin
Annotation-free delineation of prokaryotic homology groups. PLoS Comput. Biol. 18(6) (2022) - [c38]Berk A. Yakici
Phylogenetic Network Dissimilarity Measures that Take Branch Lengths into Account. RECOMB-CG 2022: 86-102 - 2020
- [j36]Xian F. Mallory
Assessing the performance of methods for copy number aberration detection from single-cell DNA sequencing data. PLoS Comput. Biol. 16(7) (2020)
2010 – 2019
- 2019
- [j35]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): i370-i378 (2019) - [c37]Peng Du, Huw A. Ogilvie, Luay Nakhleh:
Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks. ISBRA 2019: 40-51 - [c36]Zhen Cao, Jiafan Zhu, Luay Nakhleh
Empirical Performance of Tree-Based Inference of Phylogenetic Networks. WABI 2019: 21:1-21:13 - [c35]Mohammad Amin Edrisi
A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic Inference. WABI 2019: 22:1-22:13 - 2018
- [j34]Jiafan Zhu, Luay Nakhleh:
Inference of species phylogenies from bi-allelic markers using pseudo-likelihood. Bioinform. 34(13): i376-i385 (2018) - [j33]Ryan A. Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, Luay Nakhleh:
ALPHA: a toolkit for Automated Local PHylogenomic Analyses. Bioinform. 34(16): 2848-2850 (2018) - [j32]Yaxuan Wang, Luay Nakhleh:
Towards an accurate and efficient heuristic for species/gene tree co-estimation. Bioinform. 34(17): i697-i705 (2018) - [j31]Jiafan Zhu, Dingqiao Wen, Yun Yu, Heidi M. Meudt
Bayesian inference of phylogenetic networks from bi-allelic genetic markers. PLoS Comput. Biol. 14(1) (2018) - [c34]Peng Du, Luay Nakhleh:
Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence Model. BCB 2018: 376-385 - [c33]Xian Fan, Jie Xu, Luay Nakhleh:
Detecting Large Indels Using Optical Map Data. RECOMB-CG 2018: 108-127 - [c32]Ryan A. Leo Elworth, Chabrielle Allen, Travis Benedict, Peter Dulworth, Luay Nakhleh:
DGEN: A Test Statistic for Detection of General Introgression Scenarios. WABI 2018: 19:1-19:13 - 2017
- [c31]Ryan A. Leo Elworth, Luay Nakhleh:
Inferring Local Genealogies on Closely Related Genomes. RECOMB-CG 2017: 213-231 - [e1]Joao Meidanis, Luay Nakhleh:
Comparative Genomics - 15th International Workshop, RECOMB CG 2017, Barcelona, Spain, October 4-6, 2017, Proceedings. Lecture Notes in Computer Science 10562, Springer 2017, ISBN 978-3-319-67978-5 [contents] - 2016
- [j30]Jiafan Zhu, Yun Yu, Luay Nakhleh:
In the light of deep coalescence: revisiting trees within networks. BMC Bioinform. 17(S-14): 271-282 (2016) - 2015
- [c30]Yun Yu, Luay Nakhleh:
A Distance-Based Method for Inferring Phylogenetic Networks in the Presence of Incomplete Lineage Sorting. ISBRA 2015: 378-389 - 2014
- [j29]Xian Fan
Towards accurate characterization of clonal heterogeneity based on structural variation. BMC Bioinform. 15: 299 (2014) - [j28]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) - 2013
- [j27]Troy A. Ruths, Luay Nakhleh:
Boosting forward-time population genetic simulators through genotype compression. BMC Bioinform. 14: 192 (2013) - [j26]Yun Yu, Nikola Ristic, Luay Nakhleh:
Fast algorithms and heuristics for phylogenomics under ILS and hybridization. BMC Bioinform. 14(S-15): S6 (2013) - [j25]Natalie Berestovsky, Wanding Zhou, Deepak Nagrath
Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks. PLoS Comput. Biol. 9(11) (2013) - [c29]Xian Fan, Luay Nakhleh, Ken Chen
Integrated genotyping of structural variation. GlobalSIP 2013: 47-48 - [c28]Luay Nakhleh, Noah A. Rosenberg, Tandy J. Warnow:
Session introduction. Pacific Symposium on Biocomputing 2013: 247-249 - 2012
- [j24]Hyun Jung Park
Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria. BMC Bioinform. 13(S-19): S12 (2012) - [j23]Wanding Zhou, Luay Nakhleh:
Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways. J. Chem. Inf. Model. 52(10): 2684-2696 (2012) - [c27]Natalie Berestovsky, Riya Fukui, Luay Nakhleh:
On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks. CIBCB 2012: 184-191 - [c26]Hyun Jung Park
MURPAR: A Fast Heuristic for Inferring Parsimonious Phylogenetic Networks from Multiple Gene Trees. ISBRA 2012: 213-224 - [c25]Yun Zhu, Luay Nakhleh:
Reconstructing the Evolution of Molecular Interaction Networks under the DMC and Link Dynamics Models. WABI 2012: 57-68 - [i1]Yun Yu, Luay Nakhleh:
Fast Algorithms for Reconciliation under Hybridization and Incomplete Lineage Sorting. CoRR abs/1212.1909 (2012) - 2011
- [j22]Wanding Zhou, Luay Nakhleh:
The strength of chemical linkage as a criterion for pruning metabolic graphs. Bioinform. 27(14): 1957-1963 (2011) - [j21]Wanding Zhou, Luay Nakhleh:
Properties of Metabolic Graphs: Biological Organization or Representation Artifacts? BMC Bioinform. 12: 132 (2011) - [j20]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): 1543-1559 (2011) - [c24]Yun Yu, Tandy J. Warnow, Luay Nakhleh:
Algorithms for MDC-Based Multi-locus Phylogeny Inference. RECOMB 2011: 531-545 - 2010
- [j19]Luay Nakhleh:
A Metric on the Space of Reduced Phylogenetic Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 7(2): 218-222 (2010)
2000 – 2009
- 2009
- [j18]Troy A. Ruths, Derek A. Ruths, Luay Nakhleh:
GS2: an efficiently computable measure of GO-based similarity of gene sets. Bioinform. 25(9): 1178-1184 (2009) - [j17]Cuong Than, Luay Nakhleh:
Species Tree Inference by Minimizing Deep Coalescences. PLoS Comput. Biol. 5(9) (2009) - [j16]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): 495-505 (2009) - 2008
- [j15]Iyad A. Kanj, Luay Nakhleh, Ge Xia:
The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms. Algorithmica 51(2): 99-128 (2008) - [j14]Cuong Than, Derek A. Ruths, Luay Nakhleh:
PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships. BMC Bioinform. 9 (2008) - [j13]Derek A. Ruths, Luay Nakhleh, Prahlad T. Ram
Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle. BMC Syst. Biol. 2: 76 (2008) - [j12]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) - [j11]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): 153-164 (2008) - [c23]Cuong Than, Luay Nakhleh:
SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions. APBC 2008: 251-260 - [c22]Cuong Than, R. Sugino, Hideki Innan
Efficient inference of bacterial strain trees from genome-scale multilocus data. ISMB 2008: 123-131 - [c21]Cuong Than, Guohua Jin, Luay Nakhleh:
Integrating Sequence and Topology for Efficient and Accurate Detection of Horizontal Gene Transfer. RECOMB-CG 2008: 113-127 - 2007
- [j10]Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
Efficient parsimony-based methods for phylogenetic network reconstruction. Bioinform. 23(2): 123-128 (2007) - [j9]Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller:
Maximum likelihood of phylogenetic networks. Bioinform. 23(8): 1046-1047 (2007) - [j8]Cuong Than, Derek A. Ruths, Hideki Innan
Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions. J. Comput. Biol. 14(4): 517-535 (2007) - [c20]Iyad A. Kanj, Luay Nakhleh, Cuong Than, Ge Xia:
Seeing the Trees and Their Branches in the Forest is Hard. ICTCS 2007: 82-93 - [c19]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: 61-72 - 2006
- [j7]Guohua Jin, Luay Nakhleh, Sagi Snir, Tamir Tuller
Maximum likelihood of phylogenetic networks. Bioinform. 22(21): 2604-2611 (2006) - [j6]Yuri Dotsenko, Cristian Coarfa, Luay Nakhleh, John M. Mellor-Crummey
PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction. Int. J. Bioinform. Res. Appl. 2(4): 407-419 (2006) - [j5]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): 1546-1557 (2006) - [c18]Derek A. Ruths, Luay Nakhleh:
RECOMP: A Parsimony-Based Method for Detecting Recombination. APBC 2006: 59-68 - [c17]Derek A. Ruths, Luay Nakhleh:
Techniques for Assessing Phylogenetic Branch Support: A Performance Study. APBC 2006: 187-196 - [c16]Iyad A. Kanj, Luay Nakhleh, Ge Xia:
Reconstructing Evolution of Natural Languages: Complexity and Parameterized Algorithms. COCOON 2006: 299-308 - [c15]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: 108-118 - [c14]Cuong Than, Derek A. Ruths, Hideki Innan, Luay Nakhleh:
Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer. Comparative Genomics 2006: 215-229 - 2005
- [j4]Derek A. Ruths, Luay Nakhleh:
Recombination and phylogeny: effects and detection. Int. J. Bioinform. Res. Appl. 1(2): 202-212 (2005) - [j3]Luay Nakhleh, Tandy J. Warnow, C. Randal Linder, Katherine St. John
Reconstructing Reticulate Evolution in SpeciesTheory and Practice. J. Comput. Biol. 12(6): 796-811 (2005) - [j2]Luay Nakhleh, Li-San Wang:
Phylogenetic Networks: Properties and Relationship to Trees and Clusters. Trans. Comp. Sys. Biology 2: 82-99 (2005) - [c13]Luay Nakhleh, Derek A. Ruths, Li-San Wang:
RIATA-HGT: A Fast and Accurate Heuristic for Reconstructing Horizontal Gene Transfer. COCOON 2005: 84-93 - [c12]Luay Nakhleh, Guohua Jin, Fengmei Zhao, John M. Mellor-Crummey
Reconstructing Phylogenetic Networks Using Maximum Parsimony. CSB 2005: 93-102 - [c11]Z. Du, Alexandros Stamatakis
Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood. HPCC 2005: 776-785 - [c10]Luay Nakhleh, Li-San Wang:
Phylogenetic Networks, Trees, and Clusters. International Conference on Computational Science (2) 2005: 919-926 - [c9]Cristian Coarfa, Yuri Dotsenko, John M. Mellor-Crummey
PRec-I-DCM3: A Parallel Framework for Fast and Accurate Large Scale Phylogeny Reconstruction. ICPADS (2) 2005: 346-350 - 2004
- [j1]Bernard M. E. Moret
Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy. IEEE ACM Trans. Comput. Biol. Bioinform. 1(1): 13-23 (2004) - [c8]Luay Nakhleh, Tandy J. Warnow, C. Randal Linder:
Reconstructing reticulate evolution in species: theory and practice. RECOMB 2004: 337-346 - 2003
- [c7]Luay Nakhleh, Daniel P. Miranker, François Barbançon, William H. Piel, Michael J. Donoghue:
Requirements of Phylogenetic Databases. BIBE 2003: 141-148 - [c6]Esra Erdem, Vladimir Lifschitz, Luay Nakhleh, Donald Ringe:
Reconstructing the Evolutionary History of Indo-European Languages Using Answer Set Programming. PADL 2003: 160-176 - [c5]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: 315-326 - 2002
- [c4]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: 211-222 - [c3]Luay Nakhleh, Usman Roshan, Lisa Vawter, Tandy J. Warnow:
Estimating the Deviation from a Molecular Clock. WABI 2002: 287-299 - 2001
- [c2]Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow:
Designing fast converging phylogenetic methods. ISMB (Supplement of Bioinformatics) 2001: 190-198 - [c1]Luay Nakhleh, Usman Roshan, Katherine St. John, Jerry Sun, Tandy J. Warnow:
The Performance of Phylogenetic Methods on Trees of Bounded Diameter. WABI 2001: 214-226
Coauthor Index
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