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ORCIDBibTeX records: Luay Nakhleh
@inproceedings{DBLP:conf/recombcg/EdrisiOLN23,
author = {Mohammad Amin Edrisi and
Huw A. Ogilvie and
Meng Li and
Luay Nakhleh},
editor = {Katharina Jahn and
Tom{\'{a}}s Vinar},
title = {MoTERNN: Classifying the Mode of Cancer Evolution Using Recursive
Neural Networks},
booktitle = {Comparative Genomics - 20th International Conference, {RECOMB-CG}
2023, Istanbul, Turkey, April 14-15, 2023, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13883},
pages = {232--247},
publisher = {Springer},
year = {2023},
url = {https://doi.org/10.1007/978-3-031-36911-7\_15},
doi = {10.1007/978-3-031-36911-7\_15},
timestamp = {Tue, 25 Jul 2023 13:14:28 +0200},
biburl = {https://dblp.org/rec/conf/recombcg/EdrisiOLN23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/MalloryN22,
author = {Xian F. Mallory and
Luay Nakhleh},
title = {SimSCSnTree: a simulator of single-cell {DNA} sequencing data},
journal = {Bioinform.},
volume = {38},
number = {10},
pages = {2912--2914},
year = {2022},
url = {https://doi.org/10.1093/bioinformatics/btac169},
doi = {10.1093/BIOINFORMATICS/BTAC169},
timestamp = {Mon, 13 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/MalloryN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/YinON22,
author = {Yongze Yin and
Huw A. Ogilvie and
Luay Nakhleh},
title = {Annotation-free delineation of prokaryotic homology groups},
journal = {PLoS Comput. Biol.},
volume = {18},
number = {6},
year = {2022},
url = {https://doi.org/10.1371/journal.pcbi.1010216},
doi = {10.1371/JOURNAL.PCBI.1010216},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/YinON22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recombcg/YakiciON22,
author = {Berk A. Yakici and
Huw A. Ogilvie and
Luay Nakhleh},
editor = {Lingling Jin and
Dannie Durand},
title = {Phylogenetic Network Dissimilarity Measures that Take Branch Lengths
into Account},
booktitle = {Comparative Genomics - 19th International Conference, {RECOMB-CG}
2022, La Jolla, CA, USA, May 20-21, 2022, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {13234},
pages = {86--102},
publisher = {Springer},
year = {2022},
url = {https://doi.org/10.1007/978-3-031-06220-9\_6},
doi = {10.1007/978-3-031-06220-9\_6},
timestamp = {Mon, 06 Nov 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/recombcg/YakiciON22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/MalloryENN20,
author = {Xian F. Mallory and
Mohammad Amin Edrisi and
Nicholas Navin and
Luay Nakhleh},
title = {Assessing the performance of methods for copy number aberration detection
from single-cell {DNA} sequencing data},
journal = {PLoS Comput. Biol.},
volume = {16},
number = {7},
year = {2020},
url = {https://doi.org/10.1371/journal.pcbi.1008012},
doi = {10.1371/JOURNAL.PCBI.1008012},
timestamp = {Sun, 02 Oct 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/MalloryENN20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuLON19,
author = {Jiafan Zhu and
Xinhao Liu and
Huw A. Ogilvie and
Luay Nakhleh},
title = {A divide-and-conquer method for scalable phylogenetic network inference
from multilocus data},
journal = {Bioinform.},
volume = {35},
number = {14},
pages = {i370--i378},
year = {2019},
url = {https://doi.org/10.1093/bioinformatics/btz359},
doi = {10.1093/BIOINFORMATICS/BTZ359},
timestamp = {Mon, 07 Nov 2022 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuLON19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/DuON19,
author = {Peng Du and
Huw A. Ogilvie and
Luay Nakhleh},
editor = {Zhipeng Cai and
Pavel Skums and
Min Li},
title = {Unifying Gene Duplication, Loss, and Coalescence on Phylogenetic Networks},
booktitle = {Bioinformatics Research and Applications - 15th International Symposium,
{ISBRA} 2019, Barcelona, Spain, June 3-6, 2019, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {11490},
pages = {40--51},
publisher = {Springer},
year = {2019},
url = {https://doi.org/10.1007/978-3-030-20242-2\_4},
doi = {10.1007/978-3-030-20242-2\_4},
timestamp = {Thu, 20 Aug 2020 15:54:47 +0200},
biburl = {https://dblp.org/rec/conf/isbra/DuON19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/CaoZN19,
author = {Zhen Cao and
Jiafan Zhu and
Luay Nakhleh},
editor = {Katharina T. Huber and
Dan Gusfield},
title = {Empirical Performance of Tree-Based Inference of Phylogenetic Networks},
booktitle = {19th International Workshop on Algorithms in Bioinformatics, {WABI}
2019, September 8-10, 2019, Niagara Falls, NY, {USA}},
series = {LIPIcs},
volume = {143},
pages = {21:1--21:13},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2019},
url = {https://doi.org/10.4230/LIPIcs.WABI.2019.21},
doi = {10.4230/LIPICS.WABI.2019.21},
timestamp = {Mon, 23 Sep 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/CaoZN19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/EdrisiZN19,
author = {Mohammad Amin Edrisi and
Hamim Zafar and
Luay Nakhleh},
editor = {Katharina T. Huber and
Dan Gusfield},
title = {A Combinatorial Approach for Single-cell Variant Detection via Phylogenetic
Inference},
booktitle = {19th International Workshop on Algorithms in Bioinformatics, {WABI}
2019, September 8-10, 2019, Niagara Falls, NY, {USA}},
series = {LIPIcs},
volume = {143},
pages = {22:1--22:13},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2019},
url = {https://doi.org/10.4230/LIPIcs.WABI.2019.22},
doi = {10.4230/LIPICS.WABI.2019.22},
timestamp = {Sun, 25 Oct 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/wabi/EdrisiZN19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhuN18,
author = {Jiafan Zhu and
Luay Nakhleh},
title = {Inference of species phylogenies from bi-allelic markers using pseudo-likelihood},
journal = {Bioinform.},
volume = {34},
number = {13},
pages = {i376--i385},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty295},
doi = {10.1093/BIOINFORMATICS/BTY295},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhuN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ElworthABDN18,
author = {Ryan A. Leo Elworth and
Chabrielle Allen and
Travis Benedict and
Peter Dulworth and
Luay Nakhleh},
title = {{ALPHA:} a toolkit for Automated Local PHylogenomic Analyses},
journal = {Bioinform.},
volume = {34},
number = {16},
pages = {2848--2850},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty173},
doi = {10.1093/BIOINFORMATICS/BTY173},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ElworthABDN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/WangN18,
author = {Yaxuan Wang and
Luay Nakhleh},
title = {Towards an accurate and efficient heuristic for species/gene tree
co-estimation},
journal = {Bioinform.},
volume = {34},
number = {17},
pages = {i697--i705},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/bty599},
doi = {10.1093/BIOINFORMATICS/BTY599},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/WangN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ZhuWYMN18,
author = {Jiafan Zhu and
Dingqiao Wen and
Yun Yu and
Heidi M. Meudt and
Luay Nakhleh},
title = {Bayesian inference of phylogenetic networks from bi-allelic genetic
markers},
journal = {PLoS Comput. Biol.},
volume = {14},
number = {1},
year = {2018},
url = {https://doi.org/10.1371/journal.pcbi.1005932},
doi = {10.1371/JOURNAL.PCBI.1005932},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/ZhuWYMN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bcb/DuN18,
author = {Peng Du and
Luay Nakhleh},
editor = {Amarda Shehu and
Cathy H. Wu and
Christina Boucher and
Jing Li and
Hongfang Liu and
Mihai Pop},
title = {Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence
Model},
booktitle = {Proceedings of the 2018 {ACM} International Conference on Bioinformatics,
Computational Biology, and Health Informatics, {BCB} 2018, Washington,
DC, USA, August 29 - September 01, 2018},
pages = {376--385},
publisher = {{ACM}},
year = {2018},
url = {https://doi.org/10.1145/3233547.3233600},
doi = {10.1145/3233547.3233600},
timestamp = {Wed, 21 Nov 2018 12:44:25 +0100},
biburl = {https://dblp.org/rec/conf/bcb/DuN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/FanXN18,
author = {Xian Fan and
Jie Xu and
Luay Nakhleh},
editor = {Mathieu Blanchette and
A{\"{\i}}da Ouangraoua},
title = {Detecting Large Indels Using Optical Map Data},
booktitle = {Comparative Genomics - 16th International Conference, {RECOMB-CG}
2018, Magog-Orford, QC, Canada, October 9-12, 2018, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {11183},
pages = {108--127},
publisher = {Springer},
year = {2018},
url = {https://doi.org/10.1007/978-3-030-00834-5\_6},
doi = {10.1007/978-3-030-00834-5\_6},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/FanXN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/ElworthABDN18,
author = {Ryan A. Leo Elworth and
Chabrielle Allen and
Travis Benedict and
Peter Dulworth and
Luay Nakhleh},
editor = {Laxmi Parida and
Esko Ukkonen},
title = {{DGEN:} {A} Test Statistic for Detection of General Introgression
Scenarios},
booktitle = {18th International Workshop on Algorithms in Bioinformatics, {WABI}
2018, August 20-22, 2018, Helsinki, Finland},
series = {LIPIcs},
volume = {113},
pages = {19:1--19:13},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum f{\"{u}}r Informatik},
year = {2018},
url = {https://doi.org/10.4230/LIPIcs.WABI.2018.19},
doi = {10.4230/LIPICS.WABI.2018.19},
timestamp = {Tue, 11 Feb 2020 15:52:14 +0100},
biburl = {https://dblp.org/rec/conf/wabi/ElworthABDN18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ElworthN17,
author = {Ryan A. Leo Elworth and
Luay Nakhleh},
editor = {Joao Meidanis and
Luay Nakhleh},
title = {Inferring Local Genealogies on Closely Related Genomes},
booktitle = {Comparative Genomics - 15th International Workshop, {RECOMB} {CG}
2017, Barcelona, Spain, October 4-6, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10562},
pages = {213--231},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-67979-2\_12},
doi = {10.1007/978-3-319-67979-2\_12},
timestamp = {Sat, 30 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ElworthN17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@proceedings{DBLP:conf/recomb/2017cg,
editor = {Joao Meidanis and
Luay Nakhleh},
title = {Comparative Genomics - 15th International Workshop, {RECOMB} {CG}
2017, Barcelona, Spain, October 4-6, 2017, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {10562},
publisher = {Springer},
year = {2017},
url = {https://doi.org/10.1007/978-3-319-67979-2},
doi = {10.1007/978-3-319-67979-2},
isbn = {978-3-319-67978-5},
timestamp = {Mon, 13 May 2019 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/recomb/2017cg.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhuYN16,
author = {Jiafan Zhu and
Yun Yu and
Luay Nakhleh},
title = {In the light of deep coalescence: revisiting trees within networks},
journal = {{BMC} Bioinform.},
volume = {17},
number = {{S-14}},
pages = {271--282},
year = {2016},
url = {https://doi.org/10.1186/s12859-016-1269-1},
doi = {10.1186/S12859-016-1269-1},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhuYN16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/YuN15,
author = {Yun Yu and
Luay Nakhleh},
editor = {Robert W. Harrison and
Yaohang Li and
Ion I. Mandoiu},
title = {A Distance-Based Method for Inferring Phylogenetic Networks in the
Presence of Incomplete Lineage Sorting},
booktitle = {Bioinformatics Research and Applications - 11th International Symposium,
{ISBRA} 2015, Norfolk, VA, USA, June 7-10, 2015 Proceedings},
series = {Lecture Notes in Computer Science},
volume = {9096},
pages = {378--389},
publisher = {Springer},
year = {2015},
url = {https://doi.org/10.1007/978-3-319-19048-8\_32},
doi = {10.1007/978-3-319-19048-8\_32},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/isbra/YuN15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/FanZCNC14,
author = {Xian Fan and
Wanding Zhou and
Zechen Chong and
Luay Nakhleh and
Ken Chen},
title = {Towards accurate characterization of clonal heterogeneity based on
structural variation},
journal = {{BMC} Bioinform.},
volume = {15},
pages = {299},
year = {2014},
url = {https://doi.org/10.1186/1471-2105-15-299},
doi = {10.1186/1471-2105-15-299},
timestamp = {Wed, 21 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/FanZCNC14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/LiuDTSKN14,
author = {Kevin J. Liu and
Jingxuan Dai and
Kathy Truong and
Ying Song and
Michael H. Kohn and
Luay Nakhleh},
title = {An HMM-Based Comparative Genomic Framework for Detecting Introgression
in Eukaryotes},
journal = {PLoS Comput. Biol.},
volume = {10},
number = {6},
year = {2014},
url = {https://doi.org/10.1371/journal.pcbi.1003649},
doi = {10.1371/JOURNAL.PCBI.1003649},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/LiuDTSKN14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/RuthsN13,
author = {Troy A. Ruths and
Luay Nakhleh},
title = {Boosting forward-time population genetic simulators through genotype
compression},
journal = {{BMC} Bioinform.},
volume = {14},
pages = {192},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-192},
doi = {10.1186/1471-2105-14-192},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/RuthsN13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/YuRN13,
author = {Yun Yu and
Nikola Ristic and
Luay Nakhleh},
title = {Fast algorithms and heuristics for phylogenomics under {ILS} and hybridization},
journal = {{BMC} Bioinform.},
volume = {14},
number = {{S-15}},
pages = {S6},
year = {2013},
url = {https://doi.org/10.1186/1471-2105-14-S15-S6},
doi = {10.1186/1471-2105-14-S15-S6},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/YuRN13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/BerestovskyZNN13,
author = {Natalie Berestovsky and
Wanding Zhou and
Deepak Nagrath and
Luay Nakhleh},
title = {Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean
Networks},
journal = {PLoS Comput. Biol.},
volume = {9},
number = {11},
year = {2013},
url = {https://doi.org/10.1371/journal.pcbi.1003306},
doi = {10.1371/JOURNAL.PCBI.1003306},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/BerestovskyZNN13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/globalsip/FanNC13,
author = {Xian Fan and
Luay Nakhleh and
Ken Chen},
title = {Integrated genotyping of structural variation},
booktitle = {{IEEE} Global Conference on Signal and Information Processing, GlobalSIP
2013, Austin, TX, USA, December 3-5, 2013},
pages = {47--48},
publisher = {{IEEE}},
year = {2013},
url = {https://doi.org/10.1109/GlobalSIP.2013.6736808},
doi = {10.1109/GLOBALSIP.2013.6736808},
timestamp = {Wed, 21 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/globalsip/FanNC13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/NakhlehRW13,
author = {Luay Nakhleh and
Noah A. Rosenberg and
Tandy J. Warnow},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany Murray and
Teri E. Klein},
title = {Session introduction},
booktitle = {Biocomputing 2013: Proceedings of the Pacific Symposium, Kohala Coast,
Hawaii, USA, January 3-7, 2013},
pages = {247--249},
publisher = {World Scientific Publishing},
year = {2013},
url = {http://psb.stanford.edu/psb-online/proceedings/psb13/intro-ppg.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/NakhlehRW13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ParkN12,
author = {Hyun Jung Park and
Luay Nakhleh},
title = {Inference of reticulate evolutionary histories by maximum likelihood:
the performance of information criteria},
journal = {{BMC} Bioinform.},
volume = {13},
number = {{S-19}},
pages = {S12},
year = {2012},
url = {https://doi.org/10.1186/1471-2105-13-S19-S12},
doi = {10.1186/1471-2105-13-S19-S12},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcbi/ParkN12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcisd/ZhouN12,
author = {Wanding Zhou and
Luay Nakhleh},
title = {Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic
Pathways},
journal = {J. Chem. Inf. Model.},
volume = {52},
number = {10},
pages = {2684--2696},
year = {2012},
url = {https://doi.org/10.1021/ci300259u},
doi = {10.1021/CI300259U},
timestamp = {Fri, 06 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcisd/ZhouN12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cibcb/BerestovskyFN12,
author = {Natalie Berestovsky and
Riya Fukui and
Luay Nakhleh},
title = {On the performance of particle swarm optimization for parameterizing
kinetic models of cellular networks},
booktitle = {2012 {IEEE} Symposium on Computational Intelligence in Bioinformatics
and Computational Biology, {CIBCB} 2012, San Diego, CA, USA, May 9-12,
2012},
pages = {184--191},
publisher = {{IEEE}},
year = {2012},
url = {https://doi.org/10.1109/CIBCB.2012.6217229},
doi = {10.1109/CIBCB.2012.6217229},
timestamp = {Wed, 16 Oct 2019 14:14:48 +0200},
biburl = {https://dblp.org/rec/conf/cibcb/BerestovskyFN12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/ParkN12,
author = {Hyun Jung Park and
Luay Nakhleh},
editor = {Leonidas G. Bleris and
Ion I. Mandoiu and
Russell Schwartz and
Jianxin Wang},
title = {{MURPAR:} {A} Fast Heuristic for Inferring Parsimonious Phylogenetic
Networks from Multiple Gene Trees},
booktitle = {Bioinformatics Research and Applications - 8th International Symposium,
{ISBRA} 2012, Dallas, TX, USA, May 21-23, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7292},
pages = {213--224},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-30191-9\_20},
doi = {10.1007/978-3-642-30191-9\_20},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/isbra/ParkN12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/ZhuN12,
author = {Yun Zhu and
Luay Nakhleh},
editor = {Benjamin J. Raphael and
Jijun Tang},
title = {Reconstructing the Evolution of Molecular Interaction Networks under
the {DMC} and Link Dynamics Models},
booktitle = {Algorithms in Bioinformatics - 12th International Workshop, {WABI}
2012, Ljubljana, Slovenia, September 10-12, 2012. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {7534},
pages = {57--68},
publisher = {Springer},
year = {2012},
url = {https://doi.org/10.1007/978-3-642-33122-0\_5},
doi = {10.1007/978-3-642-33122-0\_5},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/ZhuN12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-1212-1909,
author = {Yun Yu and
Luay Nakhleh},
title = {Fast Algorithms for Reconciliation under Hybridization and Incomplete
Lineage Sorting},
journal = {CoRR},
volume = {abs/1212.1909},
year = {2012},
url = {http://arxiv.org/abs/1212.1909},
eprinttype = {arXiv},
eprint = {1212.1909},
timestamp = {Mon, 13 Aug 2018 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/corr/abs-1212-1909.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ZhouN11,
author = {Wanding Zhou and
Luay Nakhleh},
title = {The strength of chemical linkage as a criterion for pruning metabolic
graphs},
journal = {Bioinform.},
volume = {27},
number = {14},
pages = {1957--1963},
year = {2011},
url = {https://doi.org/10.1093/bioinformatics/btr271},
doi = {10.1093/BIOINFORMATICS/BTR271},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/ZhouN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ZhouN11,
author = {Wanding Zhou and
Luay Nakhleh},
title = {Properties of Metabolic Graphs: Biological Organization or Representation
Artifacts?},
journal = {{BMC} Bioinform.},
volume = {12},
pages = {132},
year = {2011},
url = {https://doi.org/10.1186/1471-2105-12-132},
doi = {10.1186/1471-2105-12-132},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ZhouN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/YuWN11,
author = {Yun Yu and
Tandy J. Warnow and
Luay Nakhleh},
title = {Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted
Binary Gene Trees on Single Alleles},
journal = {J. Comput. Biol.},
volume = {18},
number = {11},
pages = {1543--1559},
year = {2011},
url = {https://doi.org/10.1089/cmb.2011.0174},
doi = {10.1089/CMB.2011.0174},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/YuWN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/YuWN11,
author = {Yun Yu and
Tandy J. Warnow and
Luay Nakhleh},
editor = {Vineet Bafna and
S{\"{u}}leyman Cenk Sahinalp},
title = {Algorithms for MDC-Based Multi-locus Phylogeny Inference},
booktitle = {Research in Computational Molecular Biology - 15th Annual International
Conference, {RECOMB} 2011, Vancouver, BC, Canada, March 28-31, 2011.
Proceedings},
series = {Lecture Notes in Computer Science},
volume = {6577},
pages = {531--545},
publisher = {Springer},
year = {2011},
url = {https://doi.org/10.1007/978-3-642-20036-6\_47},
doi = {10.1007/978-3-642-20036-6\_47},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/YuWN11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/Nakhleh10,
author = {Luay Nakhleh},
title = {A Metric on the Space of Reduced Phylogenetic Networks},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {7},
number = {2},
pages = {218--222},
year = {2010},
url = {https://doi.org/10.1109/TCBB.2009.2},
doi = {10.1109/TCBB.2009.2},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/Nakhleh10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RuthsRN09,
author = {Troy A. Ruths and
Derek A. Ruths and
Luay Nakhleh},
title = {GS\({}^{\mbox{2}}\): an efficiently computable measure of GO-based
similarity of gene sets},
journal = {Bioinform.},
volume = {25},
number = {9},
pages = {1178--1184},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp128},
doi = {10.1093/BIOINFORMATICS/BTP128},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/RuthsRN09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/ThanN09,
author = {Cuong Than and
Luay Nakhleh},
title = {Species Tree Inference by Minimizing Deep Coalescences},
journal = {PLoS Comput. Biol.},
volume = {5},
number = {9},
year = {2009},
url = {https://doi.org/10.1371/journal.pcbi.1000501},
doi = {10.1371/JOURNAL.PCBI.1000501},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/ThanN09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/JinNST09,
author = {Guohua Jin and
Luay Nakhleh and
Sagi Snir and
Tamir Tuller},
title = {Parsimony Score of Phylogenetic Networks: Hardness Results and a Linear-Time
Heuristic},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {6},
number = {3},
pages = {495--505},
year = {2009},
url = {https://doi.org/10.1109/TCBB.2008.119},
doi = {10.1109/TCBB.2008.119},
timestamp = {Mon, 28 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/JinNST09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/algorithmica/KanjNX08,
author = {Iyad A. Kanj and
Luay Nakhleh and
Ge Xia},
title = {The Compatibility of Binary Characters on Phylogenetic Networks: Complexity
and Parameterized Algorithms},
journal = {Algorithmica},
volume = {51},
number = {2},
pages = {99--128},
year = {2008},
url = {https://doi.org/10.1007/s00453-007-9046-1},
doi = {10.1007/S00453-007-9046-1},
timestamp = {Wed, 17 May 2017 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/algorithmica/KanjNX08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcbi/ThanRN08,
author = {Cuong Than and
Derek A. Ruths and
Luay Nakhleh},
title = {PhyloNet: a software package for analyzing and reconstructing reticulate
evolutionary relationships},
journal = {{BMC} Bioinform.},
volume = {9},
year = {2008},
url = {https://doi.org/10.1186/1471-2105-9-322},
doi = {10.1186/1471-2105-9-322},
timestamp = {Sun, 15 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bmcbi/ThanRN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bmcsb/RuthsNR08,
author = {Derek A. Ruths and
Luay Nakhleh and
Prahlad T. Ram},
title = {Rapidly exploring structural and dynamic properties of signaling networks
using PathwayOracle},
journal = {{BMC} Syst. Biol.},
volume = {2},
pages = {76},
year = {2008},
url = {https://doi.org/10.1186/1752-0509-2-76},
doi = {10.1186/1752-0509-2-76},
timestamp = {Tue, 05 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bmcsb/RuthsNR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ploscb/RuthsMTNR08,
author = {Derek A. Ruths and
Melissa Muller and
Jen{-}Te Tseng and
Luay Nakhleh and
Prahlad T. Ram},
title = {The Signaling Petri Net-Based Simulator: {A} Non-Parametric Strategy
for Characterizing the Dynamics of Cell-Specific Signaling Networks},
journal = {PLoS Comput. Biol.},
volume = {4},
number = {2},
year = {2008},
url = {https://doi.org/10.1371/journal.pcbi.1000005},
doi = {10.1371/JOURNAL.PCBI.1000005},
timestamp = {Thu, 10 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ploscb/RuthsMTNR08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcs/KanjNTX08,
author = {Iyad A. Kanj and
Luay Nakhleh and
Cuong Than and
Ge Xia},
title = {Seeing the trees and their branches in the network is hard},
journal = {Theor. Comput. Sci.},
volume = {401},
number = {1-3},
pages = {153--164},
year = {2008},
url = {https://doi.org/10.1016/j.tcs.2008.04.019},
doi = {10.1016/J.TCS.2008.04.019},
timestamp = {Wed, 17 Feb 2021 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/tcs/KanjNTX08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/ThanN08,
author = {Cuong Than and
Luay Nakhleh},
editor = {Alvis Brazma and
Satoru Miyano and
Tatsuya Akutsu},
title = {SPR-based Tree Reconciliation: Non-binary Trees and Multiple Solutions},
booktitle = {Proceedings of the 6th Asia-Pacific Bioinformatics Conference, {APBC}
2008, 14-17 January 2008, Kyoto, Japan},
series = {Advances in Bioinformatics and Computational Biology},
volume = {6},
pages = {251--260},
publisher = {Imperial College Press},
year = {2008},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2008/apbc097a.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/apbc/ThanN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/ThanSIN08,
author = {Cuong Than and
R. Sugino and
Hideki Innan and
Luay Nakhleh},
title = {Efficient inference of bacterial strain trees from genome-scale multilocus
data},
booktitle = {Proceedings 16th International Conference on Intelligent Systems for
Molecular Biology (ISMB), Toronto, Canada, July 19-23, 2008},
pages = {123--131},
year = {2008},
url = {https://doi.org/10.1093/bioinformatics/btn149},
doi = {10.1093/BIOINFORMATICS/BTN149},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/ismb/ThanSIN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ThanJN08,
author = {Cuong Than and
Guohua Jin and
Luay Nakhleh},
editor = {Craig E. Nelson and
St{\'{e}}phane Vialette},
title = {Integrating Sequence and Topology for Efficient and Accurate Detection
of Horizontal Gene Transfer},
booktitle = {Comparative Genomics, International Workshop, {RECOMB-CG} 2008, Paris,
France, October 13-15, 2008. Proceedings},
series = {Lecture Notes in Computer Science},
volume = {5267},
pages = {113--127},
publisher = {Springer},
year = {2008},
url = {https://doi.org/10.1007/978-3-540-87989-3\_9},
doi = {10.1007/978-3-540-87989-3\_9},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ThanJN08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JinNST07,
author = {Guohua Jin and
Luay Nakhleh and
Sagi Snir and
Tamir Tuller},
title = {Efficient parsimony-based methods for phylogenetic network reconstruction},
journal = {Bioinform.},
volume = {23},
number = {2},
pages = {123--128},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btl313},
doi = {10.1093/BIOINFORMATICS/BTL313},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JinNST07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JinNST07a,
author = {Guohua Jin and
Luay Nakhleh and
Sagi Snir and
Tamir Tuller},
title = {Maximum likelihood of phylogenetic networks},
journal = {Bioinform.},
volume = {23},
number = {8},
pages = {1046--1047},
year = {2007},
url = {https://doi.org/10.1093/bioinformatics/btm075},
doi = {10.1093/BIOINFORMATICS/BTM075},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JinNST07a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/ThanRIN07,
author = {Cuong Than and
Derek A. Ruths and
Hideki Innan and
Luay Nakhleh},
title = {Confounding Factors in {HGT} Detection: Statistical Error, Coalescent
Effects, and Multiple Solutions},
journal = {J. Comput. Biol.},
volume = {14},
number = {4},
pages = {517--535},
year = {2007},
url = {https://doi.org/10.1089/cmb.2007.A010},
doi = {10.1089/CMB.2007.A010},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/ThanRIN07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ictcs/KanjNTX07,
author = {Iyad A. Kanj and
Luay Nakhleh and
Cuong Than and
Ge Xia},
editor = {Giuseppe F. Italiano and
Eugenio Moggi and
Luigi Laura},
title = {Seeing the Trees and Their Branches in the Forest is Hard},
booktitle = {Theoretical Computer Science, 10th Italian Conference, {ICTCS} 2007,
Rome, Italy, October 3-5, 2007, Proceedings},
pages = {82--93},
publisher = {World Scientific},
year = {2007},
timestamp = {Wed, 11 Jun 2008 08:55:26 +0200},
biburl = {https://dblp.org/rec/conf/ictcs/KanjNTX07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/isbra/JinNST07,
author = {Guohua Jin and
Luay Nakhleh and
Sagi Snir and
Tamir Tuller},
editor = {Ion I. Mandoiu and
Alexander Zelikovsky},
title = {A New Linear-Time Heuristic Algorithm for Computing the Parsimony
Score of Phylogenetic Networks: Theoretical Bounds and Empirical Performance},
booktitle = {Bioinformatics Research and Applications, Third International Symposium,
{ISBRA} 2007, Atlanta, GA, USA, May 7-10, 2007, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4463},
pages = {61--72},
publisher = {Springer},
year = {2007},
url = {https://doi.org/10.1007/978-3-540-72031-7\_6},
doi = {10.1007/978-3-540-72031-7\_6},
timestamp = {Tue, 14 May 2019 10:00:51 +0200},
biburl = {https://dblp.org/rec/conf/isbra/JinNST07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/JinNST06,
author = {Guohua Jin and
Luay Nakhleh and
Sagi Snir and
Tamir Tuller},
title = {Maximum likelihood of phylogenetic networks},
journal = {Bioinform.},
volume = {22},
number = {21},
pages = {2604--2611},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl452},
doi = {10.1093/BIOINFORMATICS/BTL452},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/JinNST06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijbra/DotsenkoCNMR06,
author = {Yuri Dotsenko and
Cristian Coarfa and
Luay Nakhleh and
John M. Mellor{-}Crummey and
Usman Roshan},
title = {PRec-I-DCM3: a parallel framework for fast and accurate large-scale
phylogeny reconstruction},
journal = {Int. J. Bioinform. Res. Appl.},
volume = {2},
number = {4},
pages = {407--419},
year = {2006},
url = {https://doi.org/10.1504/IJBRA.2006.011039},
doi = {10.1504/IJBRA.2006.011039},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijbra/DotsenkoCNMR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/RuthsNIRR06,
author = {Derek A. Ruths and
Luay Nakhleh and
M. Sriram Iyengar and
Shrikanth A. G. Reddy and
Prahlad T. Ram},
title = {Hypothesis Generation in Signaling Networks},
journal = {J. Comput. Biol.},
volume = {13},
number = {9},
pages = {1546--1557},
year = {2006},
url = {https://doi.org/10.1089/cmb.2006.13.1546},
doi = {10.1089/CMB.2006.13.1546},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/RuthsNIRR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/RuthsN06,
author = {Derek A. Ruths and
Luay Nakhleh},
editor = {Tao Jiang and
Ueng{-}Cheng Yang and
Yi{-}Ping Phoebe Chen and
Limsoon Wong},
title = {{RECOMP:} {A} Parsimony-Based Method for Detecting Recombination},
booktitle = {Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February
2006, Taipei, Taiwan},
pages = {59--68},
publisher = {Imperial College Press, London},
year = {2006},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2006/146.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/apbc/RuthsN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/apbc/RuthsN06a,
author = {Derek A. Ruths and
Luay Nakhleh},
editor = {Tao Jiang and
Ueng{-}Cheng Yang and
Yi{-}Ping Phoebe Chen and
Limsoon Wong},
title = {Techniques for Assessing Phylogenetic Branch Support: {A} Performance
Study},
booktitle = {Proceedings of 4th Asia-Pacific Bioinformatics Conference. 13-16 February
2006, Taipei, Taiwan},
pages = {187--196},
publisher = {Imperial College Press, London},
year = {2006},
url = {http://www.comp.nus.edu.sg/\%7Ewongls/psZ/apbc2006/197.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/apbc/RuthsN06a.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cocoon/KanjNX06,
author = {Iyad A. Kanj and
Luay Nakhleh and
Ge Xia},
editor = {Danny Z. Chen and
D. T. Lee},
title = {Reconstructing Evolution of Natural Languages: Complexity and Parameterized
Algorithms},
booktitle = {Computing and Combinatorics, 12th Annual International Conference,
{COCOON} 2006, Taipei, Taiwan, August 15-18, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4112},
pages = {299--308},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11809678\_32},
doi = {10.1007/11809678\_32},
timestamp = {Tue, 14 May 2019 10:00:35 +0200},
biburl = {https://dblp.org/rec/conf/cocoon/KanjNX06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/RuthsTNR06,
author = {Derek A. Ruths and
Jen{-}Te Tseng and
Luay Nakhleh and
Prahlad T. Ram},
editor = {Trey Ideker and
Vineet Bafna},
title = {De Novo Signaling Pathway Predictions Based on Protein-Protein Interaction,
Targeted Therapy and Protein Microarray Analysis},
booktitle = {Systems Biology and Computational Proteomics, Joint {RECOMB} 2006
Satellite Workshops on Systems Biology and on Computational Proteomics,
San Diego, CA, USA, December 1-3, 2006, Revised Selected Papers},
series = {Lecture Notes in Computer Science},
volume = {4532},
pages = {108--118},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/978-3-540-73060-6\_8},
doi = {10.1007/978-3-540-73060-6\_8},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/RuthsTNR06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/ThanRIN06,
author = {Cuong Than and
Derek A. Ruths and
Hideki Innan and
Luay Nakhleh},
editor = {Guillaume Bourque and
Nadia El{-}Mabrouk},
title = {Identifiability Issues in Phylogeny-Based Detection of Horizontal
Gene Transfer},
booktitle = {Comparative Genomics, {RECOMB} 2006 International Workshop, {RCG}
2006, Montreal, Canada, September 24-26, 2006, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {4205},
pages = {215--229},
publisher = {Springer},
year = {2006},
url = {https://doi.org/10.1007/11864127\_17},
doi = {10.1007/11864127\_17},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/ThanRIN06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/ijbra/RuthsN05,
author = {Derek A. Ruths and
Luay Nakhleh},
title = {Recombination and phylogeny: effects and detection},
journal = {Int. J. Bioinform. Res. Appl.},
volume = {1},
number = {2},
pages = {202--212},
year = {2005},
url = {https://doi.org/10.1504/IJBRA.2005.007578},
doi = {10.1504/IJBRA.2005.007578},
timestamp = {Fri, 11 Sep 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/ijbra/RuthsN05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/NakhlehWLJ05,
author = {Luay Nakhleh and
Tandy J. Warnow and
C. Randal Linder and
Katherine St. John},
title = {Reconstructing Reticulate Evolution in SpeciesTheory and Practice},
journal = {J. Comput. Biol.},
volume = {12},
number = {6},
pages = {796--811},
year = {2005},
url = {https://doi.org/10.1089/cmb.2005.12.796},
doi = {10.1089/CMB.2005.12.796},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jcb/NakhlehWLJ05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcsb/NakhlehW05,
author = {Luay Nakhleh and
Li{-}San Wang},
title = {Phylogenetic Networks: Properties and Relationship to Trees and Clusters},
journal = {Trans. Comp. Sys. Biology},
volume = {2},
pages = {82--99},
year = {2005},
url = {https://doi.org/10.1007/11567752\_6},
doi = {10.1007/11567752\_6},
timestamp = {Thu, 14 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcsb/NakhlehW05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/cocoon/NakhlehRW05,
author = {Luay Nakhleh and
Derek A. Ruths and
Li{-}San Wang},
editor = {Lusheng Wang},
title = {{RIATA-HGT:} {A} Fast and Accurate Heuristic for Reconstructing Horizontal
Gene Transfer},
booktitle = {Computing and Combinatorics, 11th Annual International Conference,
{COCOON} 2005, Kunming, China, August 16-29, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3595},
pages = {84--93},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11533719\_11},
doi = {10.1007/11533719\_11},
timestamp = {Tue, 14 May 2019 10:00:35 +0200},
biburl = {https://dblp.org/rec/conf/cocoon/NakhlehRW05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/csb/NakhlehJZM05,
author = {Luay Nakhleh and
Guohua Jin and
Fengmei Zhao and
John M. Mellor{-}Crummey},
title = {Reconstructing Phylogenetic Networks Using Maximum Parsimony},
booktitle = {Fourth International {IEEE} Computer Society Computational Systems
Bioinformatics Conference, {CSB} 2005, Stanford, CA, USA, August 8-11,
2005},
pages = {93--102},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/CSB.2005.47},
doi = {10.1109/CSB.2005.47},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/csb/NakhlehJZM05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/hpcc/DuSLRN05,
author = {Z. Du and
Alexandros Stamatakis and
F. Lin and
Usman Roshan and
Luay Nakhleh},
editor = {Laurence Tianruo Yang and
Omer F. Rana and
Beniamino Di Martino and
Jack J. Dongarra},
title = {Parallel Divide-and-Conquer Phylogeny Reconstruction by Maximum Likelihood},
booktitle = {High Performance Computing and Communications, First International
Conference, {HPCC} 2005, Sorrento, Italy, September 21-23, 2005, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {3726},
pages = {776--785},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11557654\_88},
doi = {10.1007/11557654\_88},
timestamp = {Tue, 14 May 2019 10:00:45 +0200},
biburl = {https://dblp.org/rec/conf/hpcc/DuSLRN05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/iccS/NakhlehW05,
author = {Luay Nakhleh and
Li{-}San Wang},
editor = {Vaidy S. Sunderam and
G. Dick van Albada and
Peter M. A. Sloot and
Jack J. Dongarra},
title = {Phylogenetic Networks, Trees, and Clusters},
booktitle = {Computational Science - {ICCS} 2005, 5th International Conference,
Atlanta, GA, USA, May 22-25, 2005, Proceedings, Part {II}},
series = {Lecture Notes in Computer Science},
volume = {3515},
pages = {919--926},
publisher = {Springer},
year = {2005},
url = {https://doi.org/10.1007/11428848\_117},
doi = {10.1007/11428848\_117},
timestamp = {Tue, 14 May 2019 10:00:48 +0200},
biburl = {https://dblp.org/rec/conf/iccS/NakhlehW05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/icpads/CoarfaDMNR05,
author = {Cristian Coarfa and
Yuri Dotsenko and
John M. Mellor{-}Crummey and
Luay Nakhleh and
Usman Roshan},
title = {PRec-I-DCM3: {A} Parallel Framework for Fast and Accurate Large Scale
Phylogeny Reconstruction},
booktitle = {11th International Conference on Parallel and Distributed Systems,
{ICPADS} 2005, Fuduoka, Japan, July 20-22, 2005},
pages = {346--350},
publisher = {{IEEE} Computer Society},
year = {2005},
url = {https://doi.org/10.1109/ICPADS.2005.240},
doi = {10.1109/ICPADS.2005.240},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/icpads/CoarfaDMNR05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/tcbb/MoretNWLTPST04,
author = {Bernard M. E. Moret and
Luay Nakhleh and
Tandy J. Warnow and
C. Randal Linder and
Anna Tholse and
Anneke Padolina and
Jerry Sun and
Ruth E. Timme},
title = {Phylogenetic Networks: Modeling, Reconstructibility, and Accuracy},
journal = {{IEEE} {ACM} Trans. Comput. Biol. Bioinform.},
volume = {1},
number = {1},
pages = {13--23},
year = {2004},
url = {https://doi.org/10.1109/TCBB.2004.10},
doi = {10.1109/TCBB.2004.10},
timestamp = {Mon, 03 Apr 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/tcbb/MoretNWLTPST04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/recomb/NakhlehWL04,
author = {Luay Nakhleh and
Tandy J. Warnow and
C. Randal Linder},
editor = {Philip E. Bourne and
Dan Gusfield},
title = {Reconstructing reticulate evolution in species: theory and practice},
booktitle = {Proceedings of the Eighth Annual International Conference on Computational
Molecular Biology, 2004, San Diego, California, USA, March 27-31,
2004},
pages = {337--346},
publisher = {{ACM}},
year = {2004},
url = {https://doi.org/10.1145/974614.974659},
doi = {10.1145/974614.974659},
timestamp = {Mon, 13 May 2019 09:30:09 +0200},
biburl = {https://dblp.org/rec/conf/recomb/NakhlehWL04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/bibe/NakhlehMBPD03,
author = {Luay Nakhleh and
Daniel P. Miranker and
Fran{\c{c}}ois Barban{\c{c}}on and
William H. Piel and
Michael J. Donoghue},
title = {Requirements of Phylogenetic Databases},
booktitle = {3rd {IEEE} International Symposium on BioInformatics and BioEngineering
{(BIBE} 2003), 10-12 March 2003, Bethesda, MD, {USA}},
pages = {141--148},
publisher = {{IEEE} Computer Society},
year = {2003},
url = {https://doi.org/10.1109/BIBE.2003.1188940},
doi = {10.1109/BIBE.2003.1188940},
timestamp = {Fri, 24 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/bibe/NakhlehMBPD03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/padl/ErdemLNR03,
author = {Esra Erdem and
Vladimir Lifschitz and
Luay Nakhleh and
Donald Ringe},
editor = {Ver{\'{o}}nica Dahl and
Philip Wadler},
title = {Reconstructing the Evolutionary History of Indo-European Languages
Using Answer Set Programming},
booktitle = {Practical Aspects of Declarative Languages, 5th International Symposium,
{PADL} 2003, New Orleans, LA, USA, January 13-14, 2003, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2562},
pages = {160--176},
publisher = {Springer},
year = {2003},
url = {https://doi.org/10.1007/3-540-36388-2\_12},
doi = {10.1007/3-540-36388-2\_12},
timestamp = {Tue, 14 May 2019 10:00:42 +0200},
biburl = {https://dblp.org/rec/conf/padl/ErdemLNR03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/NakhlehSWLMT03,
author = {Luay Nakhleh and
Jerry Sun and
Tandy J. Warnow and
C. Randal Linder and
Bernard M. E. Moret and
Anna Tholse},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {Towards the Development of Computational Tools for Evaluating Phylogenetic
Network Reconstruction Methods},
booktitle = {Proceedings of the 8th Pacific Symposium on Biocomputing, {PSB} 2003,
Lihue, Hawaii, USA, January 3-7, 2003},
pages = {315--326},
year = {2003},
url = {http://psb.stanford.edu/psb-online/proceedings/psb03/nakhleh.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/NakhlehSWLMT03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/NakhlehMRJSW02,
author = {Luay Nakhleh and
Bernard M. E. Moret and
Usman Roshan and
Katherine St. John and
Jerry Sun and
Tandy J. Warnow},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Teri E. Klein},
title = {The Accuracy of Fast Phylogenetic Methods for Large Datasets},
booktitle = {Proceedings of the 7th Pacific Symposium on Biocomputing, {PSB} 2002,
Lihue, Hawaii, USA, January 3-7, 2002},
pages = {211--222},
year = {2002},
url = {http://psb.stanford.edu/psb-online/proceedings/psb02/nakhleh.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/NakhlehMRJSW02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/NakhlehRVW02,
author = {Luay Nakhleh and
Usman Roshan and
Lisa Vawter and
Tandy J. Warnow},
editor = {Roderic Guig{\'{o}} and
Dan Gusfield},
title = {Estimating the Deviation from a Molecular Clock},
booktitle = {Algorithms in Bioinformatics, Second International Workshop, {WABI}
2002, Rome, Italy, September 17-21, 2002, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2452},
pages = {287--299},
publisher = {Springer},
year = {2002},
url = {https://doi.org/10.1007/3-540-45784-4\_22},
doi = {10.1007/3-540-45784-4\_22},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/NakhlehRVW02.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/ismb/NakhlehRJSW01,
author = {Luay Nakhleh and
Usman Roshan and
Katherine St. John and
Jerry Sun and
Tandy J. Warnow},
title = {Designing fast converging phylogenetic methods},
booktitle = {Proceedings of the Ninth International Conference on Intelligent Systems
for Molecular Biology, July 21-25, 2001, Copenhagen, Denmark},
pages = {190--198},
year = {2001},
timestamp = {Mon, 26 Feb 2018 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/ismb/NakhlehRJSW01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/wabi/NakhlehRJSW01,
author = {Luay Nakhleh and
Usman Roshan and
Katherine St. John and
Jerry Sun and
Tandy J. Warnow},
editor = {Olivier Gascuel and
Bernard M. E. Moret},
title = {The Performance of Phylogenetic Methods on Trees of Bounded Diameter},
booktitle = {Algorithms in Bioinformatics, First International Workshop, {WABI}
2001, Aarhus, Denmark, August 28-31, 2001, Proceedings},
series = {Lecture Notes in Computer Science},
volume = {2149},
pages = {214--226},
publisher = {Springer},
year = {2001},
url = {https://doi.org/10.1007/3-540-44696-6\_17},
doi = {10.1007/3-540-44696-6\_17},
timestamp = {Tue, 14 May 2019 10:00:40 +0200},
biburl = {https://dblp.org/rec/conf/wabi/NakhlehRJSW01.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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