Luay Nakhleh : rechercher sur Z-Library

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1

Networks: expanding evolutionary thinking

Bapteste, Eric, van Iersel, Leo, Janke, Axel, Kelchner, Scot, Kelk, Steven, McInerney, James O., Morrison, David A., Nakhleh, Luay, Steel, Mike, Stougie, Leen, Whitfield, James

Journal:

Trends in Genetics

Année:

2013

Langue:

english

Fichier:

PDF, 127 KB

english, 2013

2

A comparison of phylogenetic reconstruction methods on an Indo-European dataset

Luay Nakhleh, Tandy Warnow, Don Ringe, Steven N. Evans

Journal:

Transactions of the Philological Society

Année:

2005

Langue:

english

Fichier:

PDF, 313 KB

english, 2005

3

Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages

Luay Nakhleh, Don Ringe and Tandy Warnow

Journal:

Année:

2005

Langue:

english

Fichier:

PDF, 4.42 MB

english, 2005

4

Perfect Phylogenetic Networks: A New Methodology for Reconstructing the Evolutionary History of Natural Languages

Nakhleh, Luay, Ringe, Donald A., Warnow, Tandy

Journal:

Année:

2005

Langue:

english

Fichier:

PDF, 423 KB

english, 2005

5

Seeing the trees and their branches in the network is hard

Iyad A. Kanj, Luay Nakhleh, Cuong Than, Ge Xia

Journal:

Theoretical Computer Science

Année:

2008

Langue:

english

Fichier:

PDF, 711 KB

english, 2008

6

Properties of metabolic graphs: biological organization or representation artifacts?

Wanding Zhou, Luay Nakhleh

Journal:

BMC Bioinformatics

Année:

2011

Langue:

english

Fichier:

PDF, 1.05 MB

english, 2011

7

The Compatibility of Binary Characters on Phylogenetic Networks: Complexity and Parameterized Algorithms

Iyad A. Kanj, Luay Nakhleh, Ge Xia

Journal:

Année:

2008

Langue:

english

Fichier:

PDF, 525 KB

english, 2008

8

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

Cuong Than, Derek Ruths, Luay Nakhleh

Journal:

BMC Bioinformatics

Année:

2008

Langue:

english

Fichier:

PDF, 1.28 MB

english, 2008

9

Bootstrap-based Support of HGT Inferred by Maximum Parsimony

Hyun Jung Park, Guohua Jin, Luay Nakhleh

Journal:

BMC Evolutionary Biology

Année:

2010

Langue:

english

Fichier:

PDF, 1.18 MB

english, 2010

10

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle

Derek Ruths, Luay Nakhleh, Prahlad T Ram

Journal:

BMC Systems Biology

Année:

2008

Langue:

english

Fichier:

PDF, 2.49 MB

english, 2008

11

[ACM Press the eighth annual international conference - San Diego, California, USA (2004.03.27-2004.03.31)] Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04 - Reconstructing reticulate evolution in species

Nakhleh, Luay, Warnow, Tandy, Linder, C. Randal

Année:

2004

Langue:

english

Fichier:

PDF, 234 KB

english, 2004

12

Convergent evolution of modularity in metabolic networks through different community structures

Wanding Zhou, Luay Nakhleh

Journal:

BMC Evolutionary Biology

Année:

2012

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2012

13

Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways

Zhou, Wanding, Nakhleh, Luay

Journal:

Journal of Chemical Information and Modeling

Année:

2012

Langue:

english

Fichier:

PDF, 2.66 MB

english, 2012

14

Boosting forward-time population genetic simulators through genotype compression

Troy Ruths, Luay Nakhleh

Journal:

BMC Bioinformatics

Année:

2013

Langue:

english

Fichier:

PDF, 412 KB

english, 2013

15

Inference of reticulate evolutionary histories by maximum likelihood: the performance of information criteria

Hyun Jung Park, Luay Nakhleh

Journal:

BMC Bioinformatics

Année:

2012

Langue:

english

Fichier:

PDF, 634 KB

english, 2012

16

ncDNA and drift drive binding site accumulation

Troy Ruths, Luay Nakhleh

Journal:

BMC Evolutionary Biology

Année:

2012

Langue:

english

Fichier:

PDF, 453 KB

english, 2012

17

Computational approaches to species phylogeny inference and gene tree reconciliation

Journal:

Trends in Ecology & Evolution

Année:

2013

Langue:

english

Fichier:

PDF, 516 KB

english, 2013

18

Fast algorithms and heuristics for phylogenomics under ILS and hybridization

Yu, Yun, Ristic, Nikola, Nakhleh, Luay

Journal:

BMC Bioinformatics

Année:

2013

Langue:

english

Fichier:

PDF, 884 KB

english, 2013

19

[IEEE 2013 IEEE Global Conference on Signal and Information Processing (GlobalSIP) - Austin, TX, USA (2013.12.3-2013.12.5)] 2013 IEEE Global Conference on Signal and Information Processing - Integrated genotyping of structural variation

Fan, Xian, Nakhleh, Luay, Chen, Ken

Année:

2013

Langue:

english

Fichier:

PDF, 246 KB

english, 2013

20

Maximum likelihood inference of reticulate evolutionary histories

Yu, Yun, Dong, Jianrong, Liu, Kevin J., Nakhleh, Luay

Journal:

Proceedings of the National Academy of Sciences

Année:

2014

Langue:

english

Fichier:

PDF, 863 KB

english, 2014

21

Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles

Yu, Yun, Warnow, Tandy, Nakhleh, Luay

Journal:

Journal of Computational Biology

Année:

2011

Langue:

english

Fichier:

PDF, 1.03 MB

english, 2011

22

Reconstructing Reticulate Evolution in Species—Theory and Practice

Nakhleh, Luay, Warnow, Tandy, Linder, C. Randal, John, Katherine St.

Journal:

Journal of Computational Biology

Année:

2005

Langue:

english

Fichier:

PDF, 175 KB

english, 2005

23

Confounding Factors in HGT Detection: Statistical Error, Coalescent Effects, and Multiple Solutions

Than, Cuong, Ruths, Derek, Innan, Hideki, Nakhleh, Luay

Journal:

Journal of Computational Biology

Année:

2007

Langue:

english

Fichier:

PDF, 1.51 MB

english, 2007

24

Hypothesis Generation in Signaling Networks

Ruths, Derek A., Nakhleh, Luay, Iyengar, M. Sriram, Reddy, Shrikanth A.G., Ram, Prahlad T.

Journal:

Journal of Computational Biology

Année:

2006

Langue:

english

Fichier:

PDF, 177 KB

english, 2006

25

Interspecific introgressive origin of genomic diversity in the house mouse

Liu, Kevin J., Steinberg, Ethan, Yozzo, Alexander, Song, Ying, Kohn, Michael H., Nakhleh, Luay

Journal:

Proceedings of the National Academy of Sciences

Année:

2015

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2015

26

[IEEE 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) - San Diego, CA, USA (2012.05.9-2012.05.12)] 2012 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB) - On the performance of particle swarm optimization for parameterizing kinetic models of cellular networks

Berestovsky, Natalie, Fukui, Riya, Nakhleh, Luay

Année:

2012

Langue:

english

Fichier:

PDF, 2.77 MB

english, 2012

27

Towards accurate characterization of clonal heterogeneity based on structural variation

Fan, Xian, Zhou, Wanding, Chong, Zechen, Nakhleh, Luay, Chen, Ken

Journal:

BMC Bioinformatics

Année:

2014

Langue:

english

Fichier:

PDF, 1.88 MB

english, 2014

28

Species Tree Inference by Minimizing Deep Coalescences

Than, Cuong, Nakhleh, Luay, Li, Wen-Hsiung

Journal:

PLoS Computational Biology

Année:

2009

Langue:

english

Fichier:

PDF, 573 KB

english, 2009

29

An HMM-Based Comparative Genomic Framework for Detecting Introgression in Eukaryotes

Liu, Kevin J., Dai, Jingxuan, Truong, Kathy, Song, Ying, Kohn, Michael H., Nakhleh, Luay, Lengauer, Thomas

Journal:

PLoS Computational Biology

Année:

2014

Langue:

english

Fichier:

PDF, 1.30 MB

english, 2014

30

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks

Berestovsky, Natalie, Zhou, Wanding, Nagrath, Deepak, Nakhleh, Luay, Singh, Mona

Journal:

PLoS Computational Biology

Année:

2013

Langue:

english

Fichier:

PDF, 1.67 MB

english, 2013

31

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

Yu, Yun, Degnan, James H., Nakhleh, Luay, Felsenstein, Joseph

Journal:

Année:

2012

Langue:

english

Fichier:

PDF, 550 KB

english, 2012

32

The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks

Ruths, Derek, Muller, Melissa, Tseng, Jen-Te, Nakhleh, Luay, Ram, Prahlad T., Miyano, Satoru

Journal:

PLoS Computational Biology

Année:

2008

Langue:

english

Fichier:

PDF, 583 KB

english, 2008

33

An experimental study comparing linguistic phylogenetic reconstruction methods

Barbançon, François, Evans, Steven N., Nakhleh, Luay, Ringe, Don, Warnow, Tandy

Journal:

Année:

2013

Langue:

english

Fichier:

PDF, 575 KB

english, 2013

34

Monovar: single-nucleotide variant detection in single cells

Zafar, Hamim, Wang, Yong, Nakhleh, Luay, Navin, Nicholas, Chen, Ken

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 1.51 MB

english, 2016

35

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

Wen, Dingqiao, Yu, Yun, Hahn, Matthew W., Nakhleh, Luay

Journal:

Molecular Ecology

Année:

2016

Langue:

english

Fichier:

PDF, 1.28 MB

english, 2016

36

PRec-I-DCM3: a parallel framework for fast and accurate large-scale phylogeny reconstruction

Dotsenko, Yuri, Coarfa, Cristian, Nakhleh, Luay, Crummey, John Mellor, Roshan, Usman

Journal:

International Journal of Bioinformatics Research and Applications

Année:

2006

Langue:

english

Fichier:

PDF, 422 KB

english, 2006

37

Recombination and phylogeny: effects and detection

Ruths, Derek, Nakhleh, Luay

Journal:

International Journal of Bioinformatics Research and Applications

Année:

2005

Langue:

english

Fichier:

PDF, 483 KB

english, 2005

38

Irrational exuberance for resolved species trees

Hahn, Matthew W., Nakhleh, Luay

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 433 KB

english, 2016

39

226. Next-Generation Sleeping Beauty Integration Profiles of T-Cell Adoptive Immunotherapy

Ang, Sonny O., Dong, Jianrong, Nakhleh, Luay, Cooper, Laurence J.N.

Journal:

Molecular Therapy

Année:

2015

Langue:

english

Fichier:

PDF, 277 KB

english, 2015

40

212. Of States and Fates: Predicting T-Cell Immunity By the Numbers

O'Connor, Colleen M., Ang, Sonny O., Dong, Jianrong, Maiti, Sourindra N., Nakhleh, Luay, Cooper, Laurence J.N.

Journal:

Molecular Therapy

Année:

2015

Langue:

english

Fichier:

PDF, 289 KB

english, 2015

41

HySA: a Hybrid Structural variant Assembly approach using next-generation and single-molecule sequencing technologies

Fan, Xian, Chaisson, Mark, Nakhleh, Luay, Chen, Ken

Journal:

Genome Research

Année:

2017

Langue:

english

Fichier:

PDF, 611 KB

english, 2017

42

A maximum pseudo-likelihood approach for phylogenetic networks

Yun Yu,Luay Nakhleh

Journal:

Année:

2015

Langue:

english

Fichier:

PDF, 1.36 MB

english, 2015

43

In the light of deep coalescence: revisiting trees within networks

Jiafan Zhu,Yun Yu,Luay Nakhleh

Journal:

BMC Bioinformatics

Année:

2016

Langue:

english

Fichier:

PDF, 1.06 MB

english, 2016

44

Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks

Yun Yu,Christopher Jermaine,Luay Nakhleh

Journal:

Année:

2016

Langue:

english

Fichier:

PDF, 965 KB

english, 2016

45

[Lecture Notes in Computer Science] Comparative Genomics Volume 10562 || Fast Heuristics for Resolving Weakly Supported Branches Using Duplication, Transfers, and Losses

Meidanis, Joao, Nakhleh, Luay

Année:

2017

Langue:

english

Fichier:

PDF, 545 KB

english, 2017

46

Computational approaches for inferring tumor evolution from single-cell genomic data

Zafar, Hamim, Navin, Nicholas, Nakhleh, Luay, Chen, Ken

Journal:

Current Opinion in Systems Biology

Année:

2018

Langue:

english

Fichier:

PDF, 1.34 MB

english, 2018

47

Inferring Phylogenetic Networks Using PhyloNet

Wen, Dingqiao, Yu, Yun, Zhu, Jiafan, Nakhleh, Luay

Journal:

Systematic Biology

Année:

2018

Langue:

english

Fichier:

PDF, 167 KB

english, 2018

48

ALPHA: A Toolkit for Automated Local Phylogenomic Analyses

Elworth, R A Leo, Allen, Chabrielle, Benedict, Travis, Dulworth, Peter, Nakhleh, Luay, Schwartz, Russell

Journal:

Année:

2018

Langue:

english

Fichier:

PDF, 339 KB

english, 2018

49

Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data

Wen, Dingqiao, Nakhleh, Luay

Journal:

Systematic Biology

Année:

2017

Langue:

english

Fichier:

PDF, 1.62 MB

english, 2017

50

SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models

Zafar, Hamim, Tzen, Anthony, Navin, Nicholas, Chen, Ken, Nakhleh, Luay

Journal:

Année:

2017

Langue:

english

Fichier:

PDF, 2.12 MB

english, 2017