Luay Nakhleh: search on 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

Year:

2013

Language:

english

File:

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

Year:

2005

Language:

english

File:

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:

Year:

2005

Language:

english

File:

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:

Year:

2005

Language:

english

File:

PDF, 423 KB

english, 2005

5

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

Year:

2015

Language:

english

File:

PDF, 277 KB

english, 2015

6

A maximum pseudo-likelihood approach for phylogenetic networks

Yun Yu,Luay Nakhleh

Journal:

Year:

2015

Language:

english

File:

PDF, 1.36 MB

english, 2015

7

A divide-and-conquer method for scalable phylogenetic network inference from multilocus data

Zhu, Jiafan, Liu, Xinhao, Ogilvie, Huw A, Nakhleh, Luay K

Journal:

Year:

2019

Language:

english

File:

PDF, 668 KB

english, 2019

8

Integrated likelihood for phylogenomics under a no-common-mechanism model

Tidwell, Hunter, Nakhleh, Luay

Journal:

Year:

2020

File:

PDF, 1.60 MB

2020

9

Convergent evolution of modularity in metabolic networks through different community structures

Wanding Zhou, Luay Nakhleh

Journal:

BMC Evolutionary Biology

Year:

2012

Language:

english

File:

PDF, 1.34 MB

english, 2012

10

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

Year:

2008

Language:

english

File:

PDF, 583 KB

english, 2008

11

Towards an accurate and efficient heuristic for species/gene tree co-estimation

Wang, Yaxuan, Nakhleh, Luay

Journal:

Year:

2018

Language:

english

File:

PDF, 1.80 MB

english, 2018

12

Fast algorithms and heuristics for phylogenomics under ILS and hybridization

Yu, Yun, Ristic, Nikola, Nakhleh, Luay

Journal:

BMC Bioinformatics

Year:

2013

Language:

english

File:

PDF, 884 KB

english, 2013

13

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

Year:

2015

Language:

english

File:

PDF, 1.06 MB

english, 2015

14

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

Cuong Than, Derek Ruths, Luay Nakhleh

Journal:

BMC Bioinformatics

Year:

2008

Language:

english

File:

PDF, 1.28 MB

english, 2008

15

Bootstrap-based Support of HGT Inferred by Maximum Parsimony

Hyun Jung Park, Guohua Jin, Luay Nakhleh

Journal:

BMC Evolutionary Biology

Year:

2010

Language:

english

File:

PDF, 1.18 MB

english, 2010

16

Monovar: single-nucleotide variant detection in single cells

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

Journal:

Year:

2016

Language:

english

File:

PDF, 1.51 MB

english, 2016

17

Properties of metabolic graphs: biological organization or representation artifacts?

Wanding Zhou, Luay Nakhleh

Journal:

BMC Bioinformatics

Year:

2011

Language:

english

File:

PDF, 1.05 MB

english, 2011

18

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

Iyad A. Kanj, Luay Nakhleh, Ge Xia

Journal:

Year:

2008

Language:

english

File:

PDF, 525 KB

english, 2008

19

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

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

Journal:

Year:

2017

Language:

english

File:

PDF, 2.12 MB

english, 2017

20

Comments on the model parameters in “SiFit: inferring tumor trees from single-cell sequencing data under finite-sites models”

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

Journal:

Year:

2019

File:

PDF, 500 KB

2019

21

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:

Year:

2012

Language:

english

File:

PDF, 550 KB

english, 2012

22

An experimental study comparing linguistic phylogenetic reconstruction methods

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

Journal:

Year:

2013

Language:

english

File:

PDF, 575 KB

english, 2013

23

Stranger in a strange land: the experiences of immigrant researchers

Kamoun, Sophien, Lozano-Durán, Rosa, Nakhleh, Luay

Journal:

Year:

2017

Language:

english

File:

PDF, 286 KB

english, 2017

24

Inference of species phylogenies from bi-allelic markers using pseudo-likelihood

Zhu, Jiafan, Nakhleh, Luay

Journal:

Year:

2018

Language:

english

File:

PDF, 1.29 MB

english, 2018

25

[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

Year:

2004

Language:

english

File:

PDF, 234 KB

english, 2004

26

Towards accurate characterization of clonal heterogeneity based on structural variation

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

Journal:

BMC Bioinformatics

Year:

2014

Language:

english

File:

PDF, 1.88 MB

english, 2014

27

Maximum likelihood inference of reticulate evolutionary histories

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

Journal:

Proceedings of the National Academy of Sciences

Year:

2014

Language:

english

File:

PDF, 863 KB

english, 2014

28

Reconstructing Reticulate Evolution in Species—Theory and Practice

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

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 175 KB

english, 2005

29

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

Year:

2007

Language:

english

File:

PDF, 1.51 MB

english, 2007

30

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks

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

Journal:

PLoS Computational Biology

Year:

2013

Language:

english

File:

PDF, 1.67 MB

english, 2013

31

Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks

Yun Yu,Christopher Jermaine,Luay Nakhleh

Journal:

Year:

2016

Language:

english

File:

PDF, 965 KB

english, 2016

32

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

Year:

2006

Language:

english

File:

PDF, 177 KB

english, 2006

33

Irrational exuberance for resolved species trees

Hahn, Matthew W., Nakhleh, Luay

Journal:

Year:

2016

Language:

english

File:

PDF, 433 KB

english, 2016

34

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

Year:

2017

Language:

english

File:

PDF, 611 KB

english, 2017

35

Matrilysin/MMP-7 Cleavage of Perlecan/HSPG2 Complexed with Semaphorin 3A Supports FAK-Mediated Stromal Invasion by Prostate Cancer Cells

Grindel, Brian J., Martinez, Jerahme R., Tellman, Tristen V., Harrington, Daniel A., Zafar, Hamim, Nakhleh, Luay, Chung, Leland W., Farach-Carson, Mary C.

Journal:

Scientific Reports

Year:

2018

Language:

english

File:

PDF, 2.28 MB

english, 2018

36

Computational approaches to species phylogeny inference and gene tree reconciliation

Journal:

Trends in Ecology & Evolution

Year:

2013

Language:

english

File:

PDF, 516 KB

english, 2013

37

ALPHA: A Toolkit for Automated Local Phylogenomic Analyses

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

Journal:

Year:

2018

Language:

english

File:

PDF, 339 KB

english, 2018

38

Methods for copy number aberration detection from single-cell DNA-sequencing data

Mallory, Xian F., Edrisi, Mohammadamin, Navin, Nicholas, Nakhleh, Luay

Journal:

Year:

2020

File:

PDF, 2.28 MB

2020

39

Seeing the trees and their branches in the network is hard

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

Journal:

Theoretical Computer Science

Year:

2008

Language:

english

File:

PDF, 711 KB

english, 2008

40

[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

Year:

2012

Language:

english

File:

PDF, 2.77 MB

english, 2012

41

In the light of deep coalescence: revisiting trees within networks

Jiafan Zhu,Yun Yu,Luay Nakhleh

Journal:

BMC Bioinformatics

Year:

2016

Language:

english

File:

PDF, 1.06 MB

english, 2016

42

Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data

Wen, Dingqiao, Nakhleh, Luay

Journal:

Systematic Biology

Year:

2017

Language:

english

File:

PDF, 1.62 MB

english, 2017

43

Rapidly exploring structural and dynamic properties of signaling networks using PathwayOracle

Derek Ruths, Luay Nakhleh, Prahlad T Ram

Journal:

BMC Systems Biology

Year:

2008

Language:

english

File:

PDF, 2.49 MB

english, 2008

44

Quantifying and Assessing the Effect of Chemical Symmetry in Metabolic Pathways

Zhou, Wanding, Nakhleh, Luay

Journal:

Journal of Chemical Information and Modeling

Year:

2012

Language:

english

File:

PDF, 2.66 MB

english, 2012

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

Year:

2017

Language:

english

File:

PDF, 545 KB

english, 2017

46

[ACM Press the 2018 ACM International Conference - Washington, DC, USA (2018.08.29-2018.09.01)] Proceedings of the 2018 ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics - BCB '18 - Species Tree and Reconciliation Estimation under a Duplication-Loss-Coalescence Model

Du, Peng, Nakhleh, Luay

Year:

2018

Language:

english

File:

PDF, 1.28 MB

english, 2018

47

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

Year:

2014

Language:

english

File:

PDF, 1.30 MB

english, 2014

48

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

Hyun Jung Park, Luay Nakhleh

Journal:

BMC Bioinformatics

Year:

2012

Language:

english

File:

PDF, 634 KB

english, 2012

49

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

Year:

2006

Language:

english

File:

PDF, 422 KB

english, 2006

50

Recombination and phylogeny: effects and detection

Ruths, Derek, Nakhleh, Luay

Journal:

International Journal of Bioinformatics Research and Applications

Year:

2005

Language:

english

File:

PDF, 483 KB

english, 2005

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