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Items: 1 to 20 of 66


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

Grindel BJ, Martinez JR, Tellman TV, Harrington DA, Zafar H, Nakhleh L, Chung LW, Farach-Carson MC.

Sci Rep. 2018 May 8;8(1):7262. doi: 10.1038/s41598-018-25435-3.


ALPHA: A Toolkit for Automated Local Phylogenomic Analyses.

Elworth RAL, Allen C, Benedict T, Dulworth P, Nakhleh L.

Bioinformatics. 2018 Mar 19. doi: 10.1093/bioinformatics/bty173. [Epub ahead of print]


Inferring Phylogenetic Networks Using PhyloNet.

Wen D, Yu Y, Zhu J, Nakhleh L.

Syst Biol. 2018 Jul 1;67(4):735-740. doi: 10.1093/sysbio/syy015.


Bayesian inference of phylogenetic networks from bi-allelic genetic markers.

Zhu J, Wen D, Yu Y, Meudt HM, Nakhleh L.

PLoS Comput Biol. 2018 Jan 10;14(1):e1005932. doi: 10.1371/journal.pcbi.1005932. eCollection 2018 Jan.


Stranger in a strange land: the experiences of immigrant researchers.

Kamoun S, Lozano-DurĂ¡n R, Nakhleh L.

Genome Biol. 2017 Dec 15;18(1):232. doi: 10.1186/s13059-017-1370-4.


Coestimating Reticulate Phylogenies and Gene Trees from Multilocus Sequence Data.

Wen D, Nakhleh L.

Syst Biol. 2018 May 1;67(3):439-457. doi: 10.1093/sysbio/syx085.


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

Zafar H, Tzen A, Navin N, Chen K, Nakhleh L.

Genome Biol. 2017 Sep 19;18(1):178. doi: 10.1186/s13059-017-1311-2.


In the light of deep coalescence: revisiting trees within networks.

Zhu J, Yu Y, Nakhleh L.

BMC Bioinformatics. 2016 Nov 11;17(Suppl 14):415. doi: 10.1186/s12859-016-1269-1.


Exploring phylogenetic hypotheses via Gibbs sampling on evolutionary networks.

Yu Y, Jermaine C, Nakhleh L.

BMC Genomics. 2016 Nov 11;17(Suppl 10):784. doi: 10.1186/s12864-016-3099-y.


Correction: Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent.

Wen D, Yu Y, Nakhleh L.

PLoS Genet. 2017 Feb 8;13(2):e1006598. doi: 10.1371/journal.pgen.1006598. eCollection 2017 Feb.


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

Fan X, Chaisson M, Nakhleh L, Chen K.

Genome Res. 2017 May;27(5):793-800. doi: 10.1101/gr.214767.116. Epub 2017 Jan 19.


Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent.

Wen D, Yu Y, Nakhleh L.

PLoS Genet. 2016 May 4;12(5):e1006006. doi: 10.1371/journal.pgen.1006006. eCollection 2016 May. Erratum in: PLoS Genet. 2017 Feb 8;13(2):e1006598.


Monovar: single-nucleotide variant detection in single cells.

Zafar H, Wang Y, Nakhleh L, Navin N, Chen K.

Nat Methods. 2016 Jun;13(6):505-7. doi: 10.1038/nmeth.3835. Epub 2016 Apr 18.


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

Wen D, Yu Y, Hahn MW, Nakhleh L.

Mol Ecol. 2016 Jun;25(11):2361-72. doi: 10.1111/mec.13544. Epub 2016 Mar 10.


Irrational exuberance for resolved species trees.

Hahn MW, Nakhleh L.

Evolution. 2016 Jan;70(1):7-17. doi: 10.1111/evo.12832. Epub 2015 Dec 17.


A maximum pseudo-likelihood approach for phylogenetic networks.

Yu Y, Nakhleh L.

BMC Genomics. 2015;16 Suppl 10:S10. doi: 10.1186/1471-2164-16-S10-S10. Epub 2015 Oct 2.


Interspecific introgressive origin of genomic diversity in the house mouse.

Liu KJ, Steinberg E, Yozzo A, Song Y, Kohn MH, Nakhleh L.

Proc Natl Acad Sci U S A. 2015 Jan 6;112(1):196-201. doi: 10.1073/pnas.1406298111. Epub 2014 Dec 15.


Mutations in global regulators lead to metabolic selection during adaptation to complex environments.

Saxer G, Krepps MD, Merkley ED, Ansong C, Deatherage Kaiser BL, Valovska MT, Ristic N, Yeh PT, Prakash VP, Leiser OP, Nakhleh L, Gibbons HS, Kreuzer HW, Shamoo Y.

PLoS Genet. 2014 Dec 11;10(12):e1004872. doi: 10.1371/journal.pgen.1004872. eCollection 2014 Dec.


Maximum likelihood inference of reticulate evolutionary histories.

Yu Y, Dong J, Liu KJ, Nakhleh L.

Proc Natl Acad Sci U S A. 2014 Nov 18;111(46):16448-53. doi: 10.1073/pnas.1407950111. Epub 2014 Nov 3.


Towards accurate characterization of clonal heterogeneity based on structural variation.

Fan X, Zhou W, Chong Z, Nakhleh L, Chen K.

BMC Bioinformatics. 2014 Sep 8;15:299. doi: 10.1186/1471-2105-15-299.

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