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Items: 1 to 20 of 55


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.


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.


An HMM-based comparative genomic framework for detecting introgression in eukaryotes.

Liu KJ, Dai J, Truong K, Song Y, Kohn MH, Nakhleh L.

PLoS Comput Biol. 2014 Jun 12;10(6):e1003649. doi: 10.1371/journal.pcbi.1003649. eCollection 2014 Jun.


Mapping network motif tunability and robustness in the design of synthetic signaling circuits.

Iadevaia S, Nakhleh LK, Azencott R, Ram PT.

PLoS One. 2014 Mar 18;9(3):e91743. doi: 10.1371/journal.pone.0091743. eCollection 2014.


Fast algorithms and heuristics for phylogenomics under ILS and hybridization.

Yu Y, Ristic N, Nakhleh L.

BMC Bioinformatics. 2013;14 Suppl 15:S6. doi: 10.1186/1471-2105-14-S15-S6. Epub 2013 Oct 15.


Modeling integrated cellular machinery using hybrid Petri-Boolean networks.

Berestovsky N, Zhou W, Nagrath D, Nakhleh L.

PLoS Comput Biol. 2013;9(11):e1003306. doi: 10.1371/journal.pcbi.1003306. Epub 2013 Nov 7.


Computational approaches to species phylogeny inference and gene tree reconciliation.

Nakhleh L.

Trends Ecol Evol. 2013 Dec;28(12):719-28. doi: 10.1016/j.tree.2013.09.004. Epub 2013 Oct 1. Review.


Evolution after whole-genome duplication: a network perspective.

Zhu Y, Lin Z, Nakhleh L.

G3 (Bethesda). 2013 Nov 6;3(11):2049-57. doi: 10.1534/g3.113.008458.


An Evaluation of Methods for Inferring Boolean Networks from Time-Series Data.

Berestovsky N, Nakhleh L.

PLoS One. 2013 Jun 21;8(6):e66031. doi: 10.1371/journal.pone.0066031. Print 2013.


Networks: expanding evolutionary thinking.

Bapteste E, van Iersel L, Janke A, Kelchner S, Kelk S, McInerney JO, Morrison DA, Nakhleh L, Steel M, Stougie L, Whitfield J.

Trends Genet. 2013 Aug;29(8):439-41. doi: 10.1016/j.tig.2013.05.007. Epub 2013 Jun 11.


Boosting forward-time population genetic simulators through genotype compression.

Ruths T, Nakhleh L.

BMC Bioinformatics. 2013 Jun 14;14:192. doi: 10.1186/1471-2105-14-192.


Parsimonious inference of hybridization in the presence of incomplete lineage sorting.

Yu Y, Barnett RM, Nakhleh L.

Syst Biol. 2013 Sep;62(5):738-51. doi: 10.1093/sysbio/syt037. Epub 2013 Jun 4.


Neutral forces acting on intragenomic variability shape the Escherichia coli regulatory network topology.

Ruths T, Nakhleh L.

Proc Natl Acad Sci U S A. 2013 May 7;110(19):7754-9. doi: 10.1073/pnas.1217630110. Epub 2013 Apr 22.

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