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A maximum pseudo-likelihood approach for phylogenetic networks.

Yu Y, Nakhleh L.

BMC Genomics. 2015 Oct 2;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. 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.


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

Park HJ, Nakhleh L.

BMC Bioinformatics. 2012;13 Suppl 19:S12. doi: 10.1186/1471-2105-13-S19-S12. Epub 2012 Dec 19.


Quantifying and assessing the effect of chemical symmetry in metabolic pathways.

Zhou W, Nakhleh L.

J Chem Inf Model. 2012 Oct 22;52(10):2684-96. doi: 10.1021/ci300259u. Epub 2012 Sep 28.


Gene duplicability-connectivity-complexity across organisms and a neutral evolutionary explanation.

Zhu Y, Du P, Nakhleh L.

PLoS One. 2012;7(9):e44491. doi: 10.1371/journal.pone.0044491. Epub 2012 Sep 11.


Convergent evolution of modularity in metabolic networks through different community structures.

Zhou W, Nakhleh L.

BMC Evol Biol. 2012 Sep 14;12:181. doi: 10.1186/1471-2148-12-181.

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