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Results: 1 to 20 of 48

1.

Maximum likelihood inference of reticulate evolutionary histories.

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

Proc Natl Acad Sci U S A. 2014 Nov 3. pii: 201407950. [Epub ahead of print]

PMID:
25368173
[PubMed - as supplied by publisher]
2.

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.

PMID:
25201439
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
24922281
[PubMed - in process]
Free PMC Article
4.

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.

PMID:
24642504
[PubMed - in process]
Free PMC Article
5.

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.

PMID:
24564257
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
24244124
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

PMID:
24094331
[PubMed - indexed for MEDLINE]
8.

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.

PMID:
24048644
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

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.

PMID:
23805196
[PubMed - as supplied by publisher]
Free PMC Article
10.

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.

PMID:
23764187
[PubMed - indexed for MEDLINE]
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.

PMID:
23763838
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

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.

PMID:
23736104
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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.

PMID:
23610404
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

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.

PMID:
23281614
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

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.

PMID:
22985501
[PubMed - indexed for MEDLINE]
16.

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.

PMID:
22984517
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

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.

PMID:
22974099
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

ncDNA and drift drive binding site accumulation.

Ruths T, Nakhleh L.

BMC Evol Biol. 2012 Aug 30;12:159. doi: 10.1186/1471-2148-12-159.

PMID:
22935101
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

The probability of a gene tree topology within a phylogenetic network with applications to hybridization detection.

Yu Y, Degnan JH, Nakhleh L.

PLoS Genet. 2012;8(4):e1002660. doi: 10.1371/journal.pgen.1002660. Epub 2012 Apr 19.

PMID:
22536161
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Algorithms for MDC-based multi-locus phylogeny inference: beyond rooted binary gene trees on single alleles.

Yu Y, Warnow T, Nakhleh L.

J Comput Biol. 2011 Nov;18(11):1543-59. doi: 10.1089/cmb.2011.0174. Epub 2011 Oct 28.

PMID:
22035329
[PubMed - indexed for MEDLINE]
Free PMC Article
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