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Results: 1 to 20 of 46

1.

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
2.

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
3.

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
4.

Modeling integrated cellular machinery using hybrid Petri-Boolean networks.

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

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

PMID:
24244124
[PubMed - in process]
Free PMC Article
5.

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]
6.

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
7.

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
8.

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]
9.

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
10.

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]
11.

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
12.

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
13.

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]
14.

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
15.

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
16.

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
17.

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
18.

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
19.

Population genomics in bacteria: a case study of Staphylococcus aureus.

Takuno S, Kado T, Sugino RP, Nakhleh L, Innan H.

Mol Biol Evol. 2012 Feb;29(2):797-809. doi: 10.1093/molbev/msr249. Epub 2011 Oct 17.

PMID:
22009061
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Kinome siRNA-phosphoproteomic screen identifies networks regulating AKT signaling.

Lu Y, Muller M, Smith D, Dutta B, Komurov K, Iadevaia S, Ruths D, Tseng JT, Yu S, Yu Q, Nakhleh L, Balazsi G, Donnelly J, Schurdak M, Morgan-Lappe S, Fesik S, Ram PT, Mills GB.

Oncogene. 2011 Nov 10;30(45):4567-77. doi: 10.1038/onc.2011.164. Epub 2011 Jun 13.

PMID:
21666717
[PubMed - indexed for MEDLINE]
Free PMC Article

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