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Items: 23

1.

Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.

Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, da Rosa Farias D, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA.

Nat Genet. 2018 Nov;50(11):1618. doi: 10.1038/s41588-018-0261-2.

PMID:
30291357
2.

The prevalence of terraced treescapes in analyses of phylogenetic data sets.

Dobrin BH, Zwickl DJ, Sanderson MJ.

BMC Evol Biol. 2018 Apr 4;18(1):46. doi: 10.1186/s12862-018-1162-9.

3.

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.

Stein JC, Yu Y, Copetti D, Zwickl DJ, Zhang L, Zhang C, Chougule K, Gao D, Iwata A, Goicoechea JL, Wei S, Wang J, Liao Y, Wang M, Jacquemin J, Becker C, Kudrna D, Zhang J, Londono CEM, Song X, Lee S, Sanchez P, Zuccolo A, Ammiraju JSS, Talag J, Danowitz A, Rivera LF, Gschwend AR, Noutsos C, Wu CC, Kao SM, Zeng JW, Wei FJ, Zhao Q, Feng Q, El Baidouri M, Carpentier MC, Lasserre E, Cooke R, Rosa Farias DD, da Maia LC, Dos Santos RS, Nyberg KG, McNally KL, Mauleon R, Alexandrov N, Schmutz J, Flowers D, Fan C, Weigel D, Jena KK, Wicker T, Chen M, Han B, Henry R, Hsing YC, Kurata N, de Oliveira AC, Panaud O, Jackson SA, Machado CA, Sanderson MJ, Long M, Ware D, Wing RA.

Nat Genet. 2018 Feb;50(2):285-296. doi: 10.1038/s41588-018-0040-0. Epub 2018 Jan 22. Erratum in: Nat Genet. 2018 Nov;50(11):1618.

PMID:
29358651
4.

Impacts of Terraces on Phylogenetic Inference.

Sanderson MJ, McMahon MM, Stamatakis A, Zwickl DJ, Steel M.

Syst Biol. 2015 Sep;64(5):709-26. doi: 10.1093/sysbio/syv024. Epub 2015 May 20.

PMID:
25999395
5.

Endogenous florendoviruses are major components of plant genomes and hallmarks of virus evolution.

Geering AD, Maumus F, Copetti D, Choisne N, Zwickl DJ, Zytnicki M, McTaggart AR, Scalabrin S, Vezzulli S, Wing RA, Quesneville H, Teycheney PY.

Nat Commun. 2014 Nov 10;5:5269. doi: 10.1038/ncomms6269.

6.

A gateway for phylogenetic analysis powered by grid computing featuring GARLI 2.0.

Bazinet AL, Zwickl DJ, Cummings MP.

Syst Biol. 2014 Sep;63(5):812-8. doi: 10.1093/sysbio/syu031. Epub 2014 Apr 30.

7.

Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.

Zwickl DJ, Stein JC, Wing RA, Ware D, Sanderson MJ.

Syst Biol. 2014 Sep;63(5):645-59. doi: 10.1093/sysbio/syu027. Epub 2014 Apr 9.

PMID:
24721692
8.

A simple method for estimating informative node age priors for the fossil calibration of molecular divergence time analyses.

Nowak MD, Smith AB, Simpson C, Zwickl DJ.

PLoS One. 2013 Jun 5;8(6):e66245. doi: 10.1371/journal.pone.0066245. Print 2013.

9.

A large-scale, higher-level, molecular phylogenetic study of the insect order Lepidoptera (moths and butterflies).

Regier JC, Mitter C, Zwick A, Bazinet AL, Cummings MP, Kawahara AY, Sohn JC, Zwickl DJ, Cho S, Davis DR, Baixeras J, Brown J, Parr C, Weller S, Lees DC, Mitter KT.

PLoS One. 2013;8(3):e58568. doi: 10.1371/journal.pone.0058568. Epub 2013 Mar 12.

10.

Resolving discrepancy between nucleotides and amino acids in deep-level arthropod phylogenomics: differentiating serine codons in 21-amino-acid models.

Zwick A, Regier JC, Zwickl DJ.

PLoS One. 2012;7(11):e47450. doi: 10.1371/journal.pone.0047450. Epub 2012 Nov 20.

11.

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.

Ayres DL, Darling A, Zwickl DJ, Beerli P, Holder MT, Lewis PO, Huelsenbeck JP, Ronquist F, Swofford DL, Cummings MP, Rambaut A, Suchard MA.

Syst Biol. 2012 Jan;61(1):170-3. doi: 10.1093/sysbio/syr100. Epub 2011 Oct 1.

12.

Old gene duplication facilitates origin and diversification of an innovative communication system--twice.

Arnegard ME, Zwickl DJ, Lu Y, Zakon HH.

Proc Natl Acad Sci U S A. 2010 Dec 21;107(51):22172-7. doi: 10.1073/pnas.1011803107. Epub 2010 Dec 2.

13.

Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences.

Scaduto DI, Brown JM, Haaland WC, Zwickl DJ, Hillis DM, Metzker ML.

Proc Natl Acad Sci U S A. 2010 Dec 14;107(50):21242-7. doi: 10.1073/pnas.1015673107. Epub 2010 Nov 15.

14.

Molecular evolution of Na+ channels in teleost fishes.

Zakon HH, Jost MC, Zwickl DJ, Lu Y, Hillis DM.

Integr Zool. 2009 Mar;4(1):64-74. doi: 10.1111/j.1749-4877.2008.00136.x. Review.

15.

Evaluating the robustness of phylogenetic methods to among-site variability in substitution processes.

Holder MT, Zwickl DJ, Dessimoz C.

Philos Trans R Soc Lond B Biol Sci. 2008 Dec 27;363(1512):4013-21. doi: 10.1098/rstb.2008.0162.

16.

Molecular evolution of communication signals in electric fish.

Zakon HH, Zwickl DJ, Lu Y, Hillis DM.

J Exp Biol. 2008 Jun;211(Pt 11):1814-8. doi: 10.1242/jeb.015982. Review.

17.

Taxon sampling affects inferences of macroevolutionary processes from phylogenetic trees.

Heath TA, Zwickl DJ, Kim J, Hillis DM.

Syst Biol. 2008 Feb;57(1):160-6. doi: 10.1080/10635150701884640. No abstract available.

PMID:
18300029
18.

Sodium channel genes and the evolution of diversity in communication signals of electric fishes: convergent molecular evolution.

Zakon HH, Lu Y, Zwickl DJ, Hillis DM.

Proc Natl Acad Sci U S A. 2006 Mar 7;103(10):3675-80. Epub 2006 Feb 27.

19.

Is sparse taxon sampling a problem for phylogenetic inference?

Hillis DM, Pollock DD, McGuire JA, Zwickl DJ.

Syst Biol. 2003 Feb;52(1):124-6. No abstract available.

20.

Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support.

Wilcox TP, Zwickl DJ, Heath TA, Hillis DM.

Mol Phylogenet Evol. 2002 Nov;25(2):361-71.

PMID:
12414316
21.

Genetic algorithms and parallel processing in maximum-likelihood phylogeny inference.

Brauer MJ, Holder MT, Dries LA, Zwickl DJ, Lewis PO, Hillis DM.

Mol Biol Evol. 2002 Oct;19(10):1717-26.

PMID:
12270898
22.

Increased taxon sampling is advantageous for phylogenetic inference.

Pollock DD, Zwickl DJ, McGuire JA, Hillis DM.

Syst Biol. 2002 Aug;51(4):664-71. No abstract available.

23.

Increased taxon sampling greatly reduces phylogenetic error.

Zwickl DJ, Hillis DM.

Syst Biol. 2002 Aug;51(4):588-98.

PMID:
12228001

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