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Results: 1 to 20 of 125

1.

A consistent phylogenetic backbone for the fungi.

Ebersberger I, de Matos Simoes R, Kupczok A, Gube M, Kothe E, Voigt K, von Haeseler A.

Mol Biol Evol. 2012 May;29(5):1319-34. doi: 10.1093/molbev/msr285. Epub 2011 Nov 22.

PMID:
22114356
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

FUNYBASE: a FUNgal phYlogenomic dataBASE.

Marthey S, Aguileta G, Rodolphe F, Gendrault A, Giraud T, Fournier E, Lopez-Villavicencio M, Gautier A, Lebrun MH, Chiapello H.

BMC Bioinformatics. 2008 Oct 27;9:456. doi: 10.1186/1471-2105-9-456.

PMID:
18954438
[PubMed - indexed for MEDLINE]
Free PMC Article
3.
4.

Phylogenomic analyses predict sistergroup relationship of nucleariids and fungi and paraphyly of zygomycetes with significant support.

Liu Y, Steenkamp ET, Brinkmann H, Forget L, Philippe H, Lang BF.

BMC Evol Biol. 2009 Nov 25;9:272. doi: 10.1186/1471-2148-9-272.

PMID:
19939264
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Phylogenomics reveal a robust fungal tree of life.

Kuramae EE, Robert V, Snel B, Weiss M, Boekhout T.

FEMS Yeast Res. 2006 Dec;6(8):1213-20.

PMID:
17156018
[PubMed - indexed for MEDLINE]
6.

Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom.

Kuramae EE, Robert V, Echavarri-Erasun C, Boekhout T.

BMC Evol Biol. 2007 Aug 9;7:134.

PMID:
17688684
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

Phylogenetic relationships within the Opisthokonta based on phylogenomic analyses of conserved single-copy protein domains.

Torruella G, Derelle R, Paps J, Lang BF, Roger AJ, Shalchian-Tabrizi K, Ruiz-Trillo I.

Mol Biol Evol. 2012 Feb;29(2):531-44. doi: 10.1093/molbev/msr185. Epub 2011 Jul 18.

PMID:
21771718
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Reconstructing the fungal tree of life using phylogenomics and a preliminary investigation of the distribution of yeast prion-like proteins in the fungal kingdom.

Medina EM, Jones GW, Fitzpatrick DA.

J Mol Evol. 2011 Oct;73(3-4):116-33. doi: 10.1007/s00239-011-9461-4. Epub 2011 Sep 22.

PMID:
21938499
[PubMed - indexed for MEDLINE]
9.

Phylogenomics reveals subfamilies of fungal nonribosomal peptide synthetases and their evolutionary relationships.

Bushley KE, Turgeon BG.

BMC Evol Biol. 2010 Jan 26;10:26. doi: 10.1186/1471-2148-10-26.

PMID:
20100353
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Genomics of the fungal kingdom: insights into eukaryotic biology.

Galagan JE, Henn MR, Ma LJ, Cuomo CA, Birren B.

Genome Res. 2005 Dec;15(12):1620-31. Review. Erratum in: Genome Res. 2006 Feb;16(2):304.

PMID:
16339359
[PubMed - indexed for MEDLINE]
Free Article
11.

A fungal phylogeny based on 42 complete genomes derived from supertree and combined gene analysis.

Fitzpatrick DA, Logue ME, Stajich JE, Butler G.

BMC Evol Biol. 2006 Nov 22;6:99.

PMID:
17121679
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case.

Comas I, Moya A, González-Candelas F.

Syst Biol. 2007 Feb;56(1):1-16.

PMID:
17366133
[PubMed - indexed for MEDLINE]
13.

The impact of outgroup choice and missing data on major seed plant phylogenetics using genome-wide EST data.

de la Torre-Bárcena JE, Kolokotronis SO, Lee EK, Stevenson DW, Brenner ED, Katari MS, Coruzzi GM, DeSalle R.

PLoS One. 2009 Jun 2;4(6):e5764. doi: 10.1371/journal.pone.0005764.

PMID:
19503618
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

A phylogenomic approach to resolve the arthropod tree of life.

Meusemann K, von Reumont BM, Simon S, Roeding F, Strauss S, Kück P, Ebersberger I, Walzl M, Pass G, Breuers S, Achter V, von Haeseler A, Burmester T, Hadrys H, Wägele JW, Misof B.

Mol Biol Evol. 2010 Nov;27(11):2451-64. doi: 10.1093/molbev/msq130. Epub 2010 Jun 9.

PMID:
20534705
[PubMed - indexed for MEDLINE]
Free Article
15.

HaMStR: profile hidden markov model based search for orthologs in ESTs.

Ebersberger I, Strauss S, von Haeseler A.

BMC Evol Biol. 2009 Jul 8;9:157. doi: 10.1186/1471-2148-9-157.

PMID:
19586527
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis.

McCormack JE, Faircloth BC, Crawford NG, Gowaty PA, Brumfield RT, Glenn TC.

Genome Res. 2012 Apr;22(4):746-54. doi: 10.1101/gr.125864.111. Epub 2011 Dec 29.

PMID:
22207614
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Assessment of phylogenomic and orthology approaches for phylogenetic inference.

Dutilh BE, van Noort V, van der Heijden RT, Boekhout T, Snel B, Huynen MA.

Bioinformatics. 2007 Apr 1;23(7):815-24. Epub 2007 Jan 19.

PMID:
17237036
[PubMed - indexed for MEDLINE]
Free Article
18.

Impact of missing data on phylogenies inferred from empirical phylogenomic data sets.

Roure B, Baurain D, Philippe H.

Mol Biol Evol. 2013 Jan;30(1):197-214. doi: 10.1093/molbev/mss208. Epub 2012 Aug 28.

PMID:
22930702
[PubMed - indexed for MEDLINE]
Free Article
19.

Evolution of Rhizaria: new insights from phylogenomic analysis of uncultivated protists.

Burki F, Kudryavtsev A, Matz MV, Aglyamova GV, Bulman S, Fiers M, Keeling PJ, Pawlowski J.

BMC Evol Biol. 2010 Dec 2;10:377. doi: 10.1186/1471-2148-10-377.

PMID:
21126361
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A fungal phylogeny based on 82 complete genomes using the composition vector method.

Wang H, Xu Z, Gao L, Hao B.

BMC Evol Biol. 2009 Aug 10;9:195. doi: 10.1186/1471-2148-9-195.

PMID:
19664262
[PubMed - indexed for MEDLINE]
Free PMC Article

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