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Results: 1 to 20 of 73

1.

A simple, fast, and accurate method of phylogenomic inference.

Wu M, Eisen JA.

Genome Biol. 2008 Oct 13;9(10):R151. doi: 10.1186/gb-2008-9-10-r151.

PMID:
18851752
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.

Wu M, Scott AJ.

Bioinformatics. 2012 Apr 1;28(7):1033-4. doi: 10.1093/bioinformatics/bts079. Epub 2012 Feb 12.

PMID:
22332237
[PubMed - indexed for MEDLINE]
Free Article
3.

Rooting the eutherian tree: the power and pitfalls of phylogenomics.

Nishihara H, Okada N, Hasegawa M.

Genome Biol. 2007;8(9):R199.

PMID:
17883877
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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]
5.

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
6.

Phylogenomic resources at the UCSC Genome Browser.

Rosenbloom K, Taylor J, Schaeffer S, Kent J, Haussler D, Miller W.

Methods Mol Biol. 2008;422:133-44. doi: 10.1007/978-1-59745-581-7_9.

PMID:
18629665
[PubMed - indexed for MEDLINE]
7.

e-Science: relieving bottlenecks in large-scale genome analyses.

Craddock T, Harwood CR, Hallinan J, Wipat A.

Nat Rev Microbiol. 2008 Dec;6(12):948-54. doi: 10.1038/nrmicro2031. Review.

PMID:
19008893
[PubMed - indexed for MEDLINE]
8.

Large-scale assignment of orthology: back to phylogenetics?

Gabaldón T.

Genome Biol. 2008 Oct 30;9(10):235. doi: 10.1186/gb-2008-9-10-235. Review.

PMID:
18983710
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

Phylogenomic inference of protein molecular function: advances and challenges.

Sjölander K.

Bioinformatics. 2004 Jan 22;20(2):170-9. Review.

PMID:
14734307
[PubMed - indexed for MEDLINE]
Free Article
10.

Supertree construction in the genomic age.

Bininda-Emonds OR.

Methods Enzymol. 2005;395:745-57.

PMID:
15865993
[PubMed - indexed for MEDLINE]
11.

Co-phylog: an assembly-free phylogenomic approach for closely related organisms.

Yi H, Jin L.

Nucleic Acids Res. 2013 Apr;41(7):e75. doi: 10.1093/nar/gkt003. Epub 2013 Jan 18.

PMID:
23335788
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Functional genome annotation through phylogenomic mapping.

Srinivasan BS, Caberoy NB, Suen G, Taylor RG, Shah R, Tengra F, Goldman BS, Garza AG, Welch RD.

Nat Biotechnol. 2005 Jun;23(6):691-8.

PMID:
15940241
[PubMed - indexed for MEDLINE]
13.

FlyPhy: a phylogenomic analysis platform for Drosophila genes and gene families.

Wu J, Xu X, Xiao J, Xu L, Yi H, Gao S, Liu J, Bao Q, Zhao F, Li X.

BMC Bioinformatics. 2009 Apr 25;10:123. doi: 10.1186/1471-2105-10-123.

PMID:
19393099
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs.

Zmasek CM, Eddy SR.

BMC Bioinformatics. 2002 May 16;3:14.

PMID:
12028595
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Phylogenomic inference of protein molecular function.

Krishnamurthy N, Sjölander K.

Curr Protoc Bioinformatics. 2005 Oct;Chapter 6:Unit 6.9. doi: 10.1002/0471250953.bi0609s11.

PMID:
18428751
[PubMed - indexed for MEDLINE]
16.

Phylogenetic understanding of clonal populations in an era of whole genome sequencing.

Pearson T, Okinaka RT, Foster JT, Keim P.

Infect Genet Evol. 2009 Sep;9(5):1010-9. doi: 10.1016/j.meegid.2009.05.014. Epub 2009 May 27. Review.

PMID:
19477301
[PubMed - indexed for MEDLINE]
17.

Genome phylogenetic analysis based on extended gene contents.

Gu X, Zhang H.

Mol Biol Evol. 2004 Jul;21(7):1401-8. Epub 2004 Apr 14.

PMID:
15084675
[PubMed - indexed for MEDLINE]
Free Article
18.

Ten years of bacterial genome sequencing: comparative-genomics-based discoveries.

Binnewies TT, Motro Y, Hallin PF, Lund O, Dunn D, La T, Hampson DJ, Bellgard M, Wassenaar TM, Ussery DW.

Funct Integr Genomics. 2006 Jul;6(3):165-85. Epub 2006 May 12. Review.

PMID:
16773396
[PubMed - indexed for MEDLINE]
19.

A whole-genome phylogeny of the family Pasteurellaceae.

Bonaventura MP, Lee EK, Desalle R, Planet PJ.

Mol Phylogenet Evol. 2010 Mar;54(3):950-6. doi: 10.1016/j.ympev.2009.08.010. Epub 2009 Aug 15.

PMID:
19686857
[PubMed - indexed for MEDLINE]
20.

A phylum-level bacterial phylogenetic marker database.

Wang Z, Wu M.

Mol Biol Evol. 2013 Jun;30(6):1258-62. doi: 10.1093/molbev/mst059. Epub 2013 Mar 21.

PMID:
23519313
[PubMed - indexed for MEDLINE]
Free Article

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