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Items: 1 to 20 of 550

1.

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
2.

Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay.

Pandya GA, Holmes MH, Petersen JM, Pradhan S, Karamycheva SA, Wolcott MJ, Molins C, Jones M, Schriefer ME, Fleischmann RD, Peterson SN.

BMC Microbiol. 2009 Oct 7;9:213. doi: 10.1186/1471-2180-9-213.

3.

Comparative genome sequencing for discovery of novel polymorphisms in Bacillus anthracis.

Read TD, Salzberg SL, Pop M, Shumway M, Umayam L, Jiang L, Holtzapple E, Busch JD, Smith KL, Schupp JM, Solomon D, Keim P, Fraser CM.

Science. 2002 Jun 14;296(5575):2028-33. Epub 2002 May 9.

4.

Genome-based phylogenetic analysis of Streptomyces and its relatives.

Alam MT, Merlo ME, Takano E, Breitling R.

Mol Phylogenet Evol. 2010 Mar;54(3):763-72. doi: 10.1016/j.ympev.2009.11.019. Epub 2009 Dec 3.

PMID:
19948233
5.

Discrimination and phylogenomic classification of Bacillus anthracis-cereus-thuringiensis strains based on LC-MS/MS analysis of whole cell protein digests.

Dworzanski JP, Dickinson DN, Deshpande SV, Snyder AP, Eckenrode BA.

Anal Chem. 2010 Jan 1;82(1):145-55. doi: 10.1021/ac9015648.

PMID:
19938824
6.

Methods for obtaining and analyzing whole chloroplast genome sequences.

Jansen RK, Raubeson LA, Boore JL, dePamphilis CW, Chumley TW, Haberle RC, Wyman SK, Alverson AJ, Peery R, Herman SJ, Fourcade HM, Kuehl JV, McNeal JR, Leebens-Mack J, Cui L.

Methods Enzymol. 2005;395:348-84.

PMID:
15865976
7.

Strain-specific single-nucleotide polymorphism assays for the Bacillus anthracis Ames strain.

Van Ert MN, Easterday WR, Simonson TS, U'Ren JM, Pearson T, Kenefic LJ, Busch JD, Huynh LY, Dukerich M, Trim CB, Beaudry J, Welty-Bernard A, Read T, Fraser CM, Ravel J, Keim P.

J Clin Microbiol. 2007 Jan;45(1):47-53. Epub 2006 Nov 8.

8.

Phylogenetic discovery bias in Bacillus anthracis using single-nucleotide polymorphisms from whole-genome sequencing.

Pearson T, Busch JD, Ravel J, Read TD, Rhoton SD, U'Ren JM, Simonson TS, Kachur SM, Leadem RR, Cardon ML, Van Ert MN, Huynh LY, Fraser CM, Keim P.

Proc Natl Acad Sci U S A. 2004 Sep 14;101(37):13536-41. Epub 2004 Sep 3.

9.

Making the most of mitochondrial genomes--markers for phylogeny, molecular ecology and barcodes in Schistosoma (Platyhelminthes: Digenea).

Zarowiecki MZ, Huyse T, Littlewood DT.

Int J Parasitol. 2007 Oct;37(12):1401-18. Epub 2007 May 10.

PMID:
17570370
10.

Whole-genome prokaryotic phylogeny.

Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC.

Bioinformatics. 2005 May 15;21(10):2329-35. Epub 2004 May 27.

PMID:
15166018
11.

Whole Genome Analysis of Injectional Anthrax Identifies Two Disease Clusters Spanning More Than 13 Years.

Keim P, Grunow R, Vipond R, Grass G, Hoffmaster A, Birdsell DN, Klee SR, Pullan S, Antwerpen M, Bayer BN, Latham J, Wiggins K, Hepp C, Pearson T, Brooks T, Sahl J, Wagner DM.

EBioMedicine. 2015 Oct 6;2(11):1613-8. doi: 10.1016/j.ebiom.2015.10.004. eCollection 2015 Nov.

12.

Distance-based genome rearrangement phylogeny.

Wang LS, Warnow T, Moret BM, Jansen RK, Raubeson LA.

J Mol Evol. 2006 Oct;63(4):473-83. Epub 2006 Oct 4.

PMID:
17021931
13.
14.

A novel feature-based method for whole genome phylogenetic analysis without alignment: application to HEV genotyping and subtyping.

Liu Z, Meng J, Sun X.

Biochem Biophys Res Commun. 2008 Apr 4;368(2):223-30. doi: 10.1016/j.bbrc.2008.01.070. Epub 2008 Jan 28.

PMID:
18230342
15.

High-throughput sequencing of Bacillus anthracis in France: investigating genome diversity and population structure using whole-genome SNP discovery.

Girault G, Blouin Y, Vergnaud G, Derzelle S.

BMC Genomics. 2014 Apr 16;15:288. doi: 10.1186/1471-2164-15-288.

16.

Animal phylogenomics: multiple interspecific genome comparisons.

DeSalle R.

Methods Enzymol. 2005;395:104-33.

PMID:
15865964
17.

Accuracy of genome-wide imputation of untyped markers and impacts on statistical power for association studies.

Hao K, Chudin E, McElwee J, Schadt EE.

BMC Genet. 2009 Jun 16;10:27. doi: 10.1186/1471-2156-10-27.

18.

Integrating sequencing technologies in personal genomics: optimal low cost reconstruction of structural variants.

Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB.

PLoS Comput Biol. 2009 Jul;5(7):e1000432. doi: 10.1371/journal.pcbi.1000432. Epub 2009 Jul 10.

19.

Whole genome sequencing.

Ng PC, Kirkness EF.

Methods Mol Biol. 2010;628:215-26. doi: 10.1007/978-1-60327-367-1_12. Review.

PMID:
20238084
20.

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