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A user's guide to quantitative and comparative analysis of metagenomic datasets.
Luo C, Rodriguez-R LM, Konstantinidis KT. Luo C, et al. Methods Enzymol. 2013;531:525-47. doi: 10.1016/B978-0-12-407863-5.00023-X. Methods Enzymol. 2013. PMID: 24060135
Prokaryotic taxonomy and phylogeny in the genomic era: advancements and challenges ahead.
Konstantinidis KT, Tiedje JM. Konstantinidis KT, et al. Curr Opin Microbiol. 2007 Oct;10(5):504-9. doi: 10.1016/j.mib.2007.08.006. Epub 2007 Oct 17. Curr Opin Microbiol. 2007. PMID: 17923431 Review.
Phylogenetic analyses of ribosomal DNA-containing bacterioplankton genome fragments from a 4000 m vertical profile in the North Pacific Subtropical Gyre.
Pham VD, Konstantinidis KT, Palden T, DeLong EF. Pham VD, et al. Environ Microbiol. 2008 Sep;10(9):2313-30. doi: 10.1111/j.1462-2920.2008.01657.x. Epub 2008 May 20. Environ Microbiol. 2008. PMID: 18494796
Comparative metagenomic analysis of a microbial community residing at a depth of 4,000 meters at station ALOHA in the North Pacific subtropical gyre.
Konstantinidis KT, Braff J, Karl DM, DeLong EF. Konstantinidis KT, et al. Appl Environ Microbiol. 2009 Aug;75(16):5345-55. doi: 10.1128/AEM.00473-09. Epub 2009 Jun 19. Appl Environ Microbiol. 2009. PMID: 19542347 Free PMC article.
Genomic insights into the convergence and pathogenicity factors of Campylobacter jejuni and Campylobacter coli species.
Caro-Quintero A, Rodriguez-Castaño GP, Konstantinidis KT. Caro-Quintero A, et al. J Bacteriol. 2009 Sep;191(18):5824-31. doi: 10.1128/JB.00519-09. Epub 2009 Jul 17. J Bacteriol. 2009. PMID: 19617370 Free PMC article.
Comparative systems biology across an evolutionary gradient within the Shewanella genus.
Konstantinidis KT, Serres MH, Romine MF, Rodrigues JL, Auchtung J, McCue LA, Lipton MS, Obraztsova A, Giometti CS, Nealson KH, Fredrickson JK, Tiedje JM. Konstantinidis KT, et al. Proc Natl Acad Sci U S A. 2009 Sep 15;106(37):15909-14. doi: 10.1073/pnas.0902000106. Epub 2009 Sep 1. Proc Natl Acad Sci U S A. 2009. PMID: 19805231 Free PMC article.
Evaluating the performance of oligonucleotide microarrays for bacterial strains with increasing genetic divergence from the reference strain.
Oh S, Yoder-Himes DR, Tiedje J, Park J, Konstantinidis KT. Oh S, et al. Appl Environ Microbiol. 2010 May;76(9):2980-8. doi: 10.1128/AEM.02826-09. Epub 2010 Mar 12. Appl Environ Microbiol. 2010. PMID: 20228107 Free PMC article.
Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea.
Caro-Quintero A, Deng J, Auchtung J, Brettar I, Höfle MG, Klappenbach J, Konstantinidis KT. Caro-Quintero A, et al. ISME J. 2011 Jan;5(1):131-40. doi: 10.1038/ismej.2010.93. Epub 2010 Jul 1. ISME J. 2011. PMID: 20596068 Free PMC article.
Genome sequencing of environmental Escherichia coli expands understanding of the ecology and speciation of the model bacterial species.
Luo C, Walk ST, Gordon DM, Feldgarden M, Tiedje JM, Konstantinidis KT. Luo C, et al. Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):7200-5. doi: 10.1073/pnas.1015622108. Epub 2011 Apr 11. Proc Natl Acad Sci U S A. 2011. PMID: 21482770 Free PMC article.
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