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Items: 1 to 20 of 109

1.

AnnoTree: visualization and exploration of a functionally annotated microbial tree of life.

Mendler K, Chen H, Parks DH, Lobb B, Hug LA, Doxey AC.

Nucleic Acids Res. 2019 May 21;47(9):4442-4448. doi: 10.1093/nar/gkz246.

2.

Genome trees constructed using five different approaches suggest new major bacterial clades.

Wolf YI, Rogozin IB, Grishin NV, Tatusov RL, Koonin EV.

BMC Evol Biol. 2001 Oct 20;1:8.

3.

Origins of major archaeal clades correspond to gene acquisitions from bacteria.

Nelson-Sathi S, Sousa FL, Roettger M, Lozada-Chávez N, Thiergart T, Janssen A, Bryant D, Landan G, Schönheit P, Siebers B, McInerney JO, Martin WF.

Nature. 2015 Jan 1;517(7532):77-80. doi: 10.1038/nature13805. Epub 2014 Oct 15.

4.

The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life.

Koonin EV.

J Mol Evol. 2015 Jun;80(5-6):244-50. doi: 10.1007/s00239-015-9679-7. Epub 2015 Apr 18. Review.

5.

Functional phylogenomics analysis of bacteria and archaea using consistent genome annotation with UniFam.

Chai J, Kora G, Ahn TH, Hyatt D, Pan C.

BMC Evol Biol. 2014 Oct 9;14:207. doi: 10.1186/s12862-014-0207-y.

6.

A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea.

Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, Hooper SD, Pati A, Lykidis A, Spring S, Anderson IJ, D'haeseleer P, Zemla A, Singer M, Lapidus A, Nolan M, Copeland A, Han C, Chen F, Cheng JF, Lucas S, Kerfeld C, Lang E, Gronow S, Chain P, Bruce D, Rubin EM, Kyrpides NC, Klenk HP, Eisen JA.

Nature. 2009 Dec 24;462(7276):1056-60. doi: 10.1038/nature08656.

7.

Reconstruction of the evolution of microbial defense systems.

Puigbò P, Makarova KS, Kristensen DM, Wolf YI, Koonin EV.

BMC Evol Biol. 2017 Apr 4;17(1):94. doi: 10.1186/s12862-017-0942-y.

8.

Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes.

Puigbò P, Lobkovsky AE, Kristensen DM, Wolf YI, Koonin EV.

BMC Biol. 2014 Aug 21;12:66. doi: 10.1186/s12915-014-0066-4.

9.

Evolution of mosaic operons by horizontal gene transfer and gene displacement in situ.

Omelchenko MV, Makarova KS, Wolf YI, Rogozin IB, Koonin EV.

Genome Biol. 2003;4(9):R55. Epub 2003 Aug 29.

10.

Retroids in archaea: phylogeny and lateral origins.

Rest JS, Mindell DP.

Mol Biol Evol. 2003 Jul;20(7):1134-42. Epub 2003 May 30.

PMID:
12777534
11.

Adding genomic 'foliage' to the tree of life.

Walker A.

Nat Rev Microbiol. 2014 Feb;12(2):78. doi: 10.1038/nrmicro3203. No abstract available.

PMID:
24429416
12.

En route to a genome-based classification of Archaea and Bacteria?

Klenk HP, Göker M.

Syst Appl Microbiol. 2010 Jun;33(4):175-82. doi: 10.1016/j.syapm.2010.03.003. Epub 2010 Apr 20. Review.

PMID:
20409658
13.

Phylogeny Reconstruction with Alignment-Free Method That Corrects for Horizontal Gene Transfer.

Bromberg R, Grishin NV, Otwinowski Z.

PLoS Comput Biol. 2016 Jun 23;12(6):e1004985. doi: 10.1371/journal.pcbi.1004985. eCollection 2016 Jun.

14.

Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer.

Wolf YI, Makarova KS, Yutin N, Koonin EV.

Biol Direct. 2012 Dec 14;7:46. doi: 10.1186/1745-6150-7-46.

15.

Comparative genomics analysis of completely sequenced microbial genomes reveals the ubiquity of N-linked glycosylation in prokaryotes.

Kumar M, Balaji PV.

Mol Biosyst. 2011 May;7(5):1629-45. doi: 10.1039/c0mb00259c. Epub 2011 Mar 8.

PMID:
21387023
16.

Genomic exploration of the diversity, ecology, and evolution of the archaeal domain of life.

Spang A, Caceres EF, Ettema TJG.

Science. 2017 Aug 11;357(6351). pii: eaaf3883. doi: 10.1126/science.aaf3883. Review.

PMID:
28798101
18.

CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.

Zuo G, Hao B.

Genomics Proteomics Bioinformatics. 2015 Oct;13(5):321-31. doi: 10.1016/j.gpb.2015.08.004. Epub 2015 Nov 10.

19.

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world.

Koonin EV, Wolf YI.

Nucleic Acids Res. 2008 Dec;36(21):6688-719. doi: 10.1093/nar/gkn668. Epub 2008 Oct 23. Review.

20.

Phylo SI: a new genome-wide approach for prokaryotic phylogeny.

Shifman A, Ninyo N, Gophna U, Snir S.

Nucleic Acids Res. 2014 Feb;42(4):2391-404. doi: 10.1093/nar/gkt1138. Epub 2013 Nov 15.

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