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Items: 1 to 20 of 86

1.

Two fundamentally different classes of microbial genes.

Wolf YI, Makarova KS, Lobkovsky AE, Koonin EV.

Nat Microbiol. 2016 Nov 7;2:16208. doi: 10.1038/nmicrobiol.2016.208.

PMID:
27819663
2.

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.

3.
4.

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.

5.

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.

6.

Genomes in flux: the evolution of archaeal and proteobacterial gene content.

Snel B, Bork P, Huynen MA.

Genome Res. 2002 Jan;12(1):17-25.

7.

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.

8.

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.

9.

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.

10.

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.

11.

Flexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks.

Kang Y, Gu C, Yuan L, Wang Y, Zhu Y, Li X, Luo Q, Xiao J, Jiang D, Qian M, Ahmed Khan A, Chen F, Zhang Z, Yu J.

MBio. 2014 Nov 25;5(6):e01867. doi: 10.1128/mBio.01867-14. Erratum in: MBio. 2015;6(1). pii: e02395-14. doi: 10.1128/mBio.02395-14.

12.

The Rhizome of Lokiarchaeota Illustrates the Mosaicity of Archaeal Genomes.

Levasseur A, Merhej V, Baptiste E, Sharma V, Pontarotti P, Raoult D.

Genome Biol Evol. 2017 Oct 1;9(10):2635-2639. doi: 10.1093/gbe/evx208.

13.

Gene frequency distributions reject a neutral model of genome evolution.

Lobkovsky AE, Wolf YI, Koonin EV.

Genome Biol Evol. 2013;5(1):233-42. doi: 10.1093/gbe/evt002.

15.

Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota.

Deschamps P, Zivanovic Y, Moreira D, Rodriguez-Valera F, López-García P.

Genome Biol Evol. 2014 Jun 12;6(7):1549-63. doi: 10.1093/gbe/evu127.

16.

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.

17.

Evolutionary and Functional Relationships of the dha Regulon by Genomic Context Analysis.

Martins-Pinheiro M, Lima WC, Asif H, Oller CA, Menck CF.

PLoS One. 2016 Mar 3;11(3):e0150772. doi: 10.1371/journal.pone.0150772. eCollection 2016.

18.

Evolution of microbes and viruses: a paradigm shift in evolutionary biology?

Koonin EV, Wolf YI.

Front Cell Infect Microbiol. 2012 Sep 13;2:119. eCollection 2012. Review.

19.

A hidden reservoir of integrative elements is the major source of recently acquired foreign genes and ORFans in archaeal and bacterial genomes.

Cortez D, Forterre P, Gribaldo S.

Genome Biol. 2009;10(6):R65. doi: 10.1186/gb-2009-10-6-r65. Epub 2009 Jun 16.

20.

Clusters of orthologous genes for 41 archaeal genomes and implications for evolutionary genomics of archaea.

Makarova KS, Sorokin AV, Novichkov PS, Wolf YI, Koonin EV.

Biol Direct. 2007 Nov 27;2:33.

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