Microbial genome analysis: the COG approach
- Michael Y Galperin, David M Kristensen, Kira S Makarova, Yuri I Wolf, Eugene V Koonin
- Brief Bioinform, 10.1093/bib/bbx117
Reconstruction of the evolution of microbial defense systems
- Pere Puigbò, Kira S Makarova, David M Kristensen, Yuri I Wolf, Eugene V Koonin
- BMC Ecol Evol, 10.1186/s12862-017-0942-y
ATGC database and ATGC-COGs: an updated resource for micro- and macro-evolutionary studies of prokaryotic genomes and protein family annotation
- David M Kristensen, Yuri I Wolf, Eugene V Koonin
- Nucleic Acids Res, 10.1093/nar/gkw934
Evolutionary switches between two serine codon sets are driven by selection
- Igor B Rogozin, Frida Belinky, Vladimir Pavlenko, Svetlana A Shabalina, David M Kristensen, Eugene V Koonin
- Proc Natl Acad Sci U S A, 10.1073/pnas.1615832113
Prokaryotic Virus Orthologous Groups (pVOGs): a resource for comparative genomics and protein family annotation
- Ana Laura Grazziotin, Eugene V Koonin, David M Kristensen
- Nucleic Acids Res, 10.1093/nar/gkw975
Evolutionary Conservation of Bacterial Essential Metabolic Genes across All Bacterial Culture Media
- Oren Ish-Am, David M Kristensen, Eytan Ruppin
- PLoS One, 10.1371/journal.pone.0123785
Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes
- Pere Puigbò, Alexander E Lobkovsky, David M Kristensen, Yuri I Wolf, Eugene V Koonin
- BMC Biol, 10.1186/s12915-014-0066-4
Coupling between protein level selection and codon usage optimization in the evolution of bacteria and archaea
- Wenqi Ran, David M Kristensen, Eugene V Koonin
- mBio, 10.1128/mbio.00956-14
Classification and quantification of bacteriophage taxa in human gut metagenomes
- Alison S Waller, Takuji Yamada, David M Kristensen, …, Shinichi Sunagawa, Eugene V Koonin, Peer Bork
- ISME J, 10.1038/ismej.2014.30
Orthologous gene clusters and taxon signature genes for viruses of prokaryotes
- David M Kristensen, Alison S Waller, Takuji Yamada, Peer Bork, Arcady R Mushegian, Eugene V Koonin
- J Bacteriol, 10.1128/jb.01801-12
Computational methods for Gene Orthology inference
- David M Kristensen, Yuri I Wolf, Arcady R Mushegian, Eugene V Koonin
- Brief Bioinform, 10.1093/bib/bbr030
Evolutionarily conserved orthologous families in phages are relatively rare in their prokaryotic hosts
- David M Kristensen, Xixu Cai, Arcady Mushegian
- J Bacteriol, 10.1128/jb.01311-10