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A comprehensive evolutionary classification of proteins encoded in complete eukaryotic genomes.

Koonin EV, Fedorova ND, Jackson JD, Jacobs AR, Krylov DM, Makarova KS, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Rogozin IB, Smirnov S, Sorokin AV, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.

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Modular co-evolution of metabolic networks.

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Modeling protein network evolution under genome duplication and domain shuffling.

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The functional genomic distribution of protein divergence in two animal phyla: coevolution, genomic conflict, and constraint.

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Specificity and evolvability in eukaryotic protein interaction networks.

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Non-random genomic divergence in repetitive sequences of human and chimpanzee in genes of different functional categories.

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Testing the neutral theory of molecular evolution using genomic data: a comparison of the human and bovine transcriptome.

MacEachern S, McEwan J, Mather A, McCulloch A, Sunnucks P, Goddard M.

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The COG database: an updated version includes eukaryotes.

Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA.

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Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes.

Lee S, Kohane I, Kasif S.

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Comparative analysis of complete genomes reveals gene loss, acquisition and acceleration of evolutionary rates in Metazoa, suggests a prevalence of evolution via gene acquisition and indicates that the evolutionary rates in animals tend to be conserved.

Babenko VN, Krylov DM.