The availability of completely sequenced genomes and other genome-wide datasets have opened a new opportunity for engaging in observatory, phenomenological studies. Many exiting observations are being made, including in our own laboratory, that do not really involve concrete theoretical backgrounds or complex models. In essence, such studies are not very different from descriptive studies of the early microscope days, except our "microscopes" are now far more advanced. Such evolutionary genomic studies are aimed at describing novel biological and evolutionary phenomena. In our previous studies we have identified several such phenomenological aspects, including several observations on the evolution of alternative splicing, the evolution of several gene families, the evolution of the Elephantidae lineage, evolution of introns and the evolution of amino acid composition.
Popadin K, Mamirova L and Kondrashov FA (2007). A manually curated database of tetrapod mitochondrial tRNAs. BMC Bioinformatics 8, 441
Kondrashov FA, Koonin EV, Morgunov IG, Finogenova TV, Kondrashova MN. (2006) Evolution of glyoxylate cycle enzymes in Metazoa: evidence of multiple horizontal transfer events and pseudogene formation. Biol Direct 1, 31.
Rogaev EI, Moliaka YK, Malyarchuk BA, Kondrashov FA, Derenko MV, Chumakov I and Grigorenko AP (2006) Complete mitochondrial genome and phylogeny of Pleistocene mammoth Mammuthus primigenius. PLOS Biology 4, e73.
Jordan IK, Kondrashov FA, Adzhubei IA, Wolf YI, Koonin EV, Kondrashov AS and Sunyaev S. (2005) A universal trend of amino acid gain and loss in protein evolution. Nature 433, 633-638.
Kondrashov FA and Koonin EV. (2003) Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences. Trends in Genetics 19, 115-119.
Castillo-Davis C, Mekhedov SI, Hartl DL, Koonin EV and Kondrashov FA. (2002)
Selection for shorter introns in highly expressed genes. Nature Genetics 31, 415-418.
Kondrashov FA and Koonin EV. (2001) Origin of alternative splicing by tandem exon duplication. Human Molecular Genetics 10, 2661-2669
Rogozin IB, Kochetov AV, Kondrashov FA, Koonin EV and Milanesi L. (2001) Presence of ATG triplets in 5' untranslated regions of eukaryotic cDNAs correlates with a 'weak' context of the start codon. Bioinformatics. 17, 890-900.
Wolf YI, Kondrashov FA and Koonin EV. (2000) No footprints of primordial introns in a eukaryotic genome. Trends in Genetics 16, 333-334.