The purpose of this project is to utilize genomic data from many related organisms in order to learn more about functions of eukaryotic DNA, both coding noncoding. For coding sequences, we discovered that amino-acid composition of proteins of modern organisms is still far from equilibrium, despite over 3 billion years of evolution. Also, we ascertained the complete distribution of coefficients of selection against amino-acid replacements in human proteins. For non-coding transcribed sequences, we developed a method for identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides. We also studied the mammalian transcriptome and the function of non-coding DNA sequences. For untranscribed sequences, we investigated contexts of 5'-enhancers which are associated with tissue-specific expression of the corresponding genes.
| Yampolsky, Lev Y; Allen, Chenoa; Shabalina, Svetlana A et al. (2005) Persistence time of loss-of-function mutations at nonessential loci affecting eye color in Drosophila melanogaster. Genetics 171:2133-8 |
| Jordan, I King; Kondrashov, Fyodor A; Adzhubei, Ivan A et al. (2005) A universal trend of amino acid gain and loss in protein evolution. Nature 433:633-8 |
| Yampolsky, Lev Y; Kondrashov, Fyodor A; Kondrashov, Alexey S (2005) Distribution of the strength of selection against amino acid replacements in human proteins. Hum Mol Genet 14:3191-201 |
| Kolker, Eugene; Makarova, Kira S; Shabalina, Svetlana et al. (2004) Identification and functional analysis of 'hypothetical' genes expressed in Haemophilus influenzae. Nucleic Acids Res 32:2353-61 |
| Kondrashov, Alexey S; Rogozin, Igor B (2004) Context of deletions and insertions in human coding sequences. Hum Mutat 23:177-85 |
| Arnegard, Matthew E; Kondrashov, Alexey S (2004) Sympatric speciation by sexual selection alone is unlikely. Evolution Int J Org Evolution 58:222-37 |
| Bazykin, Georgii A; Kondrashov, Fyodor A; Ogurtsov, Aleksey Y et al. (2004) Positive selection at sites of multiple amino acid replacements since rat-mouse divergence. Nature 429:558-62 |
| Matveeva, Olga V; Foley, Brian T; Nemtsov, Vladimir A et al. (2004) Identification of regions in multiple sequence alignments thermodynamically suitable for targeting by consensus oligonucleotides: application to HIV genome. BMC Bioinformatics 5:44 |
| Shabalina, Svetlana A; Ogurtsov, Aleksey Y; Rogozin, Igor B et al. (2004) Comparative analysis of orthologous eukaryotic mRNAs: potential hidden functional signals. Nucleic Acids Res 32:1774-82 |
| Kondrashov, Fyodor A; Ogurtsov, Aleksey Y; Kondrashov, Alexey S (2004) Bioinformatical assay of human gene morbidity. Nucleic Acids Res 32:1731-7 |
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