Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions. - Dmitry A. Afonnikov; Dmitry Yu. Oshchepkov; Nikolay A. Kolchanov (Bioinform., 2001)

SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition. - Dmitry Yu. Oshchepkov; Evgenii E. Vityaev 001; Dmitry A. Grigorovich; Elena V. Ignatieva; Tamara M. Khlebodarova (Nucleic Acids Res., 2004)

Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes. - Nikolay A. Kolchanov; Tatyana I. Merkulova; Elena V. Ignatieva; Elena A. Ananko; Dmitry Yu. Oshchepkov; Victor G. Levitsky; Gennady V. Vasiliev; Nataly V. Klimova; Vasily M. Merkulov; T. Charles Hodgman (Briefings Bioinform., 2007)

Promoters of the genes encoding the transcription factors regulating the cytokine gene expression in macrophages contain putative binding sites for aryl hydrocarbon receptor. - Dagmara P. Furman; Eugenia A. Oshchepkova; Dmitry Yu. Oshchepkov; Marina Yu. Shamanina; Viatcheslav A. Mordvinov (Comput. Biol. Chem., 2009)

Analysis and recognition of the GAGA transcription factor binding sites in Drosophila genes. - E. S. Omelina; E. M. Baricheva; Dmitry Yu. Oshchepkov; Tatyana I. Merkulova (Comput. Biol. Chem., 2011)

From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites. - Ivan V. Kulakovskiy; Victor G. Levitsky; Dmitry Yu. Oshchepkov; Leonid Bryzgalov; Ilya E. Vorontsov; Vsevolod J. Makeev (J. Bioinform. Comput. Biol., 2013)

Hidden heterogeneity of transcription factor binding sites: A case study of SF-1. - Victor G. Levitsky; Dmitry Yu. Oshchepkov; Nataly V. Klimova; Elena V. Ignatieva; Gennady V. Vasiliev; Vasily M. Merkulov; Tatyana I. Merkulova (Comput. Biol. Chem., 2016)