Construction of a generalized consensus matrix for recognition of vertebrate pre-mRNA 3'-terminal processing sites. - Yury V. Kondrakhin; V. V. Shamin; Nikolay A. Kolchanov (Comput. Appl. Biosci., 1994)

Computer Tool FUNSITE for Analysis of Eukaryotic Regulatory Genomic Sequences. - Alexander E. Kel; Yury V. Kondrakhin; Ph. A. Kolpakov; O. V. Kel; Aida G. Romashchenko; Edgar Wingender; Luciano Milanesi; Nikolay A. Kolchanov (ISMB, 1995)

PROANAL version 2: multifunctional program for analysis of multiple protein sequence alignments and for studying the structure–activity relationships in protein families. - A. M. Eroshkin; V. I. Fomin; P. A. Zhilkin; V. V. Ivanisenko; Yury V. Kondrakhin (Comput. Appl. Biosci., 1995)

Eukaryotic promoter recognition by binding sites for transcription factors. - Yury V. Kondrakhin; Alexander E. Kel; Nikolay A. Kolchanov; Aida G. Romashchenko; Luciano Milanesi (Comput. Appl. Biosci., 1995)

Computer Analysis and Recognition of the Transcription Regulatory Elements in Eukaryotic Genomes. - Yury V. Kondrakhin; Fedor A. Kolpakov; Alexander E. Kel; Nikolay A. Kolchanov; Luciano Milanesi (German Conference on Bioinformatics, 1996)

Detecting direct correlations between positions in multiple alignments of amino acid sequences. - Dmitry A. Afonnikov; Yury V. Kondrakhin; Igor I. Titov; Nikolay A. Kolchanov (German Conference on Bioinformatics, 1997)

GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome. - Nikolay A. Kolchanov; Mikhail P. Ponomarenko; Alexander E. Kel; Yury V. Kondrakhin; Anatoly S. Frolov; Fedor A. Kolpakov; T. N. Goryachkovskaya; O. V. Kel; Elena A. Ananko; Elena V. Ignatieva; Olga A. Podkolodnaya; Vladimir N. Babenko; et al. (ISMB, 1998)

Integrated databases and computer systems for studying eukaryotic gene expression. - Nikolay A. Kolchanov; Mikhail P. Ponomarenko; Anatoly S. Frolov; Elena A. Ananko; Fedor A. Kolpakov; Elena V. Ignatieva; Olga A. Podkolodnaya; T. N. Goryachkovskaya; Irina L. Stepanenko; Tatyana I. Merkulova; V. V. Babenko; Y. V. Ponomarenko; et al. (Bioinform., 1999)

Recognition of interferon-inducible sites, promoters, and enhancers. - Elena A. Ananko; Yury V. Kondrakhin; Tatyana I. Merkulova; Nikolay A. Kolchanov (BMC Bioinform., 2007)

CYCLONET - an integrated database on cell cycle regulation and carcinogenesis. - Fedor A. Kolpakov; Vladimir Poroikov; Ruslan N. Sharipov; Yury V. Kondrakhin; Alexey V. Zakharov; Alexey Lagunin; Luciano Milanesi; Alexander E. Kel (Nucleic Acids Res., 2007)

Identification of Differentially Expressed Genes by Meta-Analysis of Microarray Data on Breast Cancer. - Yury V. Kondrakhin; Ruslan N. Sharipov; Alexander E. Kel; Fedor A. Kolpakov (Silico Biol., 2008)

Assessment of translational importance of mammalian mRNA sequence features based on Ribo-Seq and mRNA-Seq data. - Oxana A. Volkova; Yury V. Kondrakhin; Ivan S. Yevshin; Tagir F. Valeev; Ruslan N. Sharipov (J. Bioinform. Comput. Biol., 2016)

Comparative analysis of protein-coding and long non-coding transcripts based on RNA sequence features. - Oxana A. Volkova; Yury V. Kondrakhin; Timur A. Kashapov; Ruslan N. Sharipov (J. Bioinform. Comput. Biol., 2018)

BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data. - Fedor A. Kolpakov; Ilya R. Akberdin; Timur A. Kashapov; llya Kiselev; Semyon Kolmykov; Yury V. Kondrakhin; Elena Kutumova; Nikita Mandrik; Sergey S. Pintus; Anna Ryabova; Ruslan N. Sharipov; Ivan S. Yevshin; et al. (Nucleic Acids Res., 2019)

GTRD: a database on gene transcription regulation - 2019 update. - Ivan S. Yevshin; Ruslan N. Sharipov; Semyon Kolmykov; Yury V. Kondrakhin; Fedor A. Kolpakov (Nucleic Acids Res., 2019)

GTRD: an integrated view of transcription regulation. - Semyon Kolmykov; Ivan S. Yevshin; Mikhail Kulyashov; Ruslan N. Sharipov; Yury V. Kondrakhin; Vsevolod J. Makeev; Ivan V. Kulakovskiy; Alexander E. Kel; Fedor A. Kolpakov (Nucleic Acids Res., 2021)

BioUML - towards a universal research platform. - Fedor A. Kolpakov; Ilya R. Akberdin; Ilya Kiselev; Semyon Kolmykov; Yury V. Kondrakhin; Mikhail Kulyashov; Elena Kutumova; Sergey S. Pintus; Anna Ryabova; Ruslan N. Sharipov; Ivan S. Yevshin; Sergey Zhatchenko; et al. (Nucleic Acids Res., 2022)