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)

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)

GeneNet: a gene network database and its automated visualization. - Fedor A. Kolpakov; Elena A. Ananko; G. B. Kolesov; Nikolay A. Kolchanov (Bioinform., 1998)

Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL. - T. Heinemeyer; Edgar Wingender; Ingmar Reuter; Henning Hermjakob; Alexander E. Kel; Olga V. Kel-Margoulis; Elena V. Ignatieva; Elena A. Ananko; Olga A. Podkolodnaya; Fedor A. Kolpakov; Nikolay L. Podkolodny; Nikolay A. Kolchanov (Nucleic Acids Res., 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)

Interactive data input into the GeneNet database. - Fedor A. Kolpakov; Elena A. Ananko (Bioinform., 1999)

Transcription Regulatory Regions Database (TRRD): its status in 1999. - Nikolay A. Kolchanov; Elena A. Ananko; Olga A. Podkolodnaya; Elena V. Ignatieva; Irina L. Stepanenko; Olga V. Kel-Margoulis; Alexander E. Kel; Tatyana I. Merkulova; T. N. Goryachkovskaya; T. V. Busygina; Fedor A. Kolpakov; Nikolay L. Podkolodny; et al. (Nucleic Acids Res., 1999)

Transcription Regulatory Regions Database (TRRD): its status in 2000. - Nikolay A. Kolchanov; Olga A. Podkolodnaya; Elena A. Ananko; Elena V. Ignatieva; Irina L. Stepanenko; Olga V. Kel-Margoulis; Alexander E. Kel; Tatyana I. Merkulova; T. N. Goryachkovskaya; T. V. Busygina; Fedor A. Kolpakov; Nikolay L. Podkolodny; et al. (Nucleic Acids Res., 2000)

Methods for integration of heterogeneous information resources in molecular biology in the digital library GeneExpress. - Fedor A. Kolpakov; N. L. Podkolodnyi; Sergey V. Lavryushev; Dmitry A. Grigorovich; Mikhail P. Ponomarenko; Nikolay A. Kolchanov (Program. Comput. Softw., 2000)

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)

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language. - Dagmar Waltemath; Richard R. Adams; Frank T. Bergmann; Michael Hucka; Fedor A. Kolpakov; Andrew K. Miller; Ion I. Moraru; David P. Nickerson; Sven Sahle; Jacky L. Snoep; Nicolas Le Novère (BMC Syst. Biol., 2011)

Model composition through model reduction: a combined model of CD95 and NF-κ. - Elena Kutumova; Andrei Yu. Zinovyev; Ruslan N. Sharipov; Fedor A. Kolpakov (BMC Syst. Biol., 2013)

HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models. - Ivan V. Kulakovskiy; Ilya E. Vorontsov; Ivan S. Yevshin; Anastasiia V. Soboleva; Artem S. Kasianov; Haitham Ashoor; Wail Ba-alawi; Vladimir B. Bajic; Yulia A. Medvedeva; Fedor A. Kolpakov; Vsevolod J. Makeev (Nucleic Acids Res., 2016)

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments. - Ivan S. Yevshin; Ruslan N. Sharipov; Tagir F. Valeev; Alexander E. Kel; Fedor A. Kolpakov (Nucleic Acids Res., 2017)

HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis. - Ivan V. Kulakovskiy; Ilya E. Vorontsov; Ivan S. Yevshin; Ruslan N. Sharipov; Alla D. Fedorova; Eugene I. Rumynskiy; Yulia A. Medvedeva; Arturo Magana-Mora; Vladimir B. Bajic; Dmitri A. Papatsenko; Fedor A. Kolpakov; Vsevolod J. Makeev (Nucleic Acids Res., 2018)

Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer. - Alexander E. Kel; Ulyana Boyarskikh; Philip Stegmaier; Leonid S. Leskov; Andrey V. Sokolov; Ivan S. Yevshin; Nikita Mandrik; Daria Stelmashenko; Jeannette Koschmann; Olga V. Kel-Margoulis; Mathias Krull; Anna Martínez-Cardús; et al. (BMC Bioinform., 2019)

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)

ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs. - Alexandr Boytsov; Sergey Abramov; Ariuna Z. Aiusheeva; Alexandra M. Kasianova; Eugene Baulin; Ivan A. Kuznetsov; Yurii S. Aulchenko; Semyon Kolmykov; Ivan S. Yevshin; Fedor A. Kolpakov; Ilya E. Vorontsov; Vsevolod J. Makeev; et al. (Nucleic Acids Res., 2022)

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)

Prediction and annotation of alternative transcription starts and promoter shift in the chicken genome. - Valentina A. Grushina; Ivan S. Yevshin; Oleg A. Gusev; Fedor A. Kolpakov; Olga I. Stanishevskaya; Elena S. Fedorova; Natalia A. Zinovieva; Sergey S. Pintus (J. Bioinform. Comput. Biol., 2025)