Fedor A. Kolpakov

According to our database, Fedor A. Kolpakov authored at least 22 papers between 1996 and 2022.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of four.

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 Pintus, Anna Ryabova, Ruslan N. Sharipov, Ivan S. Yevshin, Sergey Zhatchenko, Alexander E. Kel

Nucleic Acids Res., 2022

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, Ivan V. Kulakovskiy

Nucleic Acids Res., 2022

2021

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

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

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, Alexander E. Kel

Nucleic Acids Res., 2019

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, Sebastian Moran, Manel Esteller, Fedor A. Kolpakov, Maxim Filipenko, Edgar Wingender

BMC Bioinform., 2019

2018

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

2017

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

2016

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

2013

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

2011

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

2008

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

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

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

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, Andrey N. Naumochkin, I. M. Korostishevskaya, Aida G. Romashchenko, G. Christian Overton

Nucleic Acids Res., 2000

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, Andrey N. Naumochkin, Aida G. Romashchenko

Nucleic Acids Res., 1999

Interactive data input into the GeneNet database.

Fedor A. Kolpakov, Elena A. Ananko

Bioinform., 1999

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, Alexey V. Kochetov, Nikolay L. Podkolodny, Denis G. Vorobiev, Sergey V. Lavryushev, Dmitry A. Grigorovich, Yury V. Kondrakhin, Luciano Milanesi, Edgar Wingender, Victor V. Solovyev, G. Christian Overton

Bioinform., 1999

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

GeneNet: a gene network database and its automated visualization.

Fedor A. Kolpakov, Elena A. Ananko, G. B. Kolesov, Nikolay A. Kolchanov

Bioinform., 1998

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, Irina L. Stepanenko, Aida G. Romashchenko, Tatyana I. Merkulova, Denis G. Vorobiev, Sergey V. Lavryushev, Y. V. Ponomarenko, Alexey V. Kochetov, G. B. Kolesov, Victor V. Solovyev, Luciano Milanesi, Nikolay L. Podkolodny, Edgar Wingender, T. Heinemeyer

Proceedings of the 6th International Conference on Intelligent Systems for Molecular Biology (ISMB-98), Montréal, Québec, Canada, June 28, 1998

1996

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

Proceedings of the German Conference on Bioinformatics, 1996