Fedor A. Kolpakov

23 papers A 1Journal 21Unranked 1
YearRankTypeTitle / Venue / Authors
2025 J jnl
Prediction and annotation of alternative transcription starts and promoter shift in the chicken genome.
J. Bioinform. Comput. Biol.
Valentina A. Grushina, Ivan S. Yevshin, Oleg A. Gusev, Fedor A. Kolpakov, Olga I. Stanishevskaya, Elena S. Fedorova, Natalia A. Zinovieva, Sergey S. Pintus
2022 J jnl
ANANASTRA: annotation and enrichment analysis of allele-specific transcription factor binding at SNPs.
Nucleic Acids Res.
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
2022 J jnl
BioUML - towards a universal research platform.
Nucleic Acids Res.
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, Alexander E. Kel
2021 J jnl
GTRD: an integrated view of transcription regulation.
Nucleic Acids Res.
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
2019 J jnl
BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data.
Nucleic Acids Res.
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
2019 J jnl
GTRD: a database on gene transcription regulation - 2019 update.
Nucleic Acids Res.
Ivan S. Yevshin, Ruslan N. Sharipov, Semyon Kolmykov, Yury V. Kondrakhin, Fedor A. Kolpakov
2019 J jnl
Walking pathways with positive feedback loops reveal DNA methylation biomarkers of colorectal cancer.
BMC Bioinform.
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
2018 J jnl
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis.
Nucleic Acids Res.
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
2017 J jnl
GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments.
Nucleic Acids Res.
Ivan S. Yevshin, Ruslan N. Sharipov, Tagir F. Valeev, Alexander E. Kel, Fedor A. Kolpakov
2016 J jnl
HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.
Nucleic Acids Res.
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
2013 J jnl
Model composition through model reduction: a combined model of CD95 and NF-κ.
BMC Syst. Biol.
Elena Kutumova, Andrei Yu. Zinovyev, Ruslan N. Sharipov, Fedor A. Kolpakov
2011 J jnl
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language.
BMC Syst. Biol.
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
2008 J jnl
Identification of Differentially Expressed Genes by Meta-Analysis of Microarray Data on Breast Cancer.
Silico Biol.
Yury V. Kondrakhin, Ruslan N. Sharipov, Alexander E. Kel, Fedor A. Kolpakov
2007 J jnl
CYCLONET - an integrated database on cell cycle regulation and carcinogenesis.
Nucleic Acids Res.
Fedor A. Kolpakov, Vladimir Poroikov, Ruslan N. Sharipov, Yury V. Kondrakhin, Alexey V. Zakharov, Alexey Lagunin, Luciano Milanesi, Alexander E. Kel
2000 J jnl
Methods for integration of heterogeneous information resources in molecular biology in the digital library GeneExpress.
Program. Comput. Softw.
Fedor A. Kolpakov, N. L. Podkolodnyi, Sergey V. Lavryushev, Dmitry A. Grigorovich, Mikhail P. Ponomarenko, Nikolay A. Kolchanov
2000 J jnl
Transcription Regulatory Regions Database (TRRD): its status in 2000.
Nucleic Acids Res.
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
1999 J jnl
Integrated databases and computer systems for studying eukaryotic gene expression.
Bioinform.
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
1999 J jnl
Interactive data input into the GeneNet database.
Bioinform.
Fedor A. Kolpakov, Elena A. Ananko
1999 J jnl
Transcription Regulatory Regions Database (TRRD): its status in 1999.
Nucleic Acids Res.
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
1998 J jnl
Databases on transcriptional regulation: TRANSFAC, TRRD and COMPEL.
Nucleic Acids Res.
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
1998 A conf
GenExpress: A Computer System for Description, Analysis and Recognition of Regulatory Sequences in Eukaryotic Genome.
ISMB
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
1998 J jnl
GeneNet: a gene network database and its automated visualization.
Bioinform.
Fedor A. Kolpakov, Elena A. Ananko, G. B. Kolesov, Nikolay A. Kolchanov
1996 — conf
Computer Analysis and Recognition of the Transcription Regulatory Elements in Eukaryotic Genomes.
German Conference on Bioinformatics
Yury V. Kondrakhin, Fedor A. Kolpakov, Alexander E. Kel, Nikolay A. Kolchanov, Luciano Milanesi