Model composition through model reduction: a combined model of CD95 and NF-κB signaling pathways

por Kutumova, Elena, Zinovyev, Andrei, Sharipov, Ruslan, Kolpakov, Fedor
Publicado 2013

Numerous Trigger-like Interactions of Kinases/Protein Phosphatases in Human Skeletal Muscles Can Underlie Transient Processes in Activation of Signaling Pathways during Exercise

por Vertyshev, Alexander Yu., Akberdin, Ilya R., Kolpakov, Fedor A.
Publicado 2023

GTRD: a database of transcription factor binding sites identified by ChIP-seq experiments

por Yevshin, Ivan, Sharipov, Ruslan, Valeev, Tagir, Kel, Alexander, Kolpakov, Fedor
Publicado 2017

GTRD: a database on gene transcription regulation—2019 update

por Yevshin, Ivan, Sharipov, Ruslan, Kolmykov, Semyon, Kondrakhin, Yury, Kolpakov, Fedor
Publicado 2019

Thoroughly Calibrated Modular Agent-Based Model of the Human Cardiovascular and Renal Systems for Blood Pressure Regulation in Health and Disease

por Kutumova, Elena, Kiselev, Ilya, Sharipov, Ruslan, Lifshits, Galina, Kolpakov, Fedor
Publicado 2021

Mathematical modeling of antihypertensive therapy

por Kutumova, Elena, Kiselev, Ilya, Sharipov, Ruslan, Lifshits, Galina, Kolpakov, Fedor
Publicado 2022

Transcriptomic Signatures and Upstream Regulation in Human Skeletal Muscle Adapted to Disuse and Aerobic Exercise

por Makhnovskii, Pavel A., Bokov, Roman O., Kolpakov, Fedor A., Popov, Daniil V.
Publicado 2021

Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data

por Sharipov, Ruslan N., Kondrakhin, Yury V., Ryabova, Anna S., Yevshin, Ivan S., Kolpakov, Fedor A.
Publicado 2020

CYCLONET—an integrated database on cell cycle regulation and carcinogenesis

por Kolpakov, Fedor, Poroikov, Vladimir, Sharipov, Ruslan, Kondrakhin, Yury, Zakharov, Alexey, Lagunin, Alexey, Milanesi, Luciano, Kel, Alexander
Publicado 2007

Population size estimation for quality control of ChIP-Seq datasets

por Kolmykov, Semyon K., Kondrakhin, Yury V., Yevshin, Ivan S., Sharipov, Ruslan N., Ryabova, Anna S., Kolpakov, Fedor A.
Publicado 2019

Genome-wide map of human and mouse transcription factor binding sites aggregated from ChIP-Seq data

por Vorontsov, Ilya E., Fedorova, Alla D., Yevshin, Ivan S., Sharipov, Ruslan N., Kolpakov, Fedor A., Makeev, Vsevolod J., Kulakovskiy, Ivan V.
Publicado 2018

GTRD: an integrated view of transcription regulation

por Kolmykov, Semyon, Yevshin, Ivan, Kulyashov, Mikhail, Sharipov, Ruslan, Kondrakhin, Yury, Makeev, Vsevolod J, Kulakovskiy, Ivan V, Kel, Alexander, Kolpakov, Fedor
Publicado 2020

Computational master-regulator search reveals mTOR and PI3K pathways responsible for low sensitivity of NCI-H292 and A427 lung cancer cell lines to cytotoxic action of p53 activato...

por Boyarskikh, Ulyana, Pintus, Sergey, Mandrik, Nikita, Stelmashenko, Daria, Kiselev, Ilya, Evshin, Ivan, Sharipov, Ruslan, Stegmaier, Philip, Kolpakov, Fedor, Filipenko, Maxim, Kel, Alexander
Publicado 2018

A Modular Mathematical Model of Exercise-Induced Changes in Metabolism, Signaling, and Gene Expression in Human Skeletal Muscle

por Akberdin, Ilya R., Kiselev, Ilya N., Pintus, Sergey S., Sharipov, Ruslan N., Vertyshev, Alexander Yu, Vinogradova, Olga L., Popov, Daniil V., Kolpakov, Fedor A.
Publicado 2021

Physiologically Based Pharmacokinetic Modeling of Nanoparticle Biodistribution: A Review of Existing Models, Simulation Software, and Data Analysis Tools

por Kutumova, Elena O., Akberdin, Ilya R., Kiselev, Ilya N., Sharipov, Ruslan N., Egorova, Vera S., Syrocheva, Anastasiia O., Parodi, Alessandro, Zamyatnin, Andrey A., Kolpakov, Fedor A.
Publicado 2022

Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language

por Waltemath, Dagmar, Adams, Richard, Bergmann, Frank T, Hucka, Michael, Kolpakov, Fedor, Miller, Andrew K, Moraru, Ion I, Nickerson, David, Sahle, Sven, Snoep, Jacky L, Le Novère, Nicolas
Publicado 2011

BioUML: an integrated environment for systems biology and collaborative analysis of biomedical data

por Kolpakov, Fedor, Akberdin, Ilya, Kashapov, Timur, Kiselev, llya, Kolmykov, Semyon, Kondrakhin, Yury, Kutumova, Elena, Mandrik, Nikita, Pintus, Sergey, Ryabova, Anna, Sharipov, Ruslan, Yevshin, Ivan, Kel, Alexander
Publicado 2019

BioUML—towards a universal research platform

por Kolpakov, Fedor, Akberdin, Ilya, Kiselev, Ilya, Kolmykov, Semyon, Kondrakhin, Yury, Kulyashov, Mikhail, Kutumova, Elena, Pintus, Sergey, Ryabova, Anna, Sharipov, Ruslan, Yevshin, Ivan, Zhatchenko, Sergey, Kel, Alexander
Publicado 2022

Alternative transcription start sites contribute to acute-stress-induced transcriptome response in human skeletal muscle

por Makhnovskii, Pavel A., Gusev, Oleg A., Bokov, Roman O., Gazizova, Guzel R., Vepkhvadze, Tatiana F., Lysenko, Evgeny A., Vinogradova, Olga L., Kolpakov, Fedor A., Popov, Daniil V.
Publicado 2022

Genome-Wide Atlas of Promoter Expression Reveals Contribution of Transcribed Regulatory Elements to Genetic Control of Disuse-Mediated Atrophy of Skeletal Muscle

por Pintus, Sergey S., Akberdin, Ilya R., Yevshin, Ivan, Makhnovskii, Pavel, Tyapkina, Oksana, Nigmetzyanov, Islam, Nurullin, Leniz, Devyatiyarov, Ruslan, Shagimardanova, Elena, Popov, Daniil, Kolpakov, Fedor A., Gusev, Oleg, Gazizova, Guzel R.
Publicado 2021