D. Oshchepkov

发表

Candidate SNP Markers of Atherogenesis Significantly Shifting the Affinity of TATA-Binding Protein for Human Gene Promoters Show Stabilizing Natural Selection as a Sum of Neutral Drift Accelerating Atherogenesis and Directional Natural Selection Slowing It

N. Kolchanov, M. Ponomarenko, D. Rasskazov, 2020, International journal of molecular sciences.

The Interplay of Chromatin Landscape and DNA-Binding Context Suggests Distinct Modes of EIN3 Regulation in Arabidopsis thaliana

I. Grosse, V. Mironova, V. Levitsky, 2017, Front. Plant Sci..

Effect of flanking sequences on the accuracy of the recognition of transcription factor binding sites

E. A. Ananko, T. M. Khlebodarova, N. Kolchanov, 2015, Russian Journal of Genetics: Applied Research.

Artsite Database: Comparison of In Vitro Selected and Natural Binding Sites of Eukaryotic Transcription Factors

E. A. Ananko, Denis S. Miginsky, T. M. Khlebodarova, 2006 .

Reconstruction of the mechanisms that regulate the expression of the Escherihia coli yfiA gene under stress conditions

T. M. Khlebodarova, D. Oshchepkov, V. Likhoshvai, 2013, Russian Journal of Genetics: Applied Research.

Computer Analysis of Conformational and Physicochemical Properties of Nucleotide Sequences Cleavable by DNA Topoisomerase I

N. Kolchanov, D. Oshchepkov, G. Nevinsky, 2005, Molecular Biology.

In silico prediction of transcriptional factor-binding sites.

V. Levitsky, D. Oshchepkov, 2011, Methods in molecular biology.

Human RFP2 gene promoter: unique structure and unusual strength.

A. Baranova, K. Shakhbazov, M. Skoblov, 2006, Biochemical and biophysical research communications.

A single ChIP-seq dataset is sufficient for comprehensive analysis of motifs co-occurrence with MCOT package

I. Grosse, T. Merkulova, V. Mironova, 2019, Nucleic acids research.

Genes associated with cognitive performance in the Morris water maze: an RNA-seq study

D. Oshchepkov, N. Ershov, N. Bondar, 2020, Scientific Reports.

Dynamics of IL-12 cytokine expression in human macrophages after dioxin exposure

E. Antontseva, E. Kashina, V. Mordvinov, 2014, Russian Journal of Genetics: Applied Research.

Asymmetric Conservation within Pairs of Co-occurred Motifs Mediates Weak Direct Transcription Factor Binding in ChIP-seq Data

T. Merkulova, V. Levitsky, D. Oshchepkov, 2020 .

Asymmetric Conservation within Pairs of Co-Occurred Motifs Mediates Weak Direct Binding of Transcription Factors in ChIP-Seq Data

T. Merkulova, V. Levitsky, D. Oshchepkov, 2020, International journal of molecular sciences.

Development of computational methods to search for FoxA transcription factor binding sites, their experimental verification and application to the analysis of ChIP-seq data

L. Bryzgalov, E. Antontseva, T. Merkulova, 2011, Doklady Biochemistry and Biophysics.

Analysis of data on large-scale chromatin immunoprecipitation by recognition of transcription factor binding sites

V. G. Levitskii, T. Merkulova, D. Oshchepkov, 2011, Russian Journal of Genetics: Applied Research.

Expression dynamics of the REL, RELA, and IRF1 transcription factors in U937 macrophages after dioxin exposure

E. Antontseva, E. Kashina, V. Mordvinov, 2017, Russian Journal of Genetics: Applied Research.

Dynamics of REL, RELA and IRF1 transcription factor expression in U937 macrophages after dioxin exposure

E. Antontseva, E. Kashina, V. Mordvinov, 2016 .

A Rat Model of Human Behavior Provides Evidence of Natural Selection Against Underexpression of Aggressiveness-Related Genes in Humans

M. Ponomarenko, I. Chadaeva, E. Sharypova, 2019, Front. Genet..

Web-MCOT Server for Motif Co-Occurrence Search in ChIP-Seq Data

V. Levitsky, D. Oshchepkov, E. Zemlyanskaya, 2022, International journal of molecular sciences.

Disruptive natural selection by male reproductive potential prevents underexpression of protein-coding genes on the human Y chromosome as a self-domestication syndrome

M. Ponomarenko, D. Rasskazov, I. Chadaeva, 2020, BMC Genetics.

A bioinformatic search for correspondence between differentially expressed genes of domestic versus wild animals and orthologous human genes altering reproductive potential

I. Chadaeva, E. Sharypova, D. Oshchepkov, 2022, Vavilovskii zhurnal genetiki i selektsii.

Transcription Factors as Important Regulators of Changes in Behavior through Domestication of Gray Rats: Quantitative Data from RNA Sequencing

V. Levitsky, I. Chadaeva, E. Sharypova, 2022, International journal of molecular sciences.

Construction of a biosensor sensitive to terahertz radiation based on the glutamine synthetase gene promoter

D. Oshchepkov, S. Peltek, E. Demidova, 2020 .

Hidden heterogeneity of transcription factor binding sites: A case study of SF-1

Victor G. Levitsky, Elena V. Ignatieva, Tatyana I. Merkulova, 2016, Comput. Biol. Chem..

Analysis and recognition of the GAGA transcription factor binding sites in Drosophila genes

Tatyana I. Merkulova, E. S. Omelina, E. M. Baricheva, 2011, Comput. Biol. Chem..

Stress Reactivity, Susceptibility to Hypertension, and Differential Expression of Genes in Hypertensive Compared to Normotensive Patients

N. Kolchanov, M. Ponomarenko, I. Chadaeva, 2022, International journal of molecular sciences.

Disruptive Selection of Human Immunostimulatory and Immunosuppressive Genes Both Provokes and Prevents Rheumatoid Arthritis, Respectively, as a Self-Domestication Syndrome

N. Kolchanov, M. Ponomarenko, D. Rasskazov, 2021, Frontiers in Genetics.

Bioinformatical and experimental approaches to investigation of transcription factor binding sites in vertebrate genes

E. A. Ananko, E. V. Ignatieva, N. A. Kolchanov, 2007, Biochemistry (Moscow).

Combined experimental and computational approaches to study the regulatory elements in eukaryotic genes

Victor G. Levitsky, Nikolay A. Kolchanov, Charlie Hodgman, 2007, Briefings Bioinform..

Differentially Expressed Genes and Molecular Susceptibility to Human Age-Related Diseases

N. Kolchanov, V. Ivanisenko, M. Ponomarenko, 2023, International journal of molecular sciences.

Domestication Explains Two-Thirds of Differential-Gene-Expression Variance between Domestic and Wild Animals; The Remaining One-Third Reflects Intraspecific and Interspecific Variation

N. Kolchanov, M. Ponomarenko, I. Chadaeva, 2021, Animals : an open access journal from MDPI.

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

V. Makeev, T. Merkulova, V. Levitsky, 2014, BMC Genomics.

Application of experimentally verified transcription factor binding sites models for computational analysis of ChIP-Seq data

V. Makeev, T. Merkulova, V. Levitsky, 2014, BMC Genomics.

From binding motifs in Chip-seq Data to Improved Models of transcription factor binding Sites

Victor G. Levitsky, Vsevolod J. Makeev, Dmitry Yu. Oshchepkov, 2013, J. Bioinform. Comput. Biol..

Cancer Stem Cells: «Emergency Service» for Tumors Under Generalized Cellular Stress

N. Kolchanov, D. Oshchepkov, A. Proskurina, 2019, Mathematical Biology and Bioinformatics.

SITECON: a tool for detecting conservative conformational and physicochemical properties in transcription factor binding site alignments and for site recognition

Tamara M. Khlebodarova, Evgenii Vityaev, Dmitry A. Grigorovich, 2004, Nucleic Acids Res..

Detection of target genes of FOXA transcription factors involved in proliferation control

L. Bryzgalov, T. Merkulova, D. Oshchepkov, 2008, Biochemistry (Moscow).

A Bioinformatics Model of Human Diseases on the Basis of Differentially Expressed Genes (of Domestic Versus Wild Animals) That Are Orthologs of Human Genes Associated with Reproductive-Potential Changes

N. Kolchanov, M. Ponomarenko, D. Rasskazov, 2021, International journal of molecular sciences.

Candidate SNP Markers Significantly Altering the Affinity of TATA-Binding Protein for the Promoters of Human Hub Genes for Atherogenesis, Atherosclerosis and Atheroprotection

N. Kolchanov, V. Ivanisenko, M. Ponomarenko, 2023, International journal of molecular sciences.

Rare Earth Elements Alter Redox Balance in Methylomicrobium alcaliphilum 20ZR

Anil K. Shukla, J. Adkins, D. Oshchepkov, 2018, Front. Microbiol..

The complex role of transcription factor GAGA in germline death during Drosophila spermatogenesis: transcriptomic and bioinformatic analyses

E. Baricheva, D. Oshchepkov, D. A. Karagodin, 2023, PeerJ.

E. coli aggregation and impaired cell division after terahertz irradiation

D. Oshchepkov, G. Vasiliev, S. Peltek, 2021, Scientific Reports.

Detection of conserved physico-chemical characteristics of proteins by analyzing clusters of positions with co-ordinated substitutions

Nikolay A. Kolchanov, Dmitry A. Afonnikov, Dmitry Yu. Oshchepkov, 2001, Bioinform..

Age-Dependent Changes in the Relationships between Traits Associated with the Pathogenesis of Stress-Sensitive Hypertension in ISIAH Rats

M. Ponomarenko, D. Oshchepkov, O. Redina, 2023, International journal of molecular sciences.

RatDEGdb: a knowledge base of differentially expressed genes in the rat as a model object in biomedical research

N. L. Podkolodnyy, I. Chadaeva, D. Oshchepkov, 2023, Vavilovskii zhurnal genetiki i selektsii.