Sarathi Tripathy P., Siriyappagouder P., Artem Valeryevich Nedoluzhko et al., Frontiers in Cell and Developmental Biology 2025 Vol. 13 Article 1643817
For aquaculture to be sustainable, it is very important to improve the growth rates of farmed fish by choosing the right species and their management. However, the integration of epigenetic markers in selective breeding programs remains underdeveloped, mainly due to limited understanding, particularly regarding DNA methylation’s heritability and its functional impact on growth traits. This ...
Added: March 25, 2026
Kriukov D., Efimov E., Kuzmina E. et al., , in: KDD '25: Proceedings of the 31th ACM SIGKDD Conference on Knowledge Discovery and Data Mining. Volume 2.: Association for Computing Machinery (ACM), 2025. P. 5560–5570.
The success of clinical trials of longevity drugs relies heavily on identifying integrative health and aging biomarkers, such as biological age. Epigenetic aging clocks predict the biological age of individuals using their DNA methylation profiles, commonly retrieved from blood samples. However, there is no standardized methodology to validate and compare epigenetic clock models. We propose ComputAgeBench, ...
Added: January 12, 2026
Konovalov D., Umerenkov D., Herbert A. et al., Nucleic Acids Research 2025 Vol. 53 No. 19 Article gkaf1007
Alternative DNA conformation formed by sequences called flipons are thought to play an important role in regulating various genomic processes, either repressing or enhancing transcription, chromatin organization, DNA repair, telomere maintenance, RNA splicing, translation, and stress responses. The formation of G-quadruplexes (GQs) has been investigated experimentally using various methodologies with varying degrees of overlap between ...
Added: October 30, 2025
Cherednichenko O., Poptsova M., Computers in Biology and Medicine 2025 Vol. 184 Article 109440
Non-B DNA structures, or flipons, are important functional elements that regulate a large spectrum of cellular programs. Experimental technologies for flipon detection are limited to the subsets that are active at the time of an experiment and cannot capture whole-genome functional set. Thus, the task of generating reliable whole-genome annotations of non-B DNA structures is ...
Added: March 11, 2025
Krivonosov M., Nazarenko T., Bacalini M. G. et al., Chaos, Solitons and Fractals 2022 Vol. 165 Article 112863
Despite the fact that the cause of Down Syndrome (DS) is well established, the underlying molecular mechanisms that contribute to the syndrome and the phenotype of accelerated aging remain largely unknown. DNA methylation profiles are largely altered in DS, but it remains unclear how different methylation regions and probes are structured into a network of interactions. We ...
Added: March 12, 2024
Beniaminov A., Grigory A. Puzanov, Krasnov G. et al., Frontiers in Genetics 2018 Vol. 9 No. 169
Hypermethylation of promoter CpG islands is generally recognized epigenetic mechanism responsible for gene silencing in cancer. However, molecular details on how this epigenetic mark triggers the process of gene downregulation are still elusive. Here, we used deep bisulfite sequencing and qPCR analysis to investigate the pattern of CpG methylation of ALDH1L1 promoter region and its association with ...
Added: October 11, 2022
Loginov V., Pronina I., Filippova E. et al., International Journal of Molecular Sciences 2022 Vol. 23 No. 3 Article 1300
Our work aimed to differentiate 20 aberrantly methylated miRNA genes that participate at different stages of development and metastasis of ovarian carcinoma (OvCa) using methylation-specific qPCR in a representative set of clinical samples: 102 primary tumors without and with metastases (to lymph nodes, peritoneum, or distant organs) and 30 peritoneal macroscopic metastases (PMM). Thirteen miRNA ...
Added: June 20, 2022
Konstantinovskiy N., Kirillova E., Cherniatchik R., , in: ИНСТИТУТ БИОИНФОРМАТИКИ. СБОРНИК ТЕЗИСОВ 2020/21.: St. Petersburg: Федеральное государственное автономное образовательное учреждение высшего образования "Санкт-Петербургский политехнический университет Петра Великого", 2021. P. 59–60.
Added: August 9, 2021
Tevanyan E., Poptsova M., , in: Proceedings of the MACSPro Workshop 2019Vol. 2478: CEUR Workshop Proceedings.: CEUR-WS.org, 2019. P. 139–148.
DNAsecondary structures are important functional elements thatmay influence cellular processes. One of theirpossible functions is regulation of nucleosome positioning. Here MNAse-seq and ssDNA-seq data were used to define patterns of positional relationship of DNA structures such as Z-DNA, H-DNA and G-quadruplexes with nucleosomes. Three types of patterns werefound: a structure is surrounded by nucleosomes from ...
Added: January 15, 2020
Cheloshkina K., Poptsova M., BMC Cancer 2019 Vol. 19 No. 434 P. 1–17
Background: Chromosomal rearrangements are the typical phenomena in cancer genomes causing gene disruptions and fusions, corruption of regulatory elements, damage to chromosome integrity. Among the factors contributing to genomic instability are non-B DNA structures with stem-loops and quadruplexes being the most prevalent. We aimed at investigating the impact of specifically these two classes of non-B ...
Added: March 13, 2019
Tevanyan E., Poptsova M., , in: Proceedings 2018 IEEE International Conference on Bioinformatics and Biomedicine.: Madrid: IEEE, 2018. P. 2808–2809.
Non-B DNA structures have a great potential to form and influence various genomic processes including transcription. One of the mechanisms of transcription regulation is nucleosome positioning. Even though only B-DNA can be wrapped around a nucleosome, non-B DNA structures can compete with a nucleosome for a genomic location. Here we used permanganate/S1 nuclease footprinting data ...
Added: February 3, 2019
Cheloshkina K., Poptsova M., , in: Сборник трудов 42-й междисциплинарной школы-конференции ИППИ РАН "Информационные технологии и системы 2018".: Институт проблем передачи информации им. А.А. Харкевича РАН, 2018. P. 1–5.
With the advances in the sequencing technology the International Cancer Genome Consortium (ICGC) [1] and The Cancer Genome Atlas (TCGA) [2] collected data on more than 16 000 genome-wide pairs tumor-normal tissue providing a valuable resource to study cancer mutations. In this research we focus on pre- evaluation of the relationship between cancer breakpoint hotspots ...
Added: January 15, 2019