?
AGE-RELATED CHANGES IN METHYLATION PATTERNS AT SITES OF ACTIVE HUMAN DNA REPLICATION
P. 59–60.
Konstantinovskiy N., Kirillova E., Cherniatchik R.
Language:
English
In book
St. Petersburg: Федеральное государственное автономное образовательное учреждение высшего образования "Санкт-Петербургский политехнический университет Петра Великого", 2021.
Beknazarov N., , in: Parallel Computational Technologies, 19th International Conference, PCT 2025, Moscow, Russia, April 8–10, 2025, Revised Selected Papers. (CCIS, volume 2891)Vol. 2891.: Springer, 2026. P. 3–16.
This paper addresses the challenge of efficiently training Large Language Models (LLMs) on large-scale, sparse omics datasets in high-performance computing (HPC) environments. Using over 1000 BED tracks as a representative data source, we propose a method combining interval-based chunked storage, sparse matrix transformation, and parallel data loading, integrated within a PyTorch Lightning training framework. Our ...
Added: May 19, 2026
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
Arteaga Moreano B. D., Chervov N., Poptsova M., Scientific Reports 2026 Vol. 16 No. 1 Article 4772
Accurate prediction of protein-protein interactions (PPIs) is fundamental to understanding biological processes and disease mechanisms. While deep learning offers a powerful alternative to costly experimental methods, existing approaches often overlook critical protein-surface information and rely on simplistic feature fusion techniques, thereby limiting performance. To address this, we introduce GSMFormer-PPI, a novel multimodal framework that integrates ...
Added: February 4, 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
David Arteaga, Poptsova M., Computational and Structural Biotechnology Journal 2026 Vol. 31 P. 82–93
Accurate predictions and large-scale identification of protein-protein interactions (PPIs) are crucial for understanding their inherent biological mechanisms and protein functions in virtually all biological processes. Nowadays, graph-based deep learning models have made significant contributions in modeling proteins with physicochemical and geometric features. However, most of these models rely on conventional graph construction methods, such as ...
Added: December 22, 2025
Budkina A., Korneenko E., Kotov I. et al., Viruses 2021 No. 10 P. 2006
According to various estimates, only a small percentage of existing viruses have been discovered, naturally much less being represented in the genomic databases. High-throughput sequencing technologies develop rapidly, empowering large-scale screening of various biological samples for the presence of pathogen-associated nucleotide sequences, but many organisms are yet to be attributed specific loci for identification. This ...
Added: September 19, 2025
KUDRYAVTSEVA A., Cancers 2023
Liver metastasis is a significant factor contributing to mortality associated with colorectal cancer. Establishing the biological mechanisms of metastasis is crucial for refining diagnostics and identifying therapeutic windows for interventions. Currently, little is known of the processes that govern the development of liver metastases, the role of the tumor microenvironment, the role of epigenetics, and ...
Added: July 1, 2025
Аксенова А. Ю., Жук А. С., Степченкова Е. И. et al., Экологическая генетика 2025 Т. 23 № 2 С. 1–14
Биоинформатика — это быстро развивающаяся дисциплина на стыке биологии, информатики и математики. Научно-технический прогресс в области биологических и биомедицинских наук за последние годы привел к стремительному росту объемов данных. Для анализа и интерпретации больших данных нужны мощные вычислительные инструменты и специалисты с глубокими знаниями в различных областях, включая молекулярную биологию, генетику, программирование и математику. В ...
Added: May 20, 2025
Stefan Nikolić, Ignatov D. I., Khvorykh G. et al., PeerJ Computer Science 2024 Vol. 10 Article e2454
Despite the identification of several dozen genetic loci associated with ischemic stroke (IS), the genetic bases of this disease remain largely unexplored. In this research we present the results of genome-wide association studies (GWAS) based on classical statistical testing and machine learning algorithms (logistic regression, gradient boosting on decision trees, and tabular deep learning model ...
Added: December 11, 2024
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
[б.и.], 2023.
The Workshop will be held in the Meshcheryakov Laboratory of Information Technologies (MLIT) of the Joint Institute for Nuclear Research (JINR) on July 6-8, 2022.
The workshop primarily focuses on the use of machine learning in particle astrophysics and high energy physics, but is not limited to this area. Topics of interest are various applications of ...
Added: March 12, 2024
Pavel Latyshev, Fedor Pavlov, Herbert A. et al., , in: Proceedings of 11th Moscow Conference on Computational Molecular Biology MCCMB'23.: IITP RAS, 2023.
Added: December 1, 2023
IITP RAS, 2023.
В сборнике представлены тезисы работ участников 11-ой Московской конференции по вычислительной молекулярной биологии MCCMB'23. Работы посвящены актуальным вопросам анализа аминокислотных и нуклеотидных последовательностей, структур биополимеров, молекулярной эволюции, методов высокопроизводительного секвенирования, системной биологии и биоалгоритмов. ...
Added: November 30, 2023
Cham: Springer, 2023.
Added: November 29, 2023
Alimova I., Tutubalina E., Nikolenko S. I., IEEE Access 2022 Vol. 10 P. 1432–1439
Relation extraction (RE) aims to extract relational facts from plain text, which is essential to the biomedical research field with the rapid growth of biomedical literature and generally large volumes of biomedicine-related text coming from various sources. Numerous annotated corpora and state-of-the-art models have been introduced in the past five years. However, there are no ...
Added: April 10, 2023
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
Grigory Andreevich Puzanov, Scientific Reports 2022 Vol. 12 No. 1 Article 14588
Clear cell renal carcinoma has been reported in many research studies as a rather heterogeneous disease. Identification of different subtypes and their molecular characteristics can help in choosing a more effective treatment and predicting a response to it. In this study, using multi-omics clustering of RNA-Seq data of patients with clear cell renal carcinoma from ...
Added: September 23, 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
NY: Association for Computing Machinery (ACM), 2021.
Continuing the annual tradition, the conference focuses on interdisciplinary research linking computer science, mathematics, statistics, biology, bioinformatics, biomedical informatics, and health informatics. ...
Added: December 7, 2021