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Сборник докладов VI Международной конференции "Математическая биология и биоинформатика"
Under the general editorship: Лахно В. Д.
A usual way to determine the evolutionary relatedness, or homology, of two DNA sequences is to search for traces of sequence conservation. However the lack of sequence conservation does not necessarily mean the lack of homology. Not detectable at the primary sequence level, it can be inferred when moving to the level of DNA/RNA secondary structures, which were shown to play an important role in many processes of genome functioning. Here we implemented DNAStructProfiler, an automated pipeline for reconstruction of DNA/RNA secondary structure conservation profiles that will allow researchers to reveal position-‐specific secondary structures in a set of DNA sequences. The tool can be used with any program that searches for DNA/RNA secondary structures, such as stem-‐loops, quadruplexes, triplex DNA, and any other structures of interest and is freely available at www.dnapunctuation.org/DNAStructProfiler.html. We demonstrate how the tool can be used to reveal evolutionary conserved stem-‐loop structures in human L1 retrotransposons.
Chapters
Poptsova M., Гречишникова Д., В кн.: Сборник докладов VI Международной конференции "Математическая биология и биоинформатика".: М.: Государственное учреждение Институт математических проблем биологии РАН, 2016. С. 134–135.
A usual way to determine the evolutionary relatedness, or homology, of two DNA sequences is to search for traces of sequence conservation. However the lack of sequence conservation does not necessarily mean the lack of homology. Not detectable at the primary sequence level, it can be inferred when moving to the level of DNA/RNA secondary ...
Added: March 8, 2017
Poptsova M., Заикин А. В., В кн.: Сборник докладов VI Международной конференции "Математическая биология и биоинформатика".: М.: Государственное учреждение Институт математических проблем биологии РАН, 2016.
DNA secondary structures play an important role in various processes of genome functioning from bacteria to human. A stem-loop structure is an elementary structural motif that can function as terminator, attenuator, promoter and recognition elements. Earlier we annotated bacterial genomes with stem-loop structures and found that promoter regions of transcription factors (TF) are enriched with ...
Added: March 8, 2017
Priority areas:
IT and mathematics
Language:
Russian
Kibkalo Vladislav, Chertopolokhov V., Mukhamedov A. et al., IEEE Access 2026 Vol. 14 P. 14369–14392
This study presents on-the-fly identification and multi-step prediction of nonlinear systems with delayed inputs using a dynamic neural network combined with a smooth projection onto ellipsoids. The projection enforces parameter constraints that guarantee stability, while a Lyapunov–Krasovskii analysis yields computable ultimate error bounds. Riccati-type matrix inequalities are derived, providing an efficient vectorization–projection–devectorization implementation suitable for ...
Added: May 22, 2026
Loshkareva M. E., Matveeva N., Вестник Томского государственного университета. История 2026 № 100 С. 112–118
This research is an endeavor to apply social network analysis (SNA) to the study of a medieval narrative source. The authors suppose that the use of network analysis may offer new possibilities in the study of the history of regions characterized by some political fragmentation. Authors tried to construct networks of historical interactions from 1193 ...
Added: May 22, 2026
Borovikova I., Okhrimenko G., Zamyatin V. et al., Journal of Structural Biology 2026 Vol. 218 No. 2 Article 108315
Single amino acid substitutions in the ATP-binding domain of ACVRL1, a key receptor in the bone morphogenetic protein (BMP) signaling pathway, are frequently classified as variants of uncertain significance (VUS), complicating molecular diagnosis for pulmonary arterial hypertension (PAH) and Hereditary Hemorrhagic Telangiectasia (HHT). Since aberrant ATP binding disrupts downstream SMAD1/5/8 phosphorylation, we employed molecular dynamics ...
Added: May 20, 2026
Shipilov F., Barnyakov A., Ivanov A. et al., / Series Physics "arxiv.org". 2026.
A fast simulation of the detector response is a vital task in high-energy physics (HEP). Traditional Monte-Carlo methods form the backbone of modern particle physics simulation software but are computationally expensive. We present a machine-learning-based approach to fast simulation of the Focusing Aerogel Ring Imaging Cherenkov (FARICH) detector response. Given a particle track and momentum, ...
Added: May 19, 2026
Goltseva Y., Tsokolaeva Z., Beloglazova I. et al., Stem Cell Research and Therapy 2026 Vol. 17 No. 1
Background Cardiac fibrosis represents a significant health burden, with endothelial dysfunction and damaged
perivascular microenvironment increasingly recognized as key contributors to fibrotic remodeling. The urokinase
plasminogen activator receptor (uPAR), a critical component of the urokinase system, plays a pivotal role in vascular
remodeling and fibrosis. While prior evidence indicates that uPAR deficiency leads to microvascular dysfunction and
perivascular fibrosis, ...
Added: May 19, 2026
Rabat: Association for Computational Linguistics, 2026.
Added: May 19, 2026
Bezzubov S., Malikov D., Krasnov L. et al., Scientific data 2026 Vol. 13 Article 727
Solubility is a crucial property of organic compounds, impacting their potential applications in synthetic chemistry, materials science and drug design. Moreover, in technological processes mixtures of solvents are often utilized, making the solubility assessment more complicated. Predicting solubility values in mixtures of solvents from a molecular structure can help to address this issue, although a ...
Added: May 19, 2026
Pikalov V., Meshcheryakov V., Kondratev S. et al., Technologies 2026 Vol. 14 No. 1 P. 1–27
This paper presents Aerokinesis, an IoT-based software–hardware system for intuitive gesture-driven control of quadcopter unmanned aerial vehicles (UAVs), developed within the Robot Operating System 2 (ROS2) framework. The proposed system addresses the challenge of providing an accessible human–drone interaction interface for operators in scenarios where traditional remote controllers are impractical or unavailable. The architecture comprises ...
Added: May 19, 2026
Kondratev S., Yulia Dyrchenkova, Georgiy Nikitin et al., Technologies 2026 Vol. 14 No. 1 Article 69
This paper presents Aerokinesis, an IoT-based software–hardware system for intuitive gesture-driven control of quadcopter unmanned aerial vehicles (UAVs), developed within the Robot Operating System 2 (ROS2) framework. The proposed system addresses the challenge of providing an accessible human–drone interaction interface for operators in scenarios where traditional remote controllers are impractical or unavailable. The architecture comprises ...
Added: May 19, 2026
Springer, 2025.
This book constitutes the refereed proceedings of the 19th International Conference on Parallel Computational Technologies, PCT 2025, held in Moscow, Russia, during April 8–10, 2025.
The 31 full papers included in this volume were carefully reviewed and selected from 122 submissions. These papers were organized under the following topical sections: High Performance Architectures, Tools and Technologies; ...
Added: May 18, 2026
Ronglin Z., Wei L., Jiahong C. et al., Journal of Signal Processing Systems 2026 Vol. 98 P. 1–15
To address the need for lightweight and low-latency protection in massive resource-constrained 5G Internet of Things (IoT) systems, this paper proposes Key-Controlled Modulation Hopping and Constellation Rotation (KMHCR). KMHCR is designed as a physical-layer confidentiality-enhancement mechanism that avoids bit-wise full-payload encryption in the protection pipeline. It uses a shared key derived from channel-reciprocity secret key ...
Added: May 16, 2026
Suvorov N. M., Proceedings of the Institute for System Programming of the RAS 2026 Vol. 38 No. 3(2) P. 49–66
Data Petri Nets (DPNs) extend classical Petri nets to model processes where data directly influences control-flow, enabling a comprehensive view of system behavior and possibility to detect failure points that could otherwise be hidden. Soundness is a correctness criterion that captures such failure points as deadlocks and livelocks as well as model boundedness and absence ...
Added: May 16, 2026
N. V. Mkrtchyan, Regional Research of Russia 2026 Vol. 16 No. 1 P. 170–181
The aim of the study is to assess the provision of all settlements in four regions of the Near North of Russia (Vologda, Kostroma, Kirov, and Yaroslavl oblasts) with social infrastructure institutions and to analyze whether the migration balance of settlements is associated with different provision of these institutions. The study was conducted using data ...
Added: May 16, 2026
Gaeva D. V., Barinova G. M., Romanchuk A. Y., Theoretical and Applied Climatology 2026 Vol. 157 Article 302
The objective of the paper was the spatio-temporal analysis of the dynamics of extreme climate indices for the south-eastern coast of the Baltic Sea over the 40-year period 1981–2020, employing 10 extreme indices proposed by Expert Team (ET) on Climate Change Detection and Indices (ETCCDI), characterizing hazardous phenomena as: extremely high temperatures, heat waves and ...
Added: May 13, 2026
Mkrtchyan N. V., Известия РАН. Серия географическая 2026 Т. 90 № 1 С. 231–245
Objective of the study is to assess the provision of all settlements in four regions of the Russian Near
North (Vologda, Kostroma, Kirov, and Yaroslavl oblasts) with social infrastructure facilities and to
analyze whether the migration balance of settlements is associated with varying levels of provision of
these facilities. The study is based on data collected from open ...
Added: May 13, 2026
Xiong N., Long W., He D. et al., Algorithms 2026 Vol. 19 No. 5 Article 386
In the era of data-driven education, educational social networks generate large volumes of high-dimensional and complex-structured data through learner interactions, collaborative activities, and resource-sharing behaviors, posing significant challenges to traditional unsupervised learning methods. Such data often exhibit non-convex distributions, heterogeneity, and noise sensitivity, making conventional clustering approaches insufficient for capturing their intrinsic structural relationships. To ...
Added: May 13, 2026
Velichkov B., Nikolova-Koleva I., Slavcheva M., Shumen: INCOMA Ltd, 2025.
The RANLP 2025 Student Research Workshop (RANLPStud’2025) is a special track of the established international conference Recent Advances in Natural Language Processing (RANLP’2025).
The RANLPStud is being organised for the 9th time and this year is running in parallel with the other tracks of the main RANLP 2025 conference. The target of RANLPStud’25 is to be a ...
Added: May 12, 2026
Gerges M., Kosonogov V., OBM Neurobiology 2025 Vol. 9 No. 4 Article 310
Emotion regulation (ER) involves processes by which individuals modulate the intensity, duration, and expression of emotional responses, and its dysregulation is associated with a broad spectrum of psychological disorders. While traditionally conceptualized within psychological frameworks, ER is increasingly recognized as biologically grounded, involving intricate interactions between neurochemical, hormonal, and metabolic systems. This narrative review aims ...
Added: May 12, 2026
Derkacheva A., Sakirkina M., Kraev G. et al., /. 2026.
Comprehensive data on natural hazards and their consequences are crucial for effective for risk assessment, adaptation planning, and emergency response. However, many countries face challenges with fragmented, inconsistent, and inaccessible data, particularly regarding local-scale events. To address this data gap in Russia, we developed an end-to-end processing pipeline that scrapes news from various online sources, ...
Added: April 28, 2026
Qin X., Deng Y., Shchur L. et al., / Series arXiv "math". 2026. No. 2603.02962.
We perform a Monte Carlo analysis of the Ising model on many three-dimensional lattices. By means of finite-size scaling we obtain the critical points and determine the scaling dimensions. As expected, the critical exponents agree with the three-dimensional Ising universality class for all models. The irrelevant field, as revealed by the correction-to-scaling amplitudes, appears to ...
Added: April 20, 2026
Pilé I., Deng Y., Shchur L., / Series arXiv "math". 2026. No. 2604.10254.
We investigate the spatial overlap of successive spin configurations in Markov chain Monte Carlo simulations using the local Metropolis algorithm and the Svendsen-Wang and Wolff cluster algorithms. We examine the dynamics of these algorithms for two models in different universality classes: the Ising model and the Potts model with three components. The overlap of two ...
Added: April 20, 2026
Gabdullin N., Androsov I., / Series Computer Science "arxiv.org". 2026.
Label prediction in neural networks (NNs) has O(n) complexity proportional to the number of classes. This holds true for classification using fully connected layers and cosine similarity with some set of class prototypes. In this paper we show that if NN latent space (LS) geometry is known and possesses specific properties, label prediction complexity can ...
Added: April 2, 2026
IEEE, 2025.
On behalf of the organizing committee, it is our great privilege to present this compendium of research
articles for the 11th International Conference on Automation, Robotics, and Applications (ICARA 2025),
which will be held in the vibrant city of Zagreb, Croatia from February 12 to 14, 2025. The proceedings
encapsulate the latest advancements and innovative research in the ...
Added: March 17, 2026