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Mathematical Calculation and Modeling in Biology

A Special Issue of International Journal of Molecular Sciences (ISSN 1422-0067) belonging to the section "Molecular Informatics".

Deadline for manuscript submissions: 31 March 2027 | Viewed by 865

Editor


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Guest Editor
Key Laboratory of Symbolic Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun 130012, China
Interests: mathematical modeling; computational biology; molecular biology; machine/deep learning; molecular interactions; computational drug design; disease biomarker; complex biological networks; data mining; non-coding RNA

Special Issue Information

Dear Colleagues,

The rapid development of molecular biology, high-throughput experimental technologies, and computational methods has led to an unprecedented accumulation of complex biological data at the molecular level. Mathematical calculations, mechanistic modeling, and data-driven approaches, particularly machine learning and deep learning, have become essential for extracting meaningful biological insights and enabling prediction modeling in modern biology. This Special Issue, “Mathematical Calculation and Modeling in Biology”, aims to bring together recent methodological developments in mathematical modeling, machine learning, and deep learning that address biological questions at the molecular level.

The scope of this Special Issue focuses on the development and application of mathematical models, numerical methods, and computational algorithms to investigate molecular-level biological processes. Topics of interest include molecular interaction networks, gene regulation and signaling pathways, enzyme kinetics, and protein structure. In addition, the Issue emphasizes the application of machine learning and deep learning techniques for molecular modeling, multi-omics data integration, biomolecular property prediction, and structure-function relationship analysis. Computational drug design and discovery, including drug-target interaction modeling, drug repositioning, drug resistance and sensitivity, molecular docking, and optimization of candidate compounds, are also key areas of interest.

Dr. Nan Sheng
Guest Editor

Manuscript Submission Information

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Keywords

  • mathematical modeling
  • computational biology
  • machine/deep learning
  • molecular biology
  • molecular interactions
  • gene
  • protein
  • small molecule
  • computational drug design
  • multi-omics

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Published Papers (1 paper)

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Research

19 pages, 3074 KB  
Article
Systematic Benchmarking of DNA Sequence Encoding Strategies for Predicting Regulatory Effects of Non-Coding SNPs
by Hui Jin, Yihang Bao, Wenhao Li, Chengyi Yang, Weidi Wang, Wenxiang Cai, Zhe Liu and Guan Ning Lin
Int. J. Mol. Sci. 2026, 27(15), 6657; https://doi.org/10.3390/ijms27156657 - 25 Jul 2026
Viewed by 384
Abstract
Non-coding single nucleotide polymorphisms (SNPs) are key modulators of gene regulation and have been implicated in diverse complex traits and diseases. With the growing demand for accurate functional interpretation of non-coding variants, the choice of encoding strategies becomes critical in downstream predictive modeling. [...] Read more.
Non-coding single nucleotide polymorphisms (SNPs) are key modulators of gene regulation and have been implicated in diverse complex traits and diseases. With the growing demand for accurate functional interpretation of non-coding variants, the choice of encoding strategies becomes critical in downstream predictive modeling. Despite recent advances, a systematic evaluation of encoding approaches tailored for non-coding SNPs remains lacking. To address this gap, we present a comprehensive benchmark that evaluates six representative encoding strategies, including categorical, semantic, and functional embeddings, across three quantitative trait loci (QTL)-related prediction tasks. The study encompasses nine machine learning and deep learning models and incorporates experimental controls and repeated trials to ensure robustness and reproducibility. We assess each strategy along multiple dimensions, such as interpretability, representation abundance, and computational efficiency. Rather than ranking individual methods, our analysis emphasizes the interaction between encoding strategies, model types, and preprocessing protocols, and highlights their collective influence on predictive performance. This work establishes a standardized framework for evaluating non-coding SNP representations and offers guidance for selecting and optimizing prediction pipelines in regulatory genomics. Full article
(This article belongs to the Special Issue Mathematical Calculation and Modeling in Biology)
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