Journal of Bioinformatics and Computational Biology最新文献

COLDLNA: Enhancing long-range node features extraction to improve robust generalization ability of drug-target binding affinity prediction in cold-start scenarios. COLDLNA：增强远程节点特征提取，提高冷启动场景下药物靶点结合亲和力预测的鲁棒泛化能力。

IF 0.7 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2025-09-20 DOI: 10.1142/S0219720025500131

Ting Xu, Shaohua Jiang, Weibin Ding, Peng Wang

引用次数: 0

Parameter estimation analysis of the glioblastoma immune model. 胶质母细胞瘤免疫模型参数估计分析。

IF 0.7 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2025-08-01 Epub Date: 2025-07-26 DOI: 10.1142/S0219720025500088

Biao Liu, Mengru Shen, Meiling Zhao

{"title":"Parameter estimation analysis of the glioblastoma immune model.","authors":"Biao Liu, Mengru Shen, Meiling Zhao","doi":"10.1142/S0219720025500088","DOIUrl":"10.1142/S0219720025500088","url":null,"abstract":"In exploring optimal strategies for immunotherapy in glioblastoma (GBM), one of the main challenges is enhancing treatment response. To better understand the dynamics of tumor-immune interactions, one applied Bayesian methods to estimate the parameters of glioblastoma immune model by using experimental data. One compared the effects of using uniform prior distributions versus improved prior distributions, which were adjusted based on posterior information, during parameter estimation. In addition, a comparative analysis of the results obtained by using four Markov Chain Monte Carlo (MCMC) sampling algorithms which respectively are Metropolis, DEMetropolis, DEMetropolisZ and NUTS, were performed. The results showed that the improved prior distribution significantly enhanced the accuracy of the model parameter estimates, and reduced the variance of the posterior distribution, but increased computational time and resource demands. Furthermore, DEMetropolisZ provided such efficient sampling and narrower confidence intervals within a shorter time frame, which outperformed the others. In contrast, the efficiency and stability of the Metropolis method were relatively poor. Therefore, the importance of selecting appropriate prior distributions and sampling algorithms to improve both the accuracy and efficiency of model inference were studied. The study provides valuable insights for optimizing GBM immunotherapy strategies and serves as a reference for modeling and parameter estimation of complex biological systems.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":"23 4","pages":"2550008"},"PeriodicalIF":0.7,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144849461","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Metagenomic sequence classification based on local sensitive hashing and Bi-LSTM. 基于局部敏感哈希和Bi-LSTM的宏基因组序列分类。

IF 0.7 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2025-08-01 DOI: 10.1142/S021972002550012X

Yan Qian, Lei Xiao, Yiding Zhou, Li Deng

引用次数: 0

Visual-SELEX: A technology ensemble for evaluating aptamer structural similarity via 3D visual spatial conformational analysis. visual - selex：通过三维视觉空间构象分析评估适体结构相似性的技术集成。

IF 0.7 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2025-08-01 DOI: 10.1142/S0219720025500106

Nijia Wang

{"title":"Visual-SELEX: A technology ensemble for evaluating aptamer structural similarity via 3D visual spatial conformational analysis.","authors":"Nijia Wang","doi":"10.1142/S0219720025500106","DOIUrl":"10.1142/S0219720025500106","url":null,"abstract":"To date, the study of single-stranded DNA (ssDNA) similarity has focused mainly on the similarity of bases in the same position in the nucleic acid sequence. However, focusing only on the similarity of base sequences has limitations. This similarity evaluation considers only the one-dimensional similarity of ssDNA and cannot fully capture the three-dimensional (3D) structural consistency of aptamers for nucleic acids with 3D structures. Therefore, it is necessary to develop a program that can quickly and accurately evaluate the 3D spatial consistency of ssDNA. To this end, we designed a Visual-SELEX rapid response program, which uses a screening ssDNA sequence set enriched in the DKK1 protein for analysis. The program directly generates a stable 3D structure of ssDNA through coarse-grained simulation and molecular dynamics (MD) simulation, converts the structure into a point cloud model, and then analyzes the similarity of the spatial structure of ssDNA through point cloud model alignment and superposition. The analysis results show that Visual-SELEX can accurately match ssDNAs with dissimilar base fragments but similar 3D spatial structures, providing richer 3D spatial similarity information than sequence similarity comparison alone.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":"23 4","pages":"2550010"},"PeriodicalIF":0.7,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144849462","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

NanoporeInspect: An interactive tool for evaluating nanopore sequencing quality and ligation efficiency. 一个评价纳米孔测序质量和连接效率的交互式工具。

IF 0.7 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2025-08-01 DOI: 10.1142/S0219720025500118

Maria A Grigoryeva, Maria G Khrenova, Maria I Zvereva

{"title":"NanoporeInspect: An interactive tool for evaluating nanopore sequencing quality and ligation efficiency.","authors":"Maria A Grigoryeva, Maria G Khrenova, Maria I Zvereva","doi":"10.1142/S0219720025500118","DOIUrl":"10.1142/S0219720025500118","url":null,"abstract":"In nanopore sequencing, especially in SELEX-based aptamer discovery, the correct ligation of artificial sequences (primers, adapters, barcodes) is crucial for library quality. Errors at this stage can lead to misidentification of sequences and loss of valuable information. Existing quality control tools lack focused capabilities to assess the positioning and prevalence of these artificial sequences. NanoporeInspect is a web-based tool designed to fill this gap by providing targeted insights into ligation efficacy and systematic biases within sequencing data. NanoporeInspect operates as a user-friendly, web-based platform that leverages a modern software stack with Flask, Celery and Redis to handle scalable and asynchronous task processing, and Plotly to deliver interactive visualizations. Evaluation of NanoporeInspect on various nanopore datasets demonstrated its effectiveness in discerning differences in ligation quality. Libraries with inefficient ligation showed irregular adapter and barcode distributions, indicating preparation issues, while high-quality libraries displayed uniform patterns, reflecting effective ligation.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":"23 4","pages":"2550011"},"PeriodicalIF":0.7,"publicationDate":"2025-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144849460","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Deep learning inference of miRNA expression from bulk and single-cell mRNA expression. 从大细胞和单细胞mRNA表达中深度学习推断miRNA表达。

IF 0.7 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2025-06-01 DOI: 10.1142/S021972002550009X

Rony Chowdhury Ripan, Tasbiraha Athaya, Xiaoman Li, Haiyan Hu

引用次数: 0

An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra. 从一组SILAC标记的MS/MS光谱中进行肽从头测序的算法。

IF 0.7 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2025-06-01 Epub Date: 2025-07-15 DOI: 10.1142/S0219720025500076

Fang Han, Kaizhong Zhang

{"title":"An algorithm for peptide de novo sequencing from a group of SILAC labeled MS/MS spectra.","authors":"Fang Han, Kaizhong Zhang","doi":"10.1142/S0219720025500076","DOIUrl":"10.1142/S0219720025500076","url":null,"abstract":"Shotgun proteomics coupled with high-performance liquid chromatography and mass spectrometry has been instrumental in identifying proteins in complex mixtures. Effective computational approaches are required to automate the spectra interpretation process to handle the vast amount of data collected in a single Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS) run. De novo sequencing from MS/MS has emerged as a vital technology for peptide sequencing in proteomics. To enhance the accuracy and practicality of de novo sequencing, previous algorithms have utilized multiple spectra to identify peptide sequences. Here, our study focuses on de novo sequencing of multiple tandem mass spectra of peptides with stable isotope labeling with amino acids in cell culture (SILAC) by incorporating different isotope-labeled amino acids into newly synthesized proteins. Multiple MS/MS spectra for the same peptide sequence are produced by the spectrometer after the SILAC samples undergo processing by LC-MS/MS shotgun proteomics. Taking into consideration the factors such as retention time and precursor ion mass, we aim to identify the peptide sequence with specific SILAC modifications and their locations. To do so, we propose de novo sequencing algorithms to compute the potential candidate peptide sequence by using similarity scores, followed by refinement algorithms to evaluate them. We also use real experimental data to test the algorithms.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":" ","pages":"2550007"},"PeriodicalIF":0.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144568024","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A brief review and comparative analysis of RNA secondary structure prediction tools. RNA二级结构预测工具综述及比较分析。

IF 0.7 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2025-06-01 Epub Date: 2025-07-21 DOI: 10.1142/S0219720025300011

Pranav Ballaney, Gourav Saha, Vaibhav Kulshrestha, Poojan Hasmukhray Thaker, Prakhar Hasija, Indrani Talukdar, Raviprasad Aduri

{"title":"A brief review and comparative analysis of RNA secondary structure prediction tools.","authors":"Pranav Ballaney, Gourav Saha, Vaibhav Kulshrestha, Poojan Hasmukhray Thaker, Prakhar Hasija, Indrani Talukdar, Raviprasad Aduri","doi":"10.1142/S0219720025300011","DOIUrl":"10.1142/S0219720025300011","url":null,"abstract":"Ribonucleic acid (RNA) lies at the heart of the central dogma. It spans the breadth of biological functions, from information storage to gene regulation and catalysis. RNA molecules must attain specific structures to perform these functions, and their structures depend on their sequences. Predicting the structure of RNA has been a central problem in computational biology. Various methods have been developed for this purpose - while some consider the thermodynamics of folding, others abstract away the details behind neural networks (NN). This paper presents a brief overview of the existing tools for predicting RNA secondary structures from a given single RNA sequence. Furthermore, a comparative analysis of the different prediction software packages is also presented. Performance is analyzed by running each of the available software packages on a novel dataset developed using 3D crystal structures of RNA. Software packages considered include those that can predict pseudoknots along with those that cannot. Variation in software performance based on the length and type of RNA is described.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":" ","pages":"2530001"},"PeriodicalIF":0.7,"publicationDate":"2025-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144683501","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Fractal dimensionality of a coiled helical coil. 螺旋线圈的分形维数。

IF 0.7 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2025-06-01 Epub Date: 2025-06-12 DOI: 10.1142/S0219720025710015

Subhash Kak

引用次数: 0

Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation. 具有多时滞和外部噪声调控的枯草芽孢杆菌能力基因调控电路的计算建模与动力学分析。

IF 0.9 4区生物学

Journal of Bioinformatics and Computational Biology Pub Date : 2025-04-01 Epub Date: 2025-06-05 DOI: 10.1142/S0219720025500052

Na Zhao, Haihong Liu, Fang Yan

{"title":"Computational modeling and dynamical analysis for B. subtilis competence genic regulation circuit with multiple time delays and external noisy regulation.","authors":"Na Zhao, Haihong Liu, Fang Yan","doi":"10.1142/S0219720025500052","DOIUrl":"10.1142/S0219720025500052","url":null,"abstract":"Bacillus subtilis (B. subtilis), a bacterium known to enter a competent state spontaneously, has garnered significant attention due to its intricate internal regulatory mechanisms. This study proposes a six-dimensional continuous delay differential equation (DDE) model incorporating two-time delays and a stochastic model that accounts for noise, aimed at delving deeper into the dynamic behaviors of the B. subtilis competence gene regulation circuit. Our investigation reveals that time delays play a crucial role in inducing oscillatory behavior within the continuous DDE model. Analyzing the dynamics of multiple time delays proves to be more intricate than studying a single delay. Furthermore, certain parameter adjustments significantly influence the system's dynamic characteristics. The introduction of noise also triggers oscillations, with the irregular oscillation patterns closely aligning with real-world observations. Intriguingly, the effects of parameters and noise regulation undergo significant changes when time delays are jointly considered. This analysis offers a fresh perspective on understanding B. subtilis competence and provides essential theoretical support for subsequent experimental endeavors in this domain of biomathematics.","PeriodicalId":48910,"journal":{"name":"Journal of Bioinformatics and Computational Biology","volume":"23 2","pages":"2550005"},"PeriodicalIF":0.9,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144267689","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0