Bioinformatics and Biology Insights最新文献

{"title":"Revolutionizing Chikungunya Vaccines: mRNA Breakthroughs With Molecular and Immune Simulations.","authors":"Md Habib Ullah Masum, Ahmad Abdullah Mahdeen, Abanti Barua","doi":"10.1177/11779322251324859","DOIUrl":"10.1177/11779322251324859","url":null,"abstract":"<p><p>With the ability to cause massive epidemics that have consequences on millions of individuals globally, the Chikungunya virus (CHIKV) emerges as a severe menace. Developing an effective vaccine is urgent as no effective therapeutics are available for such viral infections. Therefore, we designed a novel mRNA vaccine against CHIKV with a combination of highly antigenic and potential MHC-I, MHC-II, and B-cell epitopes from the structural polyprotein. The vaccine demonstrated well-characterized physicochemical properties, indicating its solubility and potential functional stability within the body (GRAVY score of -0.639). Structural analyses of the vaccine revealed a well-stabilized secondary and tertiary structure (Ramachandran score of 82.8% and a Z-score of -4.17). Docking studies of the vaccine with TLR-2 (-1027.7 KJ/mol) and TLR-4 (-1212.4 KJ/mol) exhibited significant affinity with detailed hydrogen bond interactions. Molecular dynamics simulations highlighted distinct conformational dynamics among the vaccine, \"vaccine-TLR-2\" and \"vaccine-TLR-4\" complexes. The vaccine's ability to elicit both innate and adaptive immune responses, including the presence of memory B-cells and T-cells, persistent B-cell immunity for a year, and the activation of TH cells leading to the release of IFN-γ and IL-2, has significant implications for its potential effectiveness. The CHIKV vaccine developed in this study shows promise as a potential candidate for future vaccine production against CHIKV, suggesting its suitability for further clinical advancement, including in vitro and in vivo experiments.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251324859"},"PeriodicalIF":2.3,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11967231/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143779130","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"The Microchimerism Literature Atlas.","authors":"Michael Christian Gruber, Daniel Kummer, Katja Sallinger, Henderson James Cleaves, Arsev Umur Aydinoğlu, Thomas Kroneis","doi":"10.1177/11779322251324104","DOIUrl":"10.1177/11779322251324104","url":null,"abstract":"<p><p>The Microchimerism Literature Atlas (MCLA) is a comprehensive online dataset to facilitate the investigation of microchimerism (MC), condition where individuals harbor cells from another individual of the same species. The MCLA provides access to more than 15 000 references from MC research, covering peer-reviewed articles and reviews from 1970 to the present. Key features include a multidimensional search function and logical operators for assembling search queries. The MCLA dataset offers a clearly structured data table view, combined with dynamic graphical data representation and visual citation analysis, aiding in the investigation and identification of research trends and patterns. The MCLA supports data export in various formats and receives regular updates. The MCLA is being developed as an essential resource for the MC research community while its framework is easily adaptable for custom literature datasets, enabling its use in other research fields.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251324104"},"PeriodicalIF":2.3,"publicationDate":"2025-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11967202/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143779132","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Development of a Novel mRNA Vaccine Against <i>Shigella</i> Pathotypes Causing Widespread Shigellosis Endemic: An In-Silico Immunoinformatic Approach.","authors":"Abdur Razzak, Otun Saha, Khandokar Fahmida Sultana, Mohammad Ruhul Amin, Abdullah Bin Zahid, Afroza Sultana, Uditi Paul Bristi, Sultana Rajia, Nikkon Sarker, Md Mizanur Rahaman, Newaz Mohammed Bahadur, Foysal Hossen","doi":"10.1177/11779322251328302","DOIUrl":"10.1177/11779322251328302","url":null,"abstract":"<p><p>Shigellosis remains a major global health concern, particularly in regions with poor sanitation and limited access to clean water. This study used immunoinformatics and reverse vaccinology to design a potential mRNA vaccine targeting <i>Shigella</i> pathotypes out of 4071 proteins from <i>Shigella sonnei</i> str. Ss046, 4 key antigenic candidates were identified: putative outer membrane protein (Q3YZL0), PapC-like porin protein (Q3YZM5), putative fimbrial-like protein (Q3Z3I2), and lipopolysaccharide (LPS)-assembly protein LptD (Q3Z5V5), ensuring broad pathotype coverage. A multitope vaccine was designed incorporating cytotoxic T lymphocyte, helper T lymphocyte, and B-cell epitopes, linked with suitable linkers and adjuvants to enhance immunogenicity. Computational analyses predicted vaccine's favorable antigenicity, solubility, and stability, while molecular docking and dynamic simulations demonstrated strong binding affinity and stability with Toll-like receptor 4 (TLR-4), indicating potential for robust immune activation. Immune simulations predicted strong humoral and cellular immune responses, characterized by significant cytokine production and long-term immune memory. Structural evaluations of the complex, including radius of gyration, root mean square deviation, root mean square fluctuation, and solvent accessibility, confirmed the vaccine's structural integrity, and stability under physiological conditions. This research contributes to the ongoing effort to alleviate the global burden of <i>Shigella</i> infections, providing a foundation for future wet laboratory investigations aimed at vaccine development.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251328302"},"PeriodicalIF":2.3,"publicationDate":"2025-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951904/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic Gene Attention Focus (DyGAF): Enhancing Biomarker Identification Through Dual-Model Attention Networks.","authors":"Md Khairul Islam, Himanshu Wagh, Hairong Wei","doi":"10.1177/11779322251325390","DOIUrl":"10.1177/11779322251325390","url":null,"abstract":"<p><p>The DyGAF model, which stands for Dynamic Gene Attention Focus, is specifically designed and tailored to address the challenges in biomarker detection, progression reporting of pathogen infection, and disease diagnostics. The DyGAF model introduced a novel dual-model attention-based mechanism within neural networks, combined with machine learning algorithms to enhance the process of biomarker identification. The model transcended traditional diagnostic approaches by meticulously analyzing gene expression data. DyGAF not only identified but also ranked genes based on their significance, revealing a comprehensive list of the top genes essential for disease detection and prognosis. In addition, KEGG pathways, Wiki Pathways, and Gene Ontology-based analyses provided a multileveled evaluation of the genes' roles. In our analyses, we tailored COVID-19 gene expression profile from nasopharyngeal swabs that offer a more nuanced view of the intricate interplay between the host and the virus. The genes ranked by the DyGAF model were compared against those selected by differential expression analysis and random forest feature selection methods for further validation of our model. DyGAF demonstrated its prowess in identifying important biomarkers that could enrich gene ontologies and pathways crucial for elucidating the pathogenesis of COVID-19. Furthermore, DyGAF was also employed for diagnosing COVID-19 patients by classifying gene-expression profiles with an accuracy of 94.23%. Benchmarking against other conventional models revealed DyGAF's superior performance, highlighting its effectiveness in identifying and categorizing COVID-19 cases. In summary, DyGAF model represents a significant advancement in genomic research, providing a more comprehensive and precise tool for identifying key genetic markers and unraveling the complex biological insights of a disease. The DyGAF model is available as a software package at the following link: https://github.com/hiddenntreasure/DyGAF.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251325390"},"PeriodicalIF":2.3,"publicationDate":"2025-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11951896/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143751083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary and epidemic dynamics of COVID-19 in Germany exemplified by three Bayesian phylodynamic case studies.","authors":"Sanni Översti, Ariane Weber, Viktor Baran, Bärbel Kieninger, Alexander Dilthey, Torsten Houwaart, Andreas Walker, Wulf Schneider-Brachert, Denise Kühnert","doi":"10.1177/11779322251321065","DOIUrl":"10.1177/11779322251321065","url":null,"abstract":"<p><p>The importance of genomic surveillance strategies for pathogens has been particularly evident during the coronavirus disease 2019 (COVID-19) pandemic, as genomic data from the causative agent, severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2), have guided public health decisions worldwide. Bayesian phylodynamic inference, integrating epidemiology and evolutionary biology, has become an essential tool in genomic epidemiological surveillance. It enables the estimation of epidemiological parameters, such as the reproductive number, from pathogen sequence data alone. Despite the phylodynamic approach being widely adopted, the abundance of phylodynamic models often makes it challenging to select the appropriate model for specific research questions. This article illustrates the application of phylodynamic birth-death-sampling models in public health using genomic data, with a focus on SARS-CoV-2. Targeting researchers less familiar with phylodynamics, it introduces a comprehensive workflow, including the conceptualisation of a research study and detailed steps for data preprocessing and postprocessing. In addition, we demonstrate the versatility of birth-death-sampling models through three case studies from Germany, utilising the BEAST2 software and its model implementations. Each case study addresses a distinct research question relevant not only to SARS-CoV-2 but also to other pathogens: Case study 1 finds traces of a superspreading event at the start of an early outbreak, exemplifying how simple models for genomic data can provide information that would otherwise only be accessible through extensive contact tracing. Case study 2 compares transmission dynamics in a nosocomial outbreak to community transmission, highlighting distinct dynamics through integrative analysis. Case study 3 investigates whether local transmission patterns align with national trends, demonstrating how phylodynamic models can disentangle complex population substructure with little additional information. For each case study, we emphasise critical points where model assumptions and data properties may misalign and outline appropriate validation assessments. Overall, we aim to provide researchers with examples on using birth-death-sampling models in genomic epidemiology, balancing theoretical and practical aspects.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251321065"},"PeriodicalIF":2.3,"publicationDate":"2025-03-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11898094/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143613195","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Gene Set Enrichment Analysis in Zebrafish Embryos Is Susceptible to False-Positive Results in the Absence of Differentially Expressed Genes.","authors":"John Dh Stead, Hyojin Lee, Andrew Williams, Sergio A Cortés Ramírez, Ella Atlas, Jan A Mennigen, Jason M O'Brien, Carole Yauk","doi":"10.1177/11779322251321071","DOIUrl":"10.1177/11779322251321071","url":null,"abstract":"<p><p>High-throughput gene expression studies commonly employ pathway analyses to infer biological meaning from lists of differentially expressed genes (DEGs). In toxicology and pharmacology studies, treatment groups are analysed against vehicle controls to identify DEGs and altered pathways. Previously, we empirically quantified false-positive rates of DEGs in gene expression data from pools of vehicle-treated zebrafish embryos to determine appropriate study designs (sample and pool size). Here, the same data were subject to Over-Representation Analysis (ORA) and Gene Set Enrichment Analysis (GSEA) to identify false-positive enriched pathways. As expected, the number of false-positive ORA results was lowest where pool and sample sizes were largest (conditions which also generated the fewest significant DEGs). In contrast, the frequency of GSEA false-positives generated through the fast GSEA (fgsea) algorithm increased with pool and sample size and was highest for simulations that generated 0 DEGs, with ribosomal gene sets significantly enriched with the highest frequency. We describe 2 distinct mechanisms by which GSEA generated these false-positive results, both of which are most likely to generate significant gene sets under conditions where expression differences are particularly low. Finally, GSEA analyses were repeated using 1 alternative GSEA algorithm (CERNO) and 11 different ranking statistics. In almost every analysis, the number of significant results was highest where pool size was highest, with ribosome as the more frequently enriched gene set, suggesting our observations to be generalizable to different implementations of GSEA. These results from zebrafish embryos suggest caution in interpreting any GSEA results in contrasts where there are no DEGs.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251321071"},"PeriodicalIF":2.3,"publicationDate":"2025-03-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11877468/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143555870","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational Development of Transmission-Blocking Vaccine Candidates Based on Fused Antigens of Pre- and Post-fertilization Gametocytes Against <i>Plasmodium falciparum</i>.","authors":"Matthew A Adeleke","doi":"10.1177/11779322241306215","DOIUrl":"10.1177/11779322241306215","url":null,"abstract":"<p><p><i>Plasmodium falciparum</i> is the most fatal species of malaria parasites in humans. Attempts at developing vaccines against the malaria parasites have not been very successful even after the approval of the RTS, S/AS01 vaccine. There is a continuous need for more effective vaccines including sexual-stage antigens that could block the transmission of malaria parasites between mosquitoes and humans. Low immunogenicity, expression, and stability are some of the challenges of transmission-blocking vaccine (TBV). This study was designed to computationally identify TBV candidates based on fused antigens by combining highly antigenic peptides from prefertilization (Pfs230, Pfs48/45) and postfertilization (Pfs25, Pfs28) gametocytes. The peptides were selected based on their antigenicity, nonallergenicity, and lack of similarity with the human proteome. Two fused antigens vaccine candidates (FAVCs) were constructed using Flagellin <i>Salmonella enterica</i> (FAVC-FSE) and Cholera toxin B (FAVC-CTB) as adjuvants. The constructs were evaluated for their physicochemical properties, structural stability, immunogenicity, and potential to elicit cross-protection across multiple <i>Plasmodium</i> species. The results yielded antigenic peptides, with antigenicity scores between 0.7589 and 1.1821. The structural analysis of FAVC-FSE and FAVC-CTB showed a Z-score of -6.70 and -4.79, a Ramachandran plot of 96.94% and 94.86% with overall quality of 94.20% and 89.85%, respectively. The FAVCs contained CD8⁺, CD4⁺, and linear B-cell epitopes with antigenicity scores between 1.2089 and 2.8623, 0.5663 and 2.4132, and 1.5196 and 2.2212, respectively. Each FAVC generated 6 conformational B-cells. High population coverage values were recorded for the FAVCs. The ability of the FAVCs to trigger immune response was evaluated through an in silico immune stimulation. The low-binding interaction energy that resulted from molecular docking and dynamics simulations showed a strong affinity of FAVCs to Toll-like receptor 5 (TLR5). The results indicate that the FAVC-FSE vaccine candidate is more promising to interrupt <i>P falciparum</i> transmission and provides a baseline for experimental validation.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322241306215"},"PeriodicalIF":2.3,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11873872/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540074","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bioinformatics-Driven Investigations of Signature Biomarkers for Triple-Negative Breast Cancer.","authors":"Shristi Handa, Sanjeev Puri, Mary Chatterjee, Veena Puri","doi":"10.1177/11779322241271565","DOIUrl":"10.1177/11779322241271565","url":null,"abstract":"<p><p>Breast cancer is a highly heterogeneous disorder characterized by dysregulated expression of number of genes and their cascades. It is one of the most common types of cancer in women posing serious health concerns globally. Recent developments and discovery of specific prognostic biomarkers have enabled its application toward developing personalized therapies. The basic premise of this study was to investigate key signature genes and signaling pathways involved in triple-negative breast cancer using bioinformatics approach. Microarray data set GSE65194 from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus was used for identification of differentially expressed genes (DEGs) using R software. Gene ontology and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analyses were carried out using the ClueGO plugin in Cytoscape software. The up-regulated DEGs were primarily engaged in the regulation of cell cycle, overexpression of spindle assembly checkpoint, and so on, whereas down-regulated DEGs were employed in alteration to major signaling pathways and metabolic reprogramming. The hub genes were identified using cytoHubba from protein-protein interaction (PPI) network for top up-regulated and down-regulated DEG's plugin in Cytoscape software. The hub genes were validated as potential signature biomarkers by evaluating the overall survival percentage in breast cancer patients.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322241271565"},"PeriodicalIF":2.3,"publicationDate":"2025-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11873876/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540073","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A \"Dock-Work\" Orange: A Dual-Receptor Biochemical Theory on the Deterrence Induced by Citrusy Aroma on Elephant Traffic Central to a Conservation Effort.","authors":"Dilantha Gunawardana","doi":"10.1177/11779322251315922","DOIUrl":"https://doi.org/10.1177/11779322251315922","url":null,"abstract":"<p><p>Conservation of elephants requires physical, chemical, and biological approaches to ensure the protection of these gargantuan pachyderms. One such approach is using orange plants (as biofencing) for the repellence of elephants, which precludes catastrophic events related to the encroachment of elephants into human habitats. Elephants have sensitive olfactory discrimination of plant volatile compounds for foraging and other behavior using G-protein-coupled receptors (GPCRs). However, 2 such receptors are the A2A and A2B receptors mediating olfaction elicited by a host of ligands, including limonene, the main volatile compound in citrus plants, which is hypothesized to be the chief repelling agent. Bioinformatics at the protein and mRNA levels (BLAST/Multiple Sequence Alignments) were employed to explore the multiple expression products of A2B receptors, namely full-length and truncated proteins produced by isoform mRNAs translated from multiple methionines, while the comparison of the limonene-binding pockets of human and elephant A2B receptors and prediction servers [Netphos 3.1; Protter] was used to focus, respectively, on the contacts limonene binding entails and the post-translational modifications that are involved in cell signaling. Finally, the link between limonene and antifeedant activity was explored by considering limonene content on trees that are preferentially foraged or avoided as part of the feeding behavior by elephants. The African bush elephant (<i>Loxodonta africana</i>) possesses a full-length A2A receptor but unlike most mammals, expresses a highly truncated A2B receptor isoform possessing only transmembrane helices 5, 6, and 7. Truncation may lead to higher traffic and expression of the A2B receptor in olfactory interfaces/pathways and aid stronger activation. In addition, all residues in the putative limonene-binding cleft are perfectly conserved between the human and African bush elephant A2B receptors, both full length and truncated. Shallow activation sites require micromolar affinity and fewer side-chain interactions, which is speculated to be the case for the truncated A2B receptor. An N-terminal extremity N-glycosylation motif is indicative of membrane localization of the truncated A2B receptor following accurate folding. A combination of truncation, indels, substitutions, and transcript isoforms are the attributed roles in the evolution of the <i>L. africana</i> A2B receptor, out of which limonene receptivity may be the key. It is also inferred how limonene may act as a dietary repellent/antifeedant to a generalist herbivore, with the documented limonene content being absent in some dietary favorites including the iconic <i>Sclerocarya birrea.</i></p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251315922"},"PeriodicalIF":2.3,"publicationDate":"2025-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11869256/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143540072","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Predicting TF-Target Gene Association Using a Heterogeneous Network and Enhanced Negative Sampling.","authors":"Thanh Tuoi Le, Xuan Tho Dang","doi":"10.1177/11779322251316130","DOIUrl":"10.1177/11779322251316130","url":null,"abstract":"<p><p>Identifying interactions between transcription factors (TFs) and target genes is crucial for understanding the molecular mechanisms involved in biological processes and diseases. Traditional biological experiments used to determine these interactions are often time-consuming, costly, and limited in scale. Current computational methods mainly predict binding sites rather than direct interactions. Although recent studies have achieved high performance in predicting TF-target gene associations, they still face a significant challenge related to constructing a robust dataset of positive and negative samples. Currently, methods do not adequately focus on selecting negative samples, resulting in incomplete coverage of potential TF-target gene relationships. This article proposes a method to select enhanced negative samples to improve the prediction performance of TF-target gene interactions. Experimental results show that the proposed method achieves an average area under the curve (AUC) value of 0.9024 ± 0.0008 through 5-fold cross-validation. These results demonstrate the model's high efficiency and accuracy, confirming its potential application in predicting TF-target gene interactions across various datasets and paving the way for large-scale biomedical research.</p>","PeriodicalId":9065,"journal":{"name":"Bioinformatics and Biology Insights","volume":"19 ","pages":"11779322251316130"},"PeriodicalIF":2.3,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11863233/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143514589","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}