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Despite revolutionary advances in genomic technologies, a persistent disconnect exists between research discoveries and clinical implementation. This translational gap stems from misaligned incentive and funding structures: researchers prioritise publications over clinical uptake, with funding ending …
Read PDF<h4>Motivation</h4>Across-chromosome phasing identifies which haplotypes of different chromosomes come from the same parent. This differs from within-chromosome phasing, which uses linkage disequilibrium patterns to determine which alleles were co-inherited within each chromosome but does not …
Read PDFChronic diseases impose a global health burden, contributing to high mortality and economic costs. Even with the recent surge in molecular data, these conditions remain largely incurable due to their biological complexity, data fragmentation, and …
Read PDF<h4>Motivation</h4>Avoiding dual-axis visualization improves quantitative interpretation. Yet for large-scale paired datasets, combining raw data with summary metrics on dual axes often hinders interpretability, while single-axis displays risk visual saturation of paired lines. These limitations may …
Read PDFModern biology increasingly relies on mathematical and computational modeling to describe complex hierarchically organized biological systems. This review considers models that cover the main levels of biological organization, from the molecular-genetic and cellular levels to …
Read PDFBACKGROUND: Acidic extracellular pH is a defining feature of many solid tumors and can influence the structural stability and activity of proteins involved in cancer progression. However, no unified computational framework exists for systematically assessing …
Read PDF<h4>Motivation</h4>MirtronDB provides a comprehensive and up-to-date resource for advancing mirtron research within RNA biology. Therefore, maintaining a specialized and continuously updated resource for mirtrons is essential to support ongoing discoveries and to serve as a …
Read PDF<h4>Background</h4>Alzheimer's disease (AD) is a progressive neurodegenerative disease. Traditional models for estimating AD onset cannot capture nonlinear interactions (epistasis) among the numerous genetic variables that contribute to AD risk.<h4>Methods</h4>We developed a feedforward neural network (FFN)-Weibull …
Read PDF<h4>Motivation</h4>AlphaFold2 significantly improved the prediction of protein complex structures. However, its accuracy is lower for interactions without coevolutionary signals, such as host-pathogen and antibody-antigen interactions. Two strategies have been developed to address this limitation: massive …
Read PDF<h4>Summary</h4>Modern omics experiments now involve multiple conditions and complex designs, producing an increasingly large set of differential expression and functional enrichment analysis results. However, no standardized data structure exists to store and contextualize these results …
Read PDF<h4>Background and purpose</h4>Colorectal cancer (CRC) is a significant global health challenge, necessitating a comprehensive molecular understanding for personalized treatments. Molecular profiling has elucidated key biomarkers that are essential for prognosis, treatment responsiveness, and targeted therapeutic …
Read PDF<h4>Motivation</h4>Predicting gene-disease associations (GDAs) can be framed as a ranking problem where genes are ranked for a query disease based on features such as phenotypic similarity. By describing phenotypes using phenotype ontologies, ontology-based semantic similarity …
Read PDF<h4>Motivation</h4>Drug-target binding affinity (DTA) prediction plays a vital role in drug repositioning. The emergence of large language models (LLMs) has introduced new perspectives for predicting DTA. Herein, we present TSEDTA, a Transformer-based neural network with …
Read PDFBioinformatics tools are increasingly important for diagnostics in clinical care and precision medicine, but despite a very active bioinformatics research community, implementation and adaptation is slow. Drawing on multidisciplinary expertise, we have identified key systemic …
Read PDF<h4>Motivation</h4>Cryo-electron microscopy (Cryo-EM) single particle analysis (SPA) is a key technique for revealing the structure of biomacromolecules by three-dimensional reconstruction. Achieving high-resolution reconstruction relies on the acquisition of a large number of authentic particles; however, …
Read PDF<h4>Motivation</h4>Enhancer-promoter interactions (EPIs) are essential for gene regulation and disease progression. Recent studies have shown that distal enhancers can regulate target genes through interactions with nearby promoters, providing important insights into transcriptional regulation mechanisms. Although …
Read PDF<h4>Motivation</h4>Accurate annotation of germline immunoglobulin (IG) and T cell receptor (TCR) loci is critical for understanding adaptive immunity.<h4>Results</h4>VDJ-Insights provides a user-friendly software package for characterizing these complex immune regions. In addition, it assesses gene segment …
Read PDF<h4>Motivation</h4>Hierarchical clustering is a fundamental problem in computational biology, with popular greedy heuristics such as average linkage dating back to the 1950s but no well-defined objective. Recently, a combinatorial optimization criterion for the problem was …
Read PDFParamyxoviruses, such as Newcastle disease virus (NDV), assemble in and bud from plasma membranes of infected cells. To explore the role of each of the NDV structural proteins in virion assembly and release, virus-like particles …
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