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Myocardial fibrosis is a common pathological feature of multiple cardiovascular diseases, including heart failure, hypertension, and myocardial infarction, and is associated with poor prognosis. Despite extensive research, clinically validated molecular biomarkers for early diagnosis and …
Read PDFAfrica continues to bear a disproportionate burden of infectious diseases, particularly antimicrobial-resistant (AMR) infections, which significantly affect public health and socio-economic development. Addressing these complex health threats requires innovative approaches to data analysis, pathogen surveillance, …
Read PDFThe COVID-19 pandemic accelerated global adoption of wastewater and environmental surveillance (WES) and revealed its value as a complement to case-based infectious disease monitoring. However, practical scientific, ethical, and legal standards for public health implementation …
Read PDF<h4>Motivation</h4>T cell receptor (TCR) and peptide interactions (TPI) are one of the most important parts of T cell immunity. Experimental identification of TPI is time-consuming and labor-intensive; therefore, it is necessary to develop computational prediction …
Read PDF[This corrects the article DOI: 10.1371/journal.pone.0343398.].
Read PDF<h4>Motivation</h4>Identifying which documents in a large database contain a query string is a fundamental problem in Information Retrieval and Computational Biology. We focus on the approximate version of this problem for genomic sequences: the result …
Read PDFMulti-omics integration combines data from transcriptomics, proteomics, and metabolomics to provide insights into biological systems. Here, we present a protocol for integrating and interpreting multi-omics data using unsupervised multi-omics factor analysis (MOFA), supervised projection-based integration …
Read PDF<h4>Motivation</h4>Building and sustaining High-Performance Computing (HPC) infrastructure for bioinformatics research in resource-limited settings presents significant technical, financial and operational challenges. Institutions in low-and middle-income regions often face constraints such as limited technical expertise, unstable infrastructure …
Read PDF<h4>Motivation</h4>Large scale loss-of-function screens utilising CRISPR or siRNA can provide profound insights into the importance of individual genes for the survival of a cancer cell and can drive the identification of therapeutic targets and biomarkers, …
Read PDF<h4>Motivation</h4>CardioVar is a machine learning framework developed to predict the pathogenicity of cardiomyopathy-associated genetic variants, providing a rapid and disease-focused classification score to support variant interpretation in cardiogenetic workflows.<h4>Results</h4>This approach supports variant interpretation within cardiac-related …
Read PDF<h4>Motivation</h4>Understanding peptide properties is often assumed to require modeling long-range molecular interactions, motivating complex graph neural networks and pretrained transformers. Whether such long-range dependencies are essential remains unclear. We investigate if simple, domain-specific molecular fingerprints …
Read PDF<h4>Motivation</h4>Network analysis has become a central strategy for dissecting complex biological and environmental systems, particularly as modern omics technologies generate increasingly large and heterogeneous datasets. However, current tools often lack the scalability, flexibility, and native …
Read PDFThe expanding role of intelligent systems in biomedical science marks a shift from passive analysis towards active participation in discovery and care. Recent scholarship has begun to frame these systems not merely as models, but …
Read PDFArtificial intelligence (AI) is often framed as replacing scientific expertise, especially in bioinformatics. We argue instead that AI is a powerful accelerant whose value depends on expert guidance in design, data curation, interpretation, and governance. …
Read PDF<h4>Motivation</h4>Mass spectrometry imaging data typically contains tens of thousands of pixels, and m/z channels which may relate to biomolecules of interest. It is impossible to visualize such highly dimensional data, and many multi-variate analyses cannot …
Read PDFChronic rhinosinusitis with nasal polyps (CRSwNP) is a prevalent inflammatory disease of the sinuses that significantly diminishes patients' quality of life. Endoplasmic reticulum stress (ERS) is strongly associated with the initiation and progression of numerous …
Read PDF<h4>Objective</h4>To identify key genes and shared pathogenic pathways associated with acute pancreatitis-associated acute lung injury (AP-ALI), through bioinformatics analysis, and to provide potential molecular targets for the diagnosis and treatment of AP-ALI.<h4>Methods</h4>The cerulein-induced severe acute …
Read PDF<h4>Motivation</h4>Accurate prediction of condition-aware drug-induced transcriptional responses is essential for drug discovery and precision medicine. Current computational models, including encoder-decoder architectures and generative adversarial network-based approaches, exhibit reasonable performance but frequently neglect biological characteristics and …
Read PDF<h4>Motivation</h4>The AGENT project established a network of actively cooperating European genebanks, integrating genomic and phenotypic data from accessions of wheat and barley. Due to specific storage demands for phenotypic and genotypic data, the project used …
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