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The analysis of large-scale next-generation sequencing (NGS) data requires substantial computational power, often necessitating the use of high-performance computing (HPC) environments. However, the command-line interfaces for these resources create a significant barrier for many researchers. …
Read PDF<h4>Motivation</h4>Integrating multi-omics data provides valuable insights into biological processes by capturing information across multiple molecular layers, enabling a comprehensive understanding of complex diseases and driving advancements in precision medicine. However, existing computational methods for multi-omics …
Read PDFAs the generation of data in the life and health sciences expands rapidly, there is a growing need for professionals and students in these fields to master core bioinformatics skills, particularly those relating to Unix-like …
Read PDF<h4>Motivation</h4>Genome annotation files (GFF3/GTF) are the standard for storing genomic feature data, yet their flexibility often results in formatting inconsistencies that create bottlenecks for downstream bioinformatics analyses. A robust, unified framework is required to parse, …
Read PDF<h4>Motivation</h4>Structure-based drug design (SBDD) has advanced with deep generative models, but bridging the gap between continuous atomic coordinates and discrete atom types remains a challenge. Current approaches, such as diffusion and flow matching models, often …
Read PDF<h4>Motivation</h4>T cell receptor (TCR) recognition of peptide-major histocompatibility complex (pMHC) complexes is central to adaptive immunity, yet rational design of immunogenic epitopes remains elusive due to complex triplet binding constraints and data scarcity. No existing …
Read PDF<h4>Motivation</h4>Realistic simulated data is critical for advancing methodological development and optimizing study design in genetics research. However, many genetic simulation tools are unable to replicate the distribution of rare variants or incorporate key genetic information, …
Read PDF<h4>Motivation</h4>The surge of genomic data from advanced sequencing technologies is outpacing current analytical pipelines. We introduce LCR-modules, an open-source suite of bioinformatics tools designed for flexible and automated cancer genome data analysis. LCR-modules enables reproducible …
Read PDF<h4>Unlabelled</h4>JMIR Bioinformatics and Biotechnology announced a strategic partnership with the MidSouth Computational Biology and Bioinformatics Society (MCBIOS) in late 2025; this partnership establishes JMIR Bioinformatics and Biotechnology as the official journal of MCBIOS. This collaboration …
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Read PDF<h4>Motivation</h4>Multiomics data analysis is essential for scientific discovery in precision medicine. However, translating analysis results of omics data analysis into novel scientific hypotheses remains a significant challenge. Human experts must manually review analysis results and …
Read PDFBACKGROUND: Bioinformatics has become an integral part of genomic medicine; however, its formal inclusion in undergraduate medical education remains limited. Early, structured exposure is essential to bridge the gap between theoretical molecular biology and its …
Read PDF<h4>Summary</h4>Annotation of HR-MS/MS spectra is a complex task that can be tackled either by expert interpretation or machine learning models that rely on large spectral/structural databases for training. Frequently, users want to find novel compounds …
Read PDFOver the past two decades, the Student Council Symposium (SCS), the flagship event of the ISCB Student Council, has grown into a vital forum for early-career researchers in computational biology. Since its inception in 2005, …
Read PDF<h4>Motivation</h4>Post-translational modifications (PTMs) alter functional states and interaction specificity largely through the conformational changes they impose on protein structure. However, most existing resources remain sequence-centric and cannot reveal how chemical modifications reshape 3D structures. To …
Read PDF<h4>Motivation</h4>Molecular maps are graphical representations of the molecular mechanisms underlying biological systems. They are a valuable tool for curating, exchanging, and understanding biological knowledge, and may serve as a backbone for data analysis and modelling. …
Read PDF<h4>Motivation</h4>Breakthrough advancements in protein tertiary and quaternary structure prediction have accelerated structural bioinformatics research activity and drug development processes. However, many biological mechanisms involve more complicated interactions, such as those between amino and nucleic acids. …
Read PDF<h4>Summary</h4>Life over the past four billion years has been shaped by proteins and their capacity to assemble into three-dimensional conformations. Protein sequence alignments have been the enabling technology for exploring the evolution and functional adaptation …
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