1012 papers
Bioinformatics sits at the exciting intersection where biology meets data science, using powerful computer tools to decode the vast complexity of living systems. From mapping the human genome to tracking how viruses evolve, this field transforms raw biological information into actionable insights that drive modern medicine and research forward without requiring a supercomputer to understand the basics.
On Gist.Science, we ensure you never miss a breakthrough by processing every new preprint in this category directly from bioRxiv. Our team provides both plain-language explanations and detailed technical summaries for each paper, making cutting-edge discoveries accessible to everyone regardless of their background.
Below are the latest bioinformatics papers added from bioRxiv, ready for you to explore with clarity and depth.
This study demonstrates that covariance non-stationarity is a prevalent and biologically significant feature in spatial transcriptomics that violates common Gaussian process assumptions, thereby necessitating a re-evaluation of how spatially varying genes are characterized and categorized.
The paper introduces Kompot, a cluster-free statistical framework that enables single-cell resolution comparative analysis of multi-condition data by modeling cell density and gene expression as continuous functions to detect both differential abundance and localized, heterogeneous transcriptional changes without relying on predefined cell types.
This study utilizes a multilayered bioinformatics approach to characterize the robust, sex-specific transcriptional signature of human skeletal muscle in response to repeated shivering, revealing how these molecular adaptations diminish with cold acclimation and offering new mechanistic insights into improved metabolic health.
This study integrates experimental biophysical analyses and computational simulations to characterize the pH-dependent structural dynamics and conformational plasticity of the Dengue virus NS2B-NS3 protease, providing critical insights for the rational design of pH-specific antiviral inhibitors.
CoTRA is an open-source, modular R/Shiny framework that unifies transparent and reproducible workflows for both bulk and single-cell RNA-seq analysis, offering extensive functionality, cross-platform compatibility, and validated performance comparable to or exceeding existing tools.
The paper introduces spatialMET, an open-source, scalable framework that provides an end-to-end workflow for spatial metabolomics analysis—including preprocessing, domain detection, and statistical testing—while overcoming limitations of existing tools through high-performance computing capabilities and reproducible Docker deployment.
This paper introduces a stratified benchmark of 1,047 rare-disease cases designed to measure and mitigate circularity in gene-prioritization evaluations by flagging annotation overlaps with source literature, alongside a version-pinned recipe for constructing a hybrid retrieval index over 2.25 million PMC Open Access articles.
This paper introduces Bravais Lattice Sampling (BLS), a geometry-guided two-phase algorithm that efficiently detects connected high-density regions in 3D discretized spaces by replacing exhaustive raster scans with sparse lattice probing and targeted expansion, achieving 100% recall with computational costs comparable to or lower than existing methods.
This paper introduces MiraProt, a modular and metadata-aware R Shiny platform for interactive downstream proteomics analysis, and demonstrates its utility by reanalyzing Mueller cell proteomes from horses with equine recurrent uveitis to reveal an interferon-responsive, cell-cycle-associated, and MHC class II-associated protein signature.
The authors developed Mural-VISTA, a semi-automated Python workflow for 3D analysis of mural cell-vessel interactions and multiscale topo-morphological metrics, which revealed cell-type-specific structural changes in pericytes and vascular smooth muscle cells driven by altered RhoA activity.