1197 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.
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.
EXTRARNAS is a reproducible, Docker-based Java framework that automates the extraction of RNA structural annotations using multiple tools and standardizes their heterogeneous outputs into BPSEQ and the new BPSEQE formats to facilitate consistent comparison of canonical and non-canonical interactions.
The paper introduces dnoise, a fast open-source Rust tool that significantly reduces the storage footprint of Bruker timsTOF native data by removing redundant points while preserving analytical accuracy in both DDA and DIA workflows.
This paper presents MetaDome 2027, a comprehensively updated resource that aggregates missense variant evidence across homologous human protein domains with GRCh38 support, significantly expanding domain coverage and providing critical pathogenic evidence to reclassify variants of uncertain significance in clinical genetics.
scPyviewer is a Python-native, web-based interactive viewer that enables non-programmers to explore AnnData single-cell datasets directly without Seurat conversion, offering feature parity with existing R Shiny tools while demonstrating superior rendering speed, lower memory usage, and the ability to handle large-scale datasets that cause R-based alternatives to fail.
The paper introduces C-PLANK, a deep learning framework trained on cellular chemoproteomics data that outperforms existing models in predicting fragment-protein interactions and successfully identified a novel SIRT3 agonist by integrating physicochemical embeddings with a systems-level biological plausibility metric.