1018 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.
FLAMESv2 is a highly modular, protocol-agnostic R/Bioconductor package designed to process and analyze long-read single-cell and spatial RNA-seq data, enabling comprehensive characterization of RNA isoforms, alternative splicing, and cellular heterogeneity across diverse experimental workflows.
The paper introduces mnDINO, a robust vision transformer-based segmentation model trained on a diverse dataset of over 5,000 annotated micronuclei to achieve high-accuracy detection of these rare subcellular structures across various microscopes and cell lines, with all resources made publicly available.
This study evaluates 30 amino acid distance measures across diverse biological datasets to demonstrate that a new consensus-based measure, DEX, derived from deep mutational scanning and experimental exchangeability data, outperforms existing metrics in modeling codon substitution patterns and predicting mean substitution frequencies.
This paper benchmarks the BEAGLE library's integration with BEAST X to demonstrate how hardware allocation and specific settings significantly impact running times on real Dengue Virus data, ultimately establishing guidelines for optimal resource allocation in phylogenetic analyses.
The paper introduces IFACE, a novel framework that aligns protein surfaces by probabilistically coupling intrinsic geometry with chemical fields to derive a unified joint distance metric, which more effectively distinguishes functional similarities and conserved catalytic pockets than traditional fold-based methods.
This paper introduces a novel methodology that integrates ESM-2 protein language models with cyclic permutation averaging to construct a comprehensive "peptide space," enabling the efficient selection of cyclic peptide libraries with uniform physicochemical coverage and superior performance in AI-driven drug discovery compared to random sequence selection.
This study evaluates eight water models paired with the AMBER Lipid21 force field for simulating POPC and DPPC bilayers, concluding that SPC/E is the optimal choice for reproducing structural properties while TIP4P-Ew best matches experimental lateral diffusion dynamics.
This paper presents the user-driven development and evaluation of Llemy, an LLM-based agentic framework designed to assist domain experts in navigating and summarizing complex molecular interaction maps through iterative prototyping and feedback.
The paper introduces DIPScan, a scalable Nextflow workflow that accurately detects deletion-containing viral genomes (DelVGs) in influenza sequencing data and corrects their interference to ensure the generation of precise consensus genomes for epidemic surveillance.
The paper introduces MultiPopPred, a novel trans-ethnic polygenic risk score method that leverages individual-level data from well-studied populations to significantly improve disease risk prediction accuracy in underrepresented South Asian populations compared to existing state-of-the-art approaches.