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.
DuplexFM is a biologically grounded framework that leverages transferable miRNA-derived representations and experimentally grounded accessibility features to significantly improve the prediction of siRNA efficacy, offering a parameter-efficient approach to unified modeling of Argonaute-mediated RNA regulation.
STR-PG introduces a topology-decoupled pangenome framework that separates stable locus representation from dynamic allele content via an external registry, enabling scalable and accurate short-read genotyping of short tandem repeats without requiring graph reconstruction when new alleles are added.
SeqDesk is an open-source, FAIR-compliant data management system designed for sequencing facilities to streamline the collection of standardized metadata, automate bioinformatics analysis, and facilitate direct submission to the European Nucleotide Archive by embedding these processes into routine operational workflows rather than treating them as retrospective tasks.
STUltra is a scalable hypergraph-based framework that integrates large-scale spatial transcriptomics data to detect spatial domains and map disease-associated genetic traits across diverse tissue contexts, overcoming batch effects and enabling the discovery of molecular architectures underlying complex diseases like congenital heart disease and Alzheimer's.
This paper introduces STORM, a principled statistical framework that unifies spatial hypothesis testing, effect size estimation, power analysis, and experimental design to rigorously analyze spatial patterns in multi-omics data.
nf-cavalier is an open-source Nextflow pipeline that automates the annotation, filtering, and visual reporting of genomic variants to facilitate the identification of causal mutations in rare Mendelian diseases.
The paper introduces pysigscore, a versatile Python framework that integrates 18 gene set scoring methods with customizable options and reliability analyses to robustly quantify signature activity in both bulk and single-cell transcriptomics data.
This registered report introduces the Signaling Pathway Reconstruction Analysis Streamliner (SPRAS) framework to enable a large-scale, systematic benchmark of 14 pathway reconstruction algorithms across 822 datasets, aiming to resolve current heterogeneity challenges and guide optimal algorithm selection for specific biological contexts.
This paper presents a deep generative decoder (DGD) capable of performing dimensionality reduction on datasets with millions of features and few samples, demonstrating that training requirements are largely independent of feature dimensionality and showing superior performance in tumor classification compared to PCA and VAE.
Scop3P-Toolkit is an open-source, executable analytical environment that integrates diverse biological annotations with structural data to provide reproducible, interactive workflows for analyzing post-translational modifications, genetic variants, and proteomics-derived peptides within their three-dimensional context.