bioRxiv: Bioinformatics Preprints · Scour

PAG-Agent: a biologist-oriented research assistant for context-aware pathway-level analysis and interpretation

Single-Cell Multi-Omics Dissection of Malignant Evolutionary Mechanisms and Construction of a Prognostic Model for Clear Cell Renal Cell Carcinoma

Robust Multi-Mutant Protein Stability Prediction from a Fine-Tuned Evolutionary Scale Model

MarkerScout: A Disease-Agnostic Machine Learning Framework for Biomarker Prediction from Multi-Scale Mechanistic Models

Auditable recovery of single-cell RNA-seq zeros with SPARE

Cellpin enables reference-based imputation and denoising of spatial transcriptomes

Development of the Mitochondrial Base Editor Analysis Package (MitoBEAP).

A Reproducible and Extensible Benchmark of Supervised Cell Type Annotation Tools for Cytometry Data

Mycol: A user-friendly app for automating analysis of microscopy images

Towards Generalizable Protein-ligand Co-folding with ACER

inGSEA: An Improved Method for Gene Set Enrichment Analysis Using a Weighted Integral Statistic

A mitochondrial-immune axis drives the transcriptomic transition from brain aging to Alzheimer's disease

DeltaMut: An Integrative Database of AlphaFold2-Derived Missense Variant Structures

Direct Detection and Atomic Modeling of Ligands in Cryo-EM Maps Using Deep Learning

KBase Research Agent: Automated Multi-Agent Workflow Construction for Reproducible Genome Analysis

VLab4Mic: prediction of structural resolvability in super-resolution microscopy

R-loop Prediction Reveals Generalization Limits of DNA Foundation Models Beyond Regulatory Genomics

Spatial Gene Set Enrichment Analysis with Applications to Spatially Resolved Transcriptomic Data

Nanobodies versus canonical antibodies: an updated comparison of their binding modes

An interpretable machine learning framework for dog breed inference and ancestry decomposition

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