Discover, rate, and discuss biology preprints.

The paper introduces a fast k-mer based algorithm to identify new genetic code variations in bacteria and archaea from assembled genomes.

This paper evaluates LLMs for plant biology tasks, identifies their limitations, and proposes GraphRAG as a solution using structured knowledge graphs for reliable, reproducible answers.

RastQC is a Rust-based sequencing QC tool that replaces FastQC, offering faster performance, lower memory use, and support for both short and long reads.

The paper introduces snail plots to assess genome assembly quality in a genome-size independent manner and shows they correlate with qualitative assessments of assembly quality.

The paper reanalyzes data showing codon-dependent differences in backbone conformation in E. coli, using corrected statistical methods and finding consistent small p-values.

The paper benchmarks SNP annotation tools and gene models across the genome, showing discrepancies in annotation and their impact on pathway analysis.

CellLoop identifies single-cell chromatin loops using a density-based framework, improving accuracy in mouse brain and embryogenesis data.

The paper introduces image analysis tools for SEM images, available as Fiji plugins and Python scripts, for quality assessment and compatibility with custom FIB-SEM instruments.

XAttn-DTA predicts drug-target affinity using graph attention networks and cross-attention fusion, achieving improved performance on benchmark datasets.

The paper identifies prognostic hub genes in oral squamous cell carcinoma using transcriptomic data and network analysis.

NovoTax identifies prokaryotic strains from proteomics data without prior knowledge, achieving accurate species and strain identification and detecting contaminants.

StarFunc combines deep learning with template information from multiple sources to improve protein function prediction, outperforming existing methods in benchmark tests.

The paper identifies a circadian critical window in myopia development using machine learning and validates its conservation across species and tissues.

SegBio provides a lightweight, user-friendly pipeline for instance segmentation of crowded biological images, achieving high performance on C. elegans datasets.

This paper introduces GenoJEPA, a genomic representation learning framework that improves efficiency and performance in downstream tasks by focusing on semantic alignment rather than nucleotide-level reconstruction.

EV-Net is a computational tool that adapts NicheNet to analyze EV cargo effects on recipient tissues, enabling prioritization of regulatory molecules from proteomics and RNA-seq data.

sctrial provides participant-level differential analysis for longitudinal single-cell experiments, reducing pseudoreplication-driven signal inflation and improving reliability of biological interpretations.

This paper introduces GP-GHS, a Bayesian method for inferring spatially varying cell-cell interaction networks from multiplexed tissue imaging data, identifying differentially active edges in colorectal cancer.

The paper improves metagenomic classification by using spaced metamers, reduced alphabets, and syncmers, enhancing precision and recall while reducing database size and increasing speed.

The paper develops BayesMonSTR to detect mosaic STR mutations at single-cell resolution and finds increased STR indels in aging cells, particularly in prefrontal cortex neurons.