Discover, rate, and discuss biology preprints.

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

The paper introduces BioSIFTR, a tool that uses shallow shotgun sequencing and biome-specific databases to generate accurate taxonomic and functional profiles, validated against deep sequencing data.

An AI-assisted C++17 port of VarDictJava gives byte-identical calls on five exome samples while running 3.7-4.8 times faster on one core and needing 8-17 times less memory.

TorchRef provides a PyTorch framework for crystallographic refinement, offering GPU acceleration and modular design for developing new refinement protocols.

This paper introduces a formal framework for deriving synteny blocks directly from sequence data to better capture genomic rearrangements without obscuring structural variation.

MetaDome now supports GRCh38 alongside GRCh37, adds coordinate lookup, and identifies 52,463 GRCh38 ClinVar missense variants of uncertain significance with uncontradicted pathogenic evidence at homologous Pfam-domain positions.

PDBe-SIFTS improves residue-level sequence-structure mapping with faster search, better scoring, and accurate alignment, comparable to expert curation.

AlphaFold3 pLDDT matches AlphaFold2 at calling disordered residues (Matthews correlation 0.693 vs 0.701); on disorder-containing complexes mean DockQ is similar, but interface features explain less variance (42% vs 58%).

This paper evaluates combining expression-based surrogate variables and genotype-based principal components in differential expression analysis, finding the combined approach improves replicability and biological recall in ALS datasets.

TurbOmics is a web-based platform that enables multi-omics integration of metabolomics, proteomics, and transcriptomics data, addressing limitations in metabolomics annotation and accessibility.

The paper introduces onsite, a framework for estimating false localization rates in phosphoproteomics, showing pyLucXor achieves high accuracy and localization count.

The paper introduces scProfiterole, a framework for clustering single-cell proteomic data using graph contrastive learning with spectral filters, showing improved cell type identification.

The paper predicts antibiotic resistance mutations in Mycobacterium tuberculosis by integrating structural context with mutation data, finding that structural clustering improves prediction accuracy.

This study benchmarks reference-based metagenomic tools for species-level detection in closely related bacterial families, finding metapresence and sylph perform best.

This paper revisits the concept of density in k-mer-based sequence analysis, introduces multiminimizers as a novel technique, and proposes deduplicated density as a new metric.

The paper validates and analyzes 12,000 AI-designed CAR-T binders from a global competition, identifying successful designs and factors improving their performance.

This paper introduces a Pareto optimization method for masked superstrings to improve the compression of pan-genome k-mer sets, achieving 12-19% better compressibility.

tangermeme provides tools to interpret deep learning models for cis-regulatory analysis, extracting human-readable insights from genomic predictions.

This study identifies and mitigates protocol-dependent gene expression bias between 3' and 5' scRNA-seq by focusing on a small set of biased genes rather than applying broad normalization.