Discover, rate, and discuss biology preprints.

The paper optimizes multiple circular sequence alignment for cyclic peptides, achieving faster performance while maintaining alignment quality.

celltypeEnrich annotates scRNA-seq clusters using consensus enrichment from 26 reference datasets, achieving 62-72% accuracy across three tissues and two species.

The paper investigates whether reconstructing level-1 blobs in phylogenetic networks is easy once the tree of blobs is known, presenting a fast algorithm that achieves comparable accuracy to existing methods.

This study identifies technical variability and best practices for interpreting PhIP-Seq data, highlighting batch effects and false negatives in antibody-antigen binding measurements.

Precomputed PPanGGOLiN pangenomes for over 4,600 prokaryotic species (Genome Taxonomy Database clusters), with plasticity regions and modules, downloadable via web, API and command line for projection onto new genomes.

The paper evaluates doublet detection methods for identifying segmentation errors in spatial transcriptomics by simulating molecular admixture between neighboring cells.

Cornet improves mutational signature discovery by modeling correlations, identifying new signatures in cancer genomes.

This study benchmarks biomedical language models for concept normalization from real-world text, finding Qwen 2 Instruct improves accuracy when combined with SapBERT.

Poly Pipeline is a spatial transcriptomics workflow validated across polyploid and diploid organisms, demonstrating effectiveness in clustering and co-expression network analysis.

This study benchmarks confidence estimation and rescoring methods for cyclic peptide-protein complex predictions, finding that pose ranking is the main limitation and that structural features improve confidence-based selection.

POAnoise improves amplicon sequencing denoising by using graph-based alignment and abundance-aware clustering, achieving higher F1-scores and more stable performance than existing methods.

This paper introduces a machine learning framework to classify phylogenetic patterns in interkingdom horizontal gene transfer, achieving high accuracy and outperforming existing methods.

CalFluxTools automates analysis of calcium flux data from high-throughput screens, providing quality control, statistical tests, and machine learning predictions for toxicity assessment.

Vritra constructs gene-specific references for metagenomic and metatranscriptomic data to enable species-resolved functional profiling and uncover gene-taxa associations.

The paper introduces ARCHER-LD, a GPU-accelerated method to compute long-range linkage disequilibrium at biobank scale, achieving significant speedups over existing tools.

ProtPipe2 provides a unified framework for downstream proteomics analysis across mass spectrometry, Olink, and SomaScan platforms, enabling consistent workflows and reusable analyses.

MakeMyFigure enables reproducible scientific figure creation by integrating data analysis, visualization, and figure assembly in a single workflow with automated documentation.

The paper introduces MaSkel and napari-MaSkel, tools for fast skeletonization and graph-based feature extraction from segmentation masks, using an optimized Lee94 thinning algorithm.

The paper identifies metabolomic signatures associated with physical resilience trajectories from middle to older age using long-term serum data.

CUBE integrates spatial protein and transcriptomic data via histology, creating a multimodal representation that captures biological structure from incompletely paired data.