Discover, rate, and discuss biology preprints.

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.

This paper introduces iMSMs to model biomolecular interactions, revealing kinetic states and transport pathways in nucleocytoplasmic transport.

Z-Hunt-DP improves Z-DNA prediction by using dynamic programming to reduce computational complexity and achieve faster, more accurate results.

SMORE performs joint dimensionality reduction and cell population discovery on single-cell methylome data, accurately recovering population structures in human datasets.

ASTRAL-X enables statistically consistent species tree inference for up to 300,000 taxa by improving scalability and reducing computational requirements.

BELL automates evidence retrieval and scoring for biological interactions, achieving high confidence in 49.5% of tested interactions and guiding curators effectively.

The paper develops and evaluates a cgMLST scheme for the Enterobacter cloacae complex using whole genome sequencing data to improve surveillance of ECC species.

This study predicts pH-sensing histidine residues in the human proteome using amino acid conservation, structural context, and benchmarking with known pH-sensors.

The paper benchmarks variant effect predictors using MAVE data, identifies reliability ceilings, and shows that correction improves performance in some regions but not others.

MIMoSA compares transcription factor binding motifs independently of their representation, showing comparable performance to PWM-based tools on benchmark datasets.