Discover, rate, and discuss biology preprints.

This paper introduces an algorithmic framework for comparing and sorting RLZ compressed sequences, achieving speedups over character-based sorting.

STPAINTER enhances spatial transcriptomics data using a pre-trained scRNA-seq atlas, enabling high-fidelity downstream analysis across cancer types.

This study identifies potential vaccine antigens in Staphylococcus aureus using computational methods, prioritizing 304 candidates based on sequence, structure, localization, and immunology features.

The paper introduces BioChirp, a system for reliable retrieval of structured biomedical data, outperforming existing agentic NL2SQL systems in accuracy and consistency.

Multiplying the AlphaFold 3 or Boltz-2 pair representation by a single scalar (1+β) at the Pairformer input, without retraining, broadens sampled ensembles toward alternative states across 86 two-state targets.

pysigscore scores gene signatures in bulk and single-cell RNA-seq data, validating its performance on multiple datasets.

The paper proposes a two-phase framework combining distribution-learning and optimization to generate bioactive peptides, achieving high confidence scores and reduced KL divergence in IL-2 and IL-13 induction tasks.

pyfraglib provides a platform for cfDNA fragmentomics analysis, including fragment extraction, feature modeling, cohort comparison, and simulation, and identifies a high-risk subgroup in CNSL patients.

The paper identifies novel biosynthetic gene clusters in marine sponge microbiomes associated with brominated alkaloids.

MBTA uses flow matching to address structural mismatch between molecular modalities, improving cross-modal translation and enabling multimodal analysis in single-cell data.

The paper compares Epi2Me and EMU workflows for full-length 16S rRNA Nanopore sequencing using mock communities, finding EMU provides more accurate species-level taxonomic assignments.

The paper develops a pseudo-longitudinal framework to estimate a buccal PACE-like aging-rate score from cross-sectional DNA methylation data, showing moderate reproducibility but limited correlation with blood-derived DunedinPACE.

This paper benchmarks 14 pathway reconstruction algorithms across 822 datasets using a standardized framework to evaluate performance, similarity, and computational efficiency.

The paper introduces MAPPIE, a method to map human protein-protein interactions into a 2D space for functional discovery, outperforming baselines in sparse interaction regions.

This paper introduces a deep generative decoder model for dimensionality reduction with millions of features and few samples, showing it outperforms PCA and VAE in tumor classification.

This paper introduces a scalable topological data analysis framework for predicting protein-protein interaction interfaces, achieving comparable performance to a geometric deep learning method with reduced computational cost.

This study evaluates computational models for predicting pharmacogenomic variant effects, finding that StructureDCA outperforms other methods in distinguishing functional variants.

pbcftools parallelizes bcftools commands for variant call sets, improving speed without sacrificing accuracy across multiple platforms and core counts.

GRIMM-II improves HLA donor matching by imputing nine loci and identifying donors with up to three mismatches in real-time.

The paper evaluates existing batch integration metrics in scRNA-seq and introduces sBEE, a new metric that provides more reliable assessments of batch mixing across diverse scenarios.