Discover, rate, and discuss biology preprints.

This paper introduces a variational inference method for Bayesian phylogenetic reconstruction, showing faster speeds than traditional Bayesian methods on real-world datasets.

This paper introduces a method to prioritize non-coding variants in rice GWAS loci using a chromatin-informed DNA language model, demonstrating its utility through case studies.

This study predicts HPAI H5N1 poultry outbreak risk in Australia using environmental and bird abundance data to create a risk map at the LGA level.

This paper introduces the Ordered Gromov-Hausdorff (OGH) metric to compare protein structures by incorporating residue order, showing it outperforms TM-score in detecting homologous proteins.

scINTILLA assesses cell-type annotation quality in single-cell datasets by combining supervised and unsupervised learning to identify label ambiguity and hidden heterogeneity.

This study reanalyzes RNA-seq data to show sex-specific effects of 17beta-estradiol on gene expression in human meniscal fibrochondrocytes, identifying distinct transcriptional programs in males and females.

ImpuT2T patches gaps in HiFi assemblies using pangenomes, improving quality over existing methods.

The paper uses Hodge decomposition to analyze information flow in KRAS proteins, showing that mutations reposition information sources while maintaining a hierarchical flow structure.

RIPPLE detects cell-type-anchored proximity gradients in spatial transcriptomics data by analyzing gene expression variation with distance to a query cell type.

Spaceland reconstructs high-resolution 3D molecular atlases from sparse spatial transcriptomics and histology, improving resolution and accuracy across multiple biological contexts.

This study compares methods for estimating biological age using HRV data, finding that the Klemera-Dubal Method has the lowest error compared to uncorrected MLR and Dubina-corrected MLR.

GPSNorm fits slide, spatial technical and biological effects in one Bayesian negative binomial model, carrying normalization uncertainty into differential expression and lowering log-fold change error in simulations.

B-SMART-Former predicts drug-drug interactions between biotech and small-molecule drugs using an explainable transformer-based model, achieving high AUROC and AUPR scores.

PGD improves visualization of single-cell trajectories by smoothing cell-level features along pseudotime, enhancing continuity and structure in complex biological processes.

Utanos provides a modular workflow for analyzing shallow whole-genome sequencing data to detect copy number aberrations and signatures.

The paper evaluates single-cell perturbation prediction models by developing a taxonomy and tool to standardize benchmarking protocols across datasets.

This study identifies 371 isoform switches in Hürthle cell carcinoma, revealing functional consequences like loss of protein domains and altered sub-cellular localization, with specific isoforms unique to tumors.

SyntenyPair Explorer provides an interactive, browser-based tool for visualizing synteny between two genomes without requiring installation or server infrastructure.

This study harmonizes cross-platform gene expression data using three techniques, evaluates ML/DL classifiers, and applies XAI methods to identify interpretable biomarkers for cardiovascular diseases.

This paper introduces a decomposition framework for perturbation response prediction, showing that aligning models with biological priors improves generalization across unseen perturbations and cell lines.