Discover, rate, and discuss biology preprints.

This study shows that regional history, not phylogeny or range size, primarily shapes demographic changes in Indo-West Pacific sea snakes over the last 200 thousand years.

The paper replicates the association between St6galnac1 and Paraprevotella abundance in stool samples from non-fasted HS rats, confirming the association across different experimental conditions.

This study compares gut microbiome features between individuals with AUD and healthy controls and examines minocycline's effects on the microbiome, finding distinct microbial composition in AUD and microbiome restructuring with minocycline.

The paper identifies over 200 new mobile transposable element families in Arabidopsis thaliana using pangenomic analysis, showing they contribute to large-effect alleles despite being rare in most strains.

The paper mitigates genotype-driven bias in single-cell DNA methylation analysis by masking variant positions, improving clustering and reducing spurious methylation differences in pooled datasets.

The paper develops a computational framework to contextualize novel isoforms identified through long-read single-cell RNA sequencing by integrating pathway analysis with expression-based neighborhoods.

This study examines how pulmonary tuberculosis affects the respiratory and gut microbiomes in Ugandan adults, finding site-specific taxonomic differences but mixed results on community composition.

This study identifies RER deficiency as a new DNA repair defect in cancer, detectable through mutational signatures and linked to therapeutic vulnerabilities.

The paper uses single-cell transcriptomics and phenotypic analysis of gene knockouts in hiPSC-derived neurons and astrocytes to identify cell-type specific and shared mechanisms of Alzheimer's disease risk genes.

Footprint-seq quantitatively maps protein-DNA interactions in vitro with high resolution and sensitivity, demonstrating its effectiveness for bacterial systems.

The paper investigates Polycomb-mediated 3D chromatin interactions and finds that cPRC1 is not essential for their formation.

This paper introduces TeloXplorer, a framework for analyzing telomere features in long-read data, showing how telomere diversity is inherited across species and populations.

The paper presents a Trisomy 21 Model Atlas comparing mouse and human models to show conserved dosage effects and context-specific transcriptional responses across tissues and developmental stages.

This paper introduces Borzoi-SE, a deep learning framework that identifies super-enhancers and detects pathogenic variants directly from DNA sequence across multiple human cell lineages.

This study uses whole-genome resequencing to analyze genetic diversity and structure in Swiss grayling populations, revealing population declines, admixture, and limited genetic contribution from hatchery releases.

cit_gsa is a single-cell RNA-seq gene set analysis method that allows covariate adjustment and handles multiple conditions, showing improved performance in complex scenarios.

The paper benchmarks structural variant analysis tools on short-read WGS data, finding that ensemble pipelines significantly reduce accuracy compared to individual tools.

The paper evaluates how response representation affects enhancer-gene prediction in human astrocytes using CRISPR-interference data and finds that whole-enhancer deletion responses improve prediction performance.

This paper presents a telomere-to-telomere genome of Holstein cattle, identifies genetic loci associated with telomere length, and highlights key biological processes involved.