Discover, rate, and discuss biology preprints.

This paper develops Deep-STARmap and Deep-RIBOmap for 3D spatial transcriptomics and translatomics in thick tissue blocks, enabling analysis of gene expression and immune interactions in human skin cancer.

amr.watch provides an interactive platform to analyze and visualize AMR trends from global WGS data, enabling ongoing situational awareness for research and policy.

This paper improves variant effect prediction by calibrating models at the residue level, enhancing both calibration and discrimination across variant subgroups.

This study identifies pseudogene-associated lncRNA genes across eight species, showing they have enhanced functional attributes and contribute to aging-related transcriptome changes.

This study uses saliva-based RNA sequencing to explore how music affects gene expression and microbiota in individuals with autism spectrum disorder, identifying key genes and microbial shifts linked to neurodevelopmental and immune processes.

This study creates a multi-omic atlas of the choroid plexus in Alzheimer's disease, identifying disease-associated cell state transitions and functional impairments.

The paper functionally measures allele-specific regulatory element activity across five human genomes to fine map causal variants in eQTLs and chromatin QTLs.

The paper imputes transcriptional patterns from ancient genomes to identify molecular targets of selection over 10,000 years of Western Eurasian history.

The paper uses eDNA metabarcoding and generalized additive models to model cetacean distribution along the Washington coast, finding spatial patterns consistent with historical records.

The paper evaluates imputation performance in East and Southeast Asian populations, showing that recent selection affects variant detection and polygenic risk score estimation.

This study integrates GWAS with eQTL and pQTL analyses to identify functionally relevant variants and molecular mechanisms in type 2 diabetes.

The paper analyzes the impact of CpG island architecture on amino acid usage and sequence complexity in human essential proteins, revealing compositional stratification and positional biases.

The paper examines how domestication affects the chromatin landscape in grain amaranth, finding that 2.5% of chromatin regions switch states during domestication, associated with selective sweeps.

FlyCADD predicts the functional impact of single nucleotide variants in Drosophila melanogaster using genomic features to prioritize variants for functional studies.

The paper assesses how supplementation affects functional genetic diversity and selective processes in Tasmanian devils, finding increased functional diversity post-supplementation without evidence of local allele swamping.

The paper generates a complete diploid genome assembly for RPE-1 cells and uses it as a matched reference to improve multi-omics data analysis and identify haplotype-specific epigenetic variation.

EPIC-unmix improves cell-type specific analysis from bulk RNA-seq by integrating single-cell reference profiles, identifying novel genes and eQTLs in Alzheimer's disease.

The paper investigates Y chromosome degeneration in Rumex hastatulus, finding widespread underexpression of Y genes and no evidence of early dosage compensation.

This paper introduces MethylAI, a deep learning framework that predicts DNA methylation states from genomic sequence and identifies sequence determinants of methylation through in silico perturbation.

The paper introduces nf-RASQUAL, a Nextflow pipeline for molQTL mapping in small datasets, applied to Atlantic salmon to identify expression and chromatin accessibility QTLs.