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This study benchmarks DNA foundation models like Evo2, revealing blind spots in variant-effect prediction and highlighting reliance on sequence regularities over biological constraints.

The paper uses unsupervised AI to identify oligonucleotide-usage zones in the human genome that match high-resolution chromosomal banding patterns.

This study shows that NAD+ supplementation restores circadian rhythms and reverses cardiac aging in mice by reprogramming the diurnal transcriptome.

This paper evaluates URINN, a metagenomic workflow for rapid UTI diagnosis, showing high accuracy in pathogen detection and antibiotic resistance prediction.

This paper introduces SCINKD, a tool to identify sex chromosome linkage groups and curate misassembled regions in a single diploid genome.

This study shows that HIRA-mediated H3.3 deposition maintains hepatocyte identity during aging, and its loss leads to metabolic dysfunction and fibrosis, which can be partially reversed by tissue regeneration.

The paper uses single-cell transcriptomics in mice to identify cell type-specific networks and prioritize genes associated with human bone mineral density GWAS findings.

The paper identifies a stage-specific chromatin accessibility state in FSHD myoblasts that resolves during differentiation, showing architectural remodeling uncoupled from DUX4 target loci.

The paper sequences the mouse pseudoautosomal region, revealing its structure and evolutionary dynamics.

This study maps chromatin accessibility and protamine incorporation during spermiogenesis, revealing compartment-specific dynamics and their role in genome stability.

The paper investigates whether genome size, replichore organization, and nucleotide skew predict bacterial growth rates, finding that skew improves predictive accuracy.

This paper demonstrates the feasibility of generating whole genomes from humpback whale blow samples for population genomics.

The paper identifies age-dependent methylation quantitative trait loci (longitudinal mQTLs) across the lifespan using blood DNAm data from two cohorts, finding consistent genotype-by-age effects and associations with multiple phenotypes.

The paper develops a method to resolve collapsed chromosomal segments in polyploid Brachypodium genomes, improving assembly quality and capturing genomic architecture.

The paper identifies splicing deficiency in non-recombining mating-type chromosomes across phytoplankton species, showing how recombination suppression leads to transcript-level dysfunction.

The paper investigates how enzymatic activity thresholds control DNA methylation patterns, finding an ultrasensitive switch mechanism influenced by enzyme interactions.

This paper presents a high-quality chromosome-level genome assembly of the Kolbroek pig, providing a genetic resource for studying genetic variation and improving breeding programs.

The paper presents a high-quality haplotype-resolved genome assembly of Zoysia japonica and identifies gene expression and regulatory variation between haplotypes.

The paper identifies 440 parent-of-origin expressed genes in pigs, revealing weak conservation of genomic imprinting across species and tissues.

This study develops a high-throughput platform using human cerebral organoids to screen for compounds that reverse HSV-1-induced neuroinflammation biomarkers associated with Alzheimer's disease.