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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.

This study identifies DNA methylation changes over time during antidepressant treatment in MDD, linking them to neuroplasticity and inflammation, and shows differences between responders and non-responders.

The paper presents a high-quality genome assembly and functional annotation of Hiroshima-derived Pacific oyster Magallana gigas, providing a genomic resource for studying genetic diversity and environmental adaptations.

This paper reviews epigenetic twin studies linking birth weight discordance to gene expression and DNA methylation, highlighting growth-related genes and epigenetic mechanisms.

This paper evaluates the reproducibility and accuracy of nanopore-only versus hybrid-assembly methylation calling in bacterial genomes, showing high concordance and precision.

The paper identifies and quantifies barcode crosstalk in Oxford Nanopore sequencing and introduces post-ligation pooling to prevent it.

The paper curates a dataset of 332 high-coverage great ape genomes to address evolutionary and diversity questions.