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MetaGLIMPSE improves low coverage sequencing imputation by combining multiple reference panels, outperforming single-panel methods for modern and ancient DNA samples across various coverage and allele frequency ranges.

The paper uses single-cell epigenomics to study brain aging in mice, finding heterochromatin instability and transcription factor dysfunction across multiple brain regions and cell types.

The paper characterizes hepatoblastoma with carcinoma features (HBCs) using multi-omics data, revealing their heterogeneous composition, worse outcomes, and origin from arrested HB cells due to WNT signaling.

This paper improves gene-regulatory network inference by using epigenomic priors, showing better accuracy with DNA methylation data compared to chromatin accessibility data.

The paper identifies lineage-specific metabolic capacities in extraintestinal pathogenic Escherichia coli clones that may contribute to their ecological success and dissemination.

Dogme is a Nextflow pipeline that automates reprocessing of ONT data for modification detection and transcript quantification, showing reproducible results across biological replicates.

This study uses population genomics to reveal fine-scale three-dimensional structure in two sympatric Sebastes species in the Northwest Atlantic, highlighting management implications.

The paper identifies trans-splicing acceptor sites in TriTryps and shows similar chromatin organization across genes, with histone-containing complexes protecting these sites.

This study constructs a single-cell chromatin accessibility atlas across mouse tissues to reveal age-related cellular and epigenomic changes, showing widespread population shifts and sex-dependent dynamics.

This study compares the EF-1α intergenic region across Babesia divergens isolates, identifying TA repeat variation and its potential regulatory impact on gene expression.

This paper introduces SBayesAPP, a Bayesian model that estimates annotation-stratified pleiotropy and co-polygenicity between complex traits using GWAS summary statistics, revealing cell-type-specific genetic correlations.

This study evaluates six methods for calling single-nucleotide variants from scRNA-seq data and finds that some methods provide phylogenetically informative genotype calls, with implications for understanding cancer progression.

The paper identifies stage-specific regulatory variants in pig skeletal muscle by analyzing chromatin accessibility, molecular QTLs, and GWAS data across prenatal and postnatal stages.

This paper describes a protocol for CRISPRi-mediated silencing of retrotransposons in hiPSCs, validated using a multiome approach combining RNA-seq, CUT&RUN, and proteomics.

This paper presents haplotype-resolved T2T gap-free genomes of Cabernet Sauvignon, revealing inversion events not seen in other V. vinifera genomes.

This study analyzes genetic diversity and admixture in Benin's cattle breeds, finding significant differentiation between taurine and zebu breeds and gene flow from zebu to taurine due to adaptive factors.

This paper presents a near telomere-to-telomere, haplotype-resolved genome of Spinifex sericeus, revealing structural variation and repetitive content that may drive genome evolution.

This study identifies retrotransposon proliferation as a driver of genome size expansion in Pseudocercospora species, with species-specific TE families and ongoing activity in some strains.

This study uses DNA methylation profiling in maternal blood to identify immune cell shifts in preeclampsia and the pregnancy-postpartum transition, finding reduced monocyte proportions in PE.

This study shows that Xi expression levels predict female-male gene expression differences and correlates with traits like BMI and hormone levels in females.