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XPCLRS detects selection signatures by improving the speed and scalability of the XP-CLR method, enabling efficient analysis of large genomic datasets.

This study compares genomic repertoires of endophytic and pathogenic Alternaria atra isolates, finding no clear genomic differences distinguishing their ecological roles.

This study identifies IRF1 as a pioneer factor that remodels chromatin and drives metabolic reprogramming in inflammatory macrophages through enhancer activation and transcriptional control.

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 DNA extraction protocols and bioinformatics workflows for Oxford Nanopore sequencing of bacterial pathogens, finding that extraction method significantly impacts workflow success and genomic resolution.

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 presents a haplotype-resolved genome for Phalaenopsis orchids, revealing genetic factors underlying trait diversity such as lip morphology and color patterns.

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.

The paper develops tools to annotate mRNA features in trypanosomatid parasites using RNA sequencing data and applies them to annotate UTRs across available genomes.

The paper identifies 1296 human genes with dual-coding regions (DCRs) and shows their conservation in mice, tissue-specific expression, and functional implications in gene regulation.