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The paper traces the origin of non-brittle rachis alleles in wheat using k-mer-based analysis of a diversity panel and a chromosome-scale wheat assembly, showing distinct origins for different Ttbtr1 alleles.

This paper characterizes the complete chloroplast genome of Adansonia digitata, compares it with other Adansonia species, and places it phylogenetically within Malvaceae.

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 barrier loci in Zosterops species by analyzing genomic differentiation across divergence stages, showing Z chromosome involvement and roles of natural and sexual selection in reproductive isolation.

This study uses single-nucleus multi-omic analysis to show cannabis use in HIV patients alters gene expression and chromatin accessibility in immune cell types, with cell-type-specific effects on inflammation and transcription factor regulation.

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

This study shows that FACT depletion in stem cells causes a sequence of chromatin disruptions leading to transcriptional collapse.

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

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.