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Measuring American black bear genetic load in fixed structural variants and runs of homozygosity

The paper assesses genetic load and structural variation in American black bear populations, finding elevated levels in an isolated population.

Isoform diversity as a complementary dimension of gene expression

The paper shows isoform diversity is a distinct dimension of gene expression, complementary to gene-level abundance, and changes with age and tissue-specific processes.

Long-read DNA sequencing reveals global hypomethylation and focal hypermethylation in SDHx-deficient pheochromocytoma and paraganglioma

The paper uses long-read sequencing to analyze DNA methylation patterns in SDHx-deficient PPGLs and finds global hypomethylation with focal hypermethylation at specific CpG islands.

Disparities in avian genomic resources highlight gaps across the Global South

The paper evaluates avian genome assemblies across geography and taxonomy, revealing underrepresentation of species in the Global South.

A single-cell transcriptomic atlas of paper wasp brains highlights Kenyon cells' role in social behavior

The paper uses single-cell transcriptomics to analyze brain cells in paper wasps, showing that Kenyon cells vary with social roles and respond to social interactions.

High piRNA abundance is a hallmark of evolutionarily persistent piRNA-producing loci.

The paper identifies high piRNA abundance as a key feature of evolutionarily persistent piRNA-producing loci across mouse and primate species.

Plumage diversity without differential expression of pigmentation genes in a rapid avian radiation

The paper investigates plumage diversity in Capuchino Seedeaters by analyzing gene expression and variants, finding that pigmentation differences arise from regulatory changes rather than differential gene expression.

How mutation rate evolves: Gene expression shapes genome-wide mutation rates in Drosophila melanogaster and Caenorhabditis elegans

The paper investigates how gene expression influences genome-wide mutation rates in Drosophila melanogaster and Caenorhabditis elegans, finding that highly expressed genes have lower mutation rates due to transcription-coupled repair.

Structural Variant Aware Identity-by-Descent Detection on Pangenome Graphs

GIBD detects IBD segments in pangenome graphs and annotates them with structural variants, outperforming existing methods in accuracy and speed.

Somatic structural variation discovery on cancer pangenome graphs

JANUS discovers somatic structural variants in cancer genomes using a pangenome graph approach, achieving high accuracy and efficiency compared to traditional methods.

Transcriptome reallocation during infection reshapes synonymous codon demand in Botrytis cinerea

The paper shows that during infection, Botrytis cinerea reallocates its transcriptome, altering synonymous codon demand across different host systems.

Contrasting Range and Demographic Histories in two Palearctic Dragonfly Species (Odonata: Anisoptera)

This study examines the relationship between climatic suitability and effective population size in two dragonfly species, finding they are not directly correlated.

Genome-wide Analysis of the VQ Gene Family and Expression Profiling in Sorghum bicolor

This study identifies and characterizes VQ genes in sorghum, showing their differential expression and potential roles in salt stress tolerance.

Sexing carnivores from faecal metagenomes: calibrating Rx for stone marten and red fox

The paper evaluates the use of the X-to-autosome ratio (Rx) for sexing carnivores from faecal metagenomes, finding it effective above a certain read depth.

Measuring satellite arrays of the human Y chromosome from sequencing reads

The paper introduces Yruler, a tool to measure Y chromosome satellite arrays from sequencing reads without alignment, revealing lineage-specific variations in satellite length and composition.

Mapping the regulatory wiring of endothelial cell differentiation reveals a critical role for Hippo mechanosignaling

The paper maps gene regulators of endothelial cell differentiation using CRISPR and single-cell RNA-seq, identifying Hippo mechanosignaling as critical for endothelial identity.

Highly prevalent cargo genes of F plasmids harbored in pathogenic Escherichia coli

The paper identifies two groups of previously uncharacterized cargo genes in F plasmids of pathogenic E. coli, potentially contributing to virulence and antimicrobial targets.

Genome-wide chromatin accessibility during early embryogenesis in a generalist cichlid fish

This study maps genome-wide chromatin accessibility in A. calliptera embryos across three stages, revealing dynamic changes in regulatory elements and transcription factor activity during early development.

WheatPanRef: a unified linear pan-reference genome for wheat genomics

WheatPanRef provides a unified linear pan-reference genome for wheat, improving read alignment and enabling integration of genomic resources across diverse accessions.

NanoPAMDA enables rapid PAM characterization of metagenome-derived Cas9 effectors

The paper identifies novel Cas9 orthologs from metagenomic data and develops NanoPAMDA to rapidly characterize their PAM preferences.