Articles

A de novo genome assembly of drought-resistant wheat (Triticum aestivum L.) genotype JIN50 and genomic analyses across other wheat germplasms identify structural variations contributing to drought responses and adaptation.

High-resolution analyses of blood-derived whole-genome sequence data from UK Biobank detect new mosaic chromosomal alterations and identify rare protein-coding variants associated with clonal expansions of copy-neutral loss-of-heterozygosity mutations.

Restricting or permitting H3K27me3 spreading concentrates or dilutes canonical PRC1 (cPRC1), respectively, which affects three-dimensional chromatin interactions. Disruption of cPRC1 compromises repression of Polycomb target genes and induces differentiation and tumor regression in H3K27M-mutant glioma.

This study uses multi-omics approaches to dissect the roles of macrophage populations in the progression of metabolic dysfunction-associated steatohepatitis. GPNMB⁺ macrophages accumulate in the portal tract in advanced disease and may have antigen-presenting capabilities.

Systematic comparisons of different masking approaches for rare variant association tests across 54 traits in UK Biobank highlight strategies for gene-level burden analyses that increase study power and replicability.

Mutations may be enriched in tumor samples because they promote carcinogenesis or because they promote clonal expansions in healthy tissue. This study mathematically disentangles these two possibilities by analyzing tumor and normal tissue sequencing datasets.

A population-scale super-pangenome constructed from 138 reference-grade genome assemblies, representing seven extant Citrullus species, highlights genomic variation associated with fruit-quality traits and accelerates watermelon breeding.

This study identifies distinct transposable element subfamilies as genetic determinants of stemness properties in normal and leukemic stem populations with clinical implications for patients with acute myeloid leukemia.

This study explores the clonal architecture of aplastic anemia across age using single-cell approaches. Somatic inactivation of specific human leukocyte antigen risk alleles is a frequent event and often occurs in multiple independent events.

Genome-wide association and fine-mapping analyses of type 1 diabetes (T1D) identify multiple genetic risk signals. Furthermore, a machine learning model, T1GRS, improves the prediction of T1D in individuals with complex risk profiles and identifies genetic subgroups.

Multi-ancestry genome-wide association analyses coupled with multi-omics integration identify new risk loci for endometriosis and adenomyosis, shed light on underlying molecular mechanisms and suggest potential therapeutic interventions.

INSPIRE addresses challenges to integrating diverse spatial transcriptomics datasets by combining deep learning with non-negative matrix factorization, revealing shared and context-specific spatial gene programs and tissue organization across scales.

Profiling of pleural mesothelioma samples from 91 patients identifies four DNA methylation subtypes that correlate with response to immune checkpoint inhibition and survival

Telomere-to-telomere genome assemblies for two diploid and four tetraploid peanut varieties provide insights into peanut genome organization, evolutionary dynamics and phenotypic differentiation.

SpaMosaic is a mosaic integration method for spatial omics data that enables cross-modality and cross-batch integration using contrastive learning and graph neural networks.

Genome-wide analyses identify genetic loci and plasma proteins associated with polycystic ovary syndrome (PCOS). This study highlights the hormonal and metabolic foundations of the disease and explores the impact of polygenic risk for PCOS in both sexes.

This paper identifies the ‘master regulators’ that maintain cell transcriptional states in diffuse midline gliomas and shows that targeting them in combination could represent a promising therapeutic avenue for the disease.

Multi-ancestry and ancestry-stratified genome-wide analyses identify genetic variants associated with refractive error and enable construction of an enhanced polygenic predictor incorporating functional annotations.

A pangenome of the Rosa subgenus constructed from genomes of 26 Rosa accessions, including 23 newly assembled, highlights widespread structural variations and key genes associated with ornamental traits for rose breeding.

Targeted sequencing of neurodegenerative disease genes and transcriptome-wide sequencing in postmortem brain and spinal cord samples from individuals with amyotrophic lateral sclerosis or frontotemporal dementia identify somatic mutations as likely drivers of disease pathology.