Research articles

Genome-wide analyses identify variants associated with infertility and reproductive hormone levels but find limited polygenic overlap between reproductive hormone levels and infertility at the population level.

This study shows that RWT4, a wheat tandem kinase, confers resistance to the fungal pathogen Magnaporthe oryzae by directly binding to the pathogen effector AvrPWT4 and activating host defense.

Analysis of pre- and post-chemotherapy samples collected from 22 patients with high-risk neuroblastoma using single-nucleus RNA and ATAC sequencing and spatial omics characterizes therapy-related changes in cell composition and the tumor microenvironment.

Recurrent de novo mutations at nucleotide positions 4 and 35 of RNU2-2 cause a neurodevelopmental disorder whose prominent features include intellectual disability, developmental delay and a complex seizure phenotype.

This paper describes a framework for classifying small insertions and deletions from genomic data and applies it to a large dataset comprising seven tumor types. The analysis highlights new insertion and deletion signatures and a classifier of postreplicative repair dysfunction.

This study introduces a ChickenGTEx atlas of regulatory variants across 28 tissues and illustrates its utility in deciphering association signals for 39 complex traits in chickens.

Common-variant and rare-variant association analyses combining datasets from multiple populations yield insights into the genetic architecture of all-cause heart failure across the allele-frequency spectrum.

Cluster hierarchy optimization by iterative random forests (CHOIR) offers a robust and accurate method to identify cell clusters across a variety of single-cell resolution data with statistical support.

A telomere-to-telomere genome assembly of allohexaploid bread wheat cv. Chinese Spring (CS-IAAS), along with transcriptomic and proteomic data, highlights wheat genome complexity and its structural and functional features.

Phosphorylation of KAP1 by DNA-PKcs at enhancers regulated by diverse stimuli prevents association with 7SK small nuclear RNPs and CDK9 SUMOylation, thereby activating the P-TEFb complex and promoting enhancer RNA transcription.

Multiomics and ecological spatial analysis (MESA) calculates ecodiversity-inspired metrics in spatially resolved omics integrated with single-cell data, enabling the quantitative comparison of tissue states across a range of conditions.

Multi-omic analysis of the adult human prostate identifies spatially resolved cell populations with potential links to prostate carcinogenesis.

Whole-genome sequencing and mutational signature analysis of 265 head and neck cancer samples collected from eight different countries provide insight into the vital contribution of tobacco smoke in disease etiology.

Chromosome-level genome assemblies of allotetraploid Nicotiana tabacum and its ancestors, along with their transcriptomes, epigenomes and genotype and phenotype data for 5,196 N. tabacum germplasms, provide insights into genome evolution and complex trait regulation.

Analysis of whole-genome sequencing data from Iceland and the UK Biobank identifies an excess burden of rare loss-of-function variants in HECTD2 and AKAP11 in individuals diagnosed with bipolar disorder.

Transcriptome-wide m⁶A RNA methylation profile in 162 primary prostate tumors identifies m⁶A association with prognostic clinical features and disease aggression.

gLike infers population demographic histories with a variety of complex admixture events by analysis of graphs of states, which conceptualize the relationships of all lineages found in trees encoded in the ancestral recombination graph.

The cobraa model extends the pairwise sequentially Markovian coalescent to identify structured population history by examination of the model transition matrix. Applied to human polymorphism data, cobraa identifies an ancient admixture event ancestral to all modern humans.