Research articles

Samples from 19 patients with non-small-cell lung cancer treated with a combination of chemotherapy and immune checkpoint blockade are profiled with single-cell RNA sequencing and spatial transcriptomics to identify factors associated with treatment resistance.

This analysis of single-cell RNA sequencing data from peripheral blood mononuclear cells for 474 individuals of diverse Asian ancestries in the Asian Immune Diversity Atlas links cell-type-specific splicing variation with autoimmune and inflammatory disease risk.

Multi-ancestry genome-wide analyses identify new risk loci for age-related macular degeneration. Ancestry-specific analyses identify distinct effects at major risk loci, including smaller effect sizes for CFH risk alleles in haplotypes of African ancestry.

Single-cell Proliferation Rate Inference in Non-homogeneous Tumors through Evolutionary Routes (SPRINTER) allows users to infer proliferation rates of individual clones within a tumor from single-cell DNA sequencing data. Applying SPRINTER to human tumor datasets highlighted a link between proliferation and metastatic potential.

ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offering a refined view of the cis-regulatory code.

An integrated single-cell multiomic analysis of complex karyotype acute myeloid leukemia characterizes intratumoral heterogeneity and highlights links to therapeutic sensitivities.

Spatial and single-nucleus analyses in human postmortem Alzheimer’s disease (AD) brain tissues at early and late stages from individuals with and without Down syndrome, as well as in AD mouse models, show sex and species-specific phenotypic changes.

Genome-wide association analyses comprising 14,256 cases and 1,199,156 controls and incorporating correlated cardiac magnetic resonance imaging traits provide insights into the molecular etiology of dilated cardiomyopathy.

Genome-wide association and multitrait analyses for dilated cardiomyopathy (DCM) using 9,365 cases and 946,368 controls provide insights into the mechanisms underlying DCM and myocardial resilience

Single-cell DNA sequencing identifies recurrent copy number changes in healthy breast tissue from women with wild-type or germline BRCA1 or BRCA2 mutations.

This Pediatric Cell Atlas study analyzes temporal cortex single-nucleus RNA sequencing datasets from eight diverse donors from 4 to 50 years of age, describing gene expression dynamics over the course of brain maturation.

Popular Vote (popV) is a simple, ensemble popular vote approach for cell type annotation in single-cell omic data, flexibly incorporating various methods in an open-source Python framework. Across various challenging input datasets, popV offers consistent, accurate performance.

A framework combining combinatorial CRISPR knockout in breast, lung and oropharyngeal cancer in vitro models with public data identifies synthetic lethal interactions, such as perturbed KDM5C sensitizing cells to PARP7 inhibition.

This study identifies Basal-B cells as a transient cell state during prostate homeostasis and androgen-mediated regeneration. These cells exist in humans and increase in number with prostatitis and inflammation.

Genome-wide association study of cerebrospinal fluid and brain metabolites highlights the unique genetic architecture of metabolite levels and metabolite–trait associations with brain-related phenotypes.

A second hit to Brca1 in heterozygous mice leads to accelerated tumor development compared to wild-type mice in which both alleles are simultaneously deleted. This is because of an epigenetic state associated with Brca1 haploinsufficiency that impacts AP-1 and Wnt10a.

Proteogenomic analysis of human cerebrospinal fluid by measuring 6,361 proteins in 3,506 individuals identifies new protein QTLs and highlights genetic regulation involved in neurological processes.

Multiomics joint analyses based on a structural variant (SV) map from 16 genome assemblies and 2,105 resequenced accession genomes shed light on the regulatory effect of SVs on gene expression and trait variation in Brassica napus.

By constructing a graph-based grapevine pangenome reference (Grapepan v.1.0) and incorporating structural variations and phenotypic maps, the study investigates the genetic basis of agronomic traits, empowering grapevine genomic breeding.

A calcium-dependent protein kinase ZmCPK39 regulates quantitative resistance to multiple foliar diseases in maize through the ZmCPK39–ZmDi19–ZmPR10 immune module.