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BEAN is a Bayesian approach for analyzing base editing screens with improved effect size quantification and variant classification. Applied to low-density lipoprotein (LDL)-associated common variants and saturation base editing of LDLR, BEAN identifies new LDL uptake genes and offers insights into variant structure–pathogenicity mechanisms.
A comprehensive variation map constructed by deep sequencing 1,904 accessions of weedy and cultivated broomcorn millet sheds light on the genetic architecture of agronomic traits during domestication.
A new acorn barnacles genome assembly, together with transcriptomic and proteomic datasets and functional experiments, identify bcs-6 and bsf, as new genes involved in the settlement process by facilitating energy metabolism and stabilizing the alternating layers of chitin and calcites, respectively.
High-quality genome assemblies of grain and vegetable cowpeas and re-sequencing of 344 accessions characterize genomic variations between cowpea subspecies and their domestication and improvement under selection.
DNA methylation data of whole blood from Han Chinese individuals are used to map mQTLs, finding that cis- and trans-mQTLs show distinct patterns of East Asians (EA) ancestry-specific colocalization with complex trait variation.
Multi-ancestry genome-wide analyses identify 95 loci associated with post-traumatic stress disorder and implicate candidate genes, pathways and neurobiological systems underlying its pathophysiology.
Analysis of genetic modifiers of 599 developmental disorder genes in the UK Biobank found that rare variant burden within this set, as well as the common polygenic background, can alter the expressivity of cognitive and socioeconomic traits in an additive manner.
A multi-ancestry genome-wide association study of liver cirrhosis and its associated endophenotypes identifies and validates 14 risk variants. Integrative common and rare variant analyses provide insights into the genetic architecture of liver cirrhosis.
A single-cell-based approach allows the daughters of a damaged cell to be separately tracked following single mitotic events. This technique highlights the different ways in which ultraviolet light and reactive oxygen species cause mutagenesis.
A comprehensive time series characterization of a mouse model of cholestatic liver injury with spatial enhanced resolution omics sequencing and single-cell RNA sequencing identifies zonal responses to insult, such as cholangiocyte signaling recruiting lipid-associated macrophages.
A Stereo-seq and scRNA-seq atlas of mouse liver in homeostasis and regeneration after partial hepatectomy identifies zonated genes, pathways, cell–cell interactions and gene regulatory networks. Functional validation finds that cooperation between TBL1XR1 and β-catenin activates hepatocyte proliferation.
Chromosome-level genome assemblies of allotetraploid Coffea arabica and representatives of its diploid progenitors, Coffeaeugenioides and Coffeacanephora, provide insights into Arabica’s diversification history.
A pan-genome of Arabidopsis thaliana constructed using chromosome-level genome assemblies of 69 diverse accessions reveals a conserved genome structure throughout the global species range.
SCENT is a nonparametric method that models association between chromatin accessibility and gene expression in single-cell multimodal datasets, enabling construction of cell-type-specific enhancer–gene maps to aid mapping of candidate causal variants and genes for common diseases.
Analyses of whole-exome sequencing data identify rare loss-of-function variants in BSN associated with adult-onset obesity, type 2 diabetes and fatty liver disease, with stronger effect sizes than those observed for variants in known obesity risk genes such as MC4R.
This study of Chinese endometrioid endometrial carcinomas describes the proteogenomic differences between early-onset and late-onset tumors, finding that SIGLEC10 mutation may contribute to tumorigenesis and progestin resistance in early cases.
Whole-genome sequencing in a Canadian cohort of 327 children with cerebral palsy compared to pediatric controls identifies novel pathogenic single-nucleotide variants/indels and copy number variations. In addition, mitochondrial variants in known disease genes were identified. This highlights the importance of genomic testing for individuals with cerebral palsy.
Incorporating protein-altering copy number variants ascertained from UK Biobank whole-exome sequencing data into analyses of rare predicted loss-of-function variants identifies complex trait associations not detectable using standard analysis methods.
Single-cell transcriptomics and expression quantitative trait locus mapping in 114 lung tissue samples, including 66 with interstitial lung disease, highlight the cell-type-specific functions of risk variants contributing to disease pathobiology.
Single-cell RNA sequencing analysis of over 800,000 human adult breast cells from 55 female donors identifies 41 cell subtypes and highlights age- and parity-dependent effects. Samples from healthy women with germline mutations in BRCA1 or BRCA2 showed signs of T cell exhaustion.