Quickdraws is a mixed-model association tool with a noninfinitesimal prior for analyzing binary and quantitative traits, using a scalable variational inference that allows analysis of biobank-scale cohorts.

Programmable Enrichment via RNA FlowFISH by sequencing (PERFF-seq) isolates rare cells based on RNA marker transcripts for single-cell RNA sequencing profiling of complex tissues, with applicability to a broad variety of samples and cell types.

Borzoi adapts the Enformer sequence-to-expression model to directly predict RNA-seq coverage, enabling the in-silico analysis of variant effects across multiple layers of gene regulation.

This genomic analysis of tandem kinase proteins across 104 plant species highlights their mechanisms of convergent molecular evolution and potential roles in plant immunity.

A gap-free telomere-to-telomere genome assembly for a ram of Hu sheep uncovers genes and variants associated with domestication and selection for wool fineness.

Analysis of 170 human genomes assembled using long-read sequencing provides a map of structural variation within regions of segmental duplication and identifies novel candidate protein-coding genes supported by full-length Iso-Seq reads.

A large-scale CRISPR-mediated deep mutational scanning approach is used to interrogate the function of mutations in the endogenous locus of TP53 mapping to the DNA-binding domain.

Genome-wide analysis and genetic manipulation at loci regulated by p53, E2F4 and RFX7 show that convergent promoters with similar epigenetic features can be co-regulated and simultaneously expressed in the same direction.

A genomic and transcriptomic analysis of nonmuscle-invasive bladder cancer identifies four molecular subtypes, and associates whole-genome duplication and immune exhaustion with tumor progression.

Analysis of medulloblastomas in humans and mice shows that the functional consequences of ZIC1 mutations are exquisitely dependent on the cells of origin that give rise to different subgroups of medulloblastoma.

A haplotype-resolved genome of hybrid sugarcane cultivar XTT22 and population analyses of Saccharum accessions highlight the genome evolution of allopolyploids and provide opportunities for sugarcane breeding.

Multi-ancestry fine-mapping of breast cancer susceptibility regions identifies candidate causal variants and prioritizes likely effector genes supported by functional genomic evidence.

Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free differential expression analysis.

Analysis of the blood DNA virome in patients with COVID-19 and autoimmune disease associates endogenous HHV-6 (eHHV-6) and high anellovirus load with increased disease risk, most notably for systemic lupus erythematosus. eHHV-6 carriers show a distinct immune response.

Generalized binary covariance decomposition (GBCD) applies empirical Bayes matrix factorization to identify shared and sample-specific gene expression signatures in single-cell RNA sequencing data, and can more accurately capture inter- and intrasample heterogeneity than existing methods.

A deleterious mutation in the tomato transcription factor SSP2 was enriched during domestication. Repairing the deleterious mutation in cultivated tomato by base editing leads to compact growth and early fruit yield.

Gene-based rare variant aggregation study with the levels of 1,294 plasma and 1,396 urine metabolites from paired specimens of 4,737 participants reveals graded effects of rare, putatively damaging variants on gene function and human traits.

Tissue–gene fine-mapping (TGFM) generalizes the SuSiE method to fine-map causal tissues and genes at disease loci using external eQTL data, offering improved calibration owing to modeling of cis-predicted expression uncertainty.

This study introduces AdipoExpress, an eQTL meta-analysis of 2,344 subcutaneous adipose tissue samples, which triples the size of previous studies and expands the discovery of eQTLs colocalized with GWAS signals for cardiometabolic traits.

Genome-wide analyses identify variants associated with sinus node dysfunction, distal conduction disease and pacemaker implantation, implicating ion channel function, cardiac developmental programs and sarcomeric structure in bradyarrhythmia susceptibility.