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This paper develops beCasKAS, a method to directly detect off-target base editor activity in primary cells, revealing distinct off-target profiles and enabling risk stratification of edits.

This study assembles human Robertsonian chromosomes, identifies a common breakpoint and centromere epigenetic changes, and explores structural features enabling their formation.

The paper investigates how fluctuations in OCT4, SOX2, and NANOG concentrations affect their genomic binding in mouse embryonic stem cells, revealing distinct concentration-dependent behaviors.

This study uses high-depth whole genome sequencing of single colon crypts to show they are often polyclonal, revealing cell-to-cell heterogeneity previously unattainable with lower sensitivity methods.

Spacelink integrates spatial transcriptomics with genetics to identify spatially variable genes linked to disease, showing improved detection power and disease informativeness.

The paper presents a single cell multiomic atlas of human lung development, identifying regulatory elements and gene programs, and linking genetic variants to pulmonary function.

The paper constructs a reference genome for Starmerella batistae and annotates 29 Starmerella species, revealing a close evolutionary relationship with Schizosaccharomyces pombe and suggesting alternative sophorolipid production pathways.

The paper presents a high-resolution atlas of transcriptional regulatory elements in human tissues and disease states using PRO-cap and deep learning models to prioritize noncoding variants.

The paper analyzes naturally occurring somatic insertions in the human genome using whole-genome sequencing, finding replication slippage as a dominant mechanism for these events.

The paper introduces GPS Pipeline, a scalable and portable genomic analysis tool for Streptococcus pneumoniae, enabling public health outputs with minimal expertise.

The paper presents HIV Atlas, a reference-quality annotation of HIV-1 and SIV transcriptional diversity, and demonstrates its utility in improving transcriptome analysis.

The paper develops and validates a 30K SNP genotyping tool for flax breeding, showing high polymorphism and genotyping accuracy.

This study examines the impact of Spiroplasma infection on testes gene expression in G. f. fuscipes, finding significant downregulation of genes related to sperm motility and energy metabolism.

This study shows ecDNA forms nuclear condensates and reorganizes chromatin to enhance oncogenic transcription across cancer types.

This study applies direct nanopore sequencing to sputum samples to accelerate MTB transmission surveillance, achieving epidemiologically useful results in half the samples analyzed.

The paper identifies cell-type-specific enhancer-gene interactions in cardiac cells and maps disease-associated SNPs to enhancers in endothelial cells.

SPACE improves spatial domain detection by clustering spatially variable genes while adjusting for cell type effects without requiring prior knowledge of clusters or cell types.

This study identifies 19 high-confidence fusion genes in 12 pediatric B-ALL patients using whole transcriptome sequencing, revealing novel and unreported fusion events.