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SPARK generates simulated nascent RNA sequencing data to benchmark computational tools for analyzing transcriptional dynamics.

This study characterizes age- and chamber-specific gene expression patterns in guinea pig and human hearts, identifying conserved maturation markers to support guinea pigs as a preclinical model for pediatric cardiology.

This study identifies DNA methylation and gene expression changes in heart failure patients before and after LVAD therapy, linking extracellular matrix and cytoskeletal remodeling to myocardial recovery.

The paper investigates how 3D nuclear positioning and compartmentalization of genes influence transcriptional responses to mechanical confinement using Hi-C and transcriptome analyses.

Nona is a multimodal masking framework that unifies sequence-to-function models, language models, and generative models for functional genomics, improving predictions and revealing privacy vulnerabilities in ATAC-seq data.

The paper uses AI-assisted image phenotyping to analyze pod traits in mungbean, identifies SNPs associated with pod morphology, and demonstrates improved genomic prediction accuracy.

This study investigates the origin and early genome evolution of Arabidopsis suecica, identifying de novo adaptation and functional compensation between homeologous genes.

TelOMpy measures individual telomere lengths from optical genome mapping data, showing high variation and diet-induced shortening in mice.

This study identifies linear plasmids in six Rhizobiaceae strains, revealing their presence in nonpathogenic and plant tumorigenic bacteria and suggesting they may be more widespread than previously thought.

The paper investigates how Polycomb proteins regulate gene expression in human cortical neurons through long-range chromatin interactions, showing their role in cell-type specification.

This study creates a single-cell and spatially resolved atlas of human esophageal squamous cell carcinoma, identifying key tumor and fibroblast subgroups and their interactions in the tumor microenvironment.

The paper identifies active human neural enhancers and CRISPRa gRNAs that upregulate NDD risk genes, providing a resource for cis-regulatory therapy development.

The paper identifies transcriptional and methylation signatures in umbilical cord blood linked to BPD risk in preterm infants.

RainBar enables pooled live-cell imaging with single-cell resolution by using optical barcoding to track perturbations and analyze dynamic phenotypes.

The paper quantifies telomere content variation across 26 global human populations and finds significant differences between African-ancestry populations in the Americas and other superpopulations.

The paper traces the evolutionary impact of transposons on human inflammatory enhancers and shows their role in disease susceptibility through population genetics analysis.

The paper jointly profiles neuronal morphology and gene expression during iPSC differentiation to better understand neuronal development and disease modeling.

This study evaluates multiple MPRA and STARR-seq datasets to identify enhancers, finding inconsistencies due to technical factors and proposing a unified pipeline to improve cross-assay agreement.

This study generates genomic and epigenomic maps of mouse centromeres and pericentromeres using long-read sequencing and epigenetic analyses, revealing satellite DNA composition and chromatin state differences.

This study analyzes ancient DNA from Iron Age Saka pastoralists in Kyrgyzstan, revealing genetic patterns consistent with patrilocality and female-mediated genetic diversity.