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The paper uses genomic and epigenomic data to identify mechanisms underlying the origin of structural variations in the human genome.

This study uses RNA sequencing to compare the transcriptional responses of Escherichia coli to PFAS and non-fluorinated compounds across growth phases, revealing distinct gene expression changes induced by PFAS.

This study identifies stable reference genes for RT-qPCR in the wild bee Ceratina calcarata across developmental stages and environments.

LRMD detects misassemblies in genome assemblies using long-read alignments without a reference, improving sensitivity and F1-score over existing tools.

The paper infers enhancer activity from cfDNA fragmentation patterns and proposes a chromatin fiber model to explain these signatures.

This paper introduces a FACS-based preprocessing workflow for PBMCs that improves scRNA-seq throughput and preserves biological integrity while enabling rare cell enrichment and cross-donor multiplexing.

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.