ATAC-seq

This paper introduces RAD-seq, a method to quantify RNA accessibility by protein binding, and shows it can detect RBP footprints and RNA structure changes under stress.

This study examines caudate nucleus aging across species and diseases, identifying shared and disorder-specific age-related changes in cell types and regulatory features.

This study shows SMARCA4 mutations in T-ALL lead to chemotherapy resistance by altering chromatin remodeling at AP-1 regulatory regions, reducing stress response genes.

This study shows that during nutrient starvation, chromatin accessibility decreases genome-wide, but RNA abundance increases selectively in stress-adaptive genes, indicating limited predictive power of ATAC-seq for transcript abundance.

This paper introduces RFA, a 3D-aware GRN filter, and finds it anticorrelates with eQTL via local distance-decay but does not predict ΔRNA.

The paper identifies KRT17-Stratifin complex as a protective barrier in dysplastic alveolar basaloid cells during chronic fibrosis, revealing mechanisms of alveolar metaplasia and its functional relevance.

The paper optimizes ATAC-see for high-throughput chromatin accessibility imaging in aging and reprogramming, revealing age-related chromatin changes and reprogramming-induced remodeling.

This study shows that increased mitochondrial metabolism in Down syndrome iPSCs impairs neuroectoderm commitment by reducing ciliation, and this effect can be reversed by inhibiting mitochondrial calcium uptake.

The paper uses single-nucleus multiome sequencing to analyze subchondral bone in OA, finding increased osteocyte SMAD2/3 activity and chondrocyte-derived FN1 signaling with disease severity.

Transient low-dose inhibition of DNA polymerase α enhances human cell reprogramming by promoting chromatin plasticity while maintaining genomic stability.

mito-overview integrates mitochondrial coverage, allele fractions, annotations, and read co-occurrence to identify and analyze candidate variants in mitochondrial genomic reports.

XChrom predicts chromatin accessibility across cells and genomic regions using genomic sequence and cell identity, outperforming existing methods and enabling cross-species analysis.

The paper introduces Watershed-DL, a framework integrating sequence-to-omics predictions and multi-omics data to prioritize rare variants, finding it increases prioritized variants by 61.4% and identifies candidate disease alleles.

The paper identifies immune cell type-specific gene expression regulated by tandem repeats using multi-omics data from large cohorts.

This study identifies HNF-1β's role in recruiting the NuRD complex to activate gene transcription through chromatin remodeling and acetylation.

This study shows that CDH1 loss in human mammary epithelial cells remodels gene expression and lineage identity toward a luminal progenitor-like state, contributing to ILC oncogenesis.

SPARK reconstructs enhancer-based gene regulatory networks using single-cell multiomics data and prior knowledge, revealing regulatory links associated with immune disease GWAS variants.

This study profiles B cell activation states using multi-omics data to identify genetic mechanisms underlying immune-mediated diseases.

This study examines epigenomic and spatial changes during human reprogramming, finding distinct molecular and spatial patterns in productive versus unsuccessful trajectories.

The paper identifies SP1 as a transcription factor necessary for human atrial cardiomyocyte identity, showing it interacts with NR2F2 to drive gene regulation.

The paper identifies population-associated differences in chromatin regulation in prostate cancer, linking reduced CTCF accessibility to aggressive tumor biology in Black men.

StarTrak infers cellular migration and phylogeny by integrating somatic variants, spatial data, and transcriptomics at single-pixel resolution in spatial genomics.

The paper characterizes nucleosome organization across 23 cancer types using ATAC-seq and shows its utility for cancer classification and detection using cell-free DNA.

The paper identifies ZBTB7B as a master regulator of salivary acinar cell function through transcriptional and regulatory analyses in human and mouse salivary glands.

GEMS associates GWAS variants with cell types using sequence-to-function predictions, revealing cell-type-specific mechanisms for disease risk variants.

SMODER deconvolves spatial multi-omics data by prioritizing RNA for cell-type identification and integrating other modalities, improving accuracy and spatial coherence.

The paper characterizes the molecular and metabolic changes in auditory neuroprogenitors induced by CHIR-DS treatment and demonstrates their utility in neuronal screening.

The paper uses CRISPR activation to engineer regulatory states in RPE-1 cells, revealing hidden genetic effects in AMD by analyzing chromatin accessibility and transcriptional interactions.

N3-kethoxal labeling of single-stranded DNA within CUT&Tag maps Pol II transcription bubbles; bubble density tracks nascent transcription, shifts with transcription inhibitors and TFIIS loss, and peaks at histone genes.