ATAC-seq

miniODP: a reusable framework for building multi-omics resources in understudied organisms

miniODP provides a framework for building multi-omics resources in understudied organisms, including a benchmark using zebrafish data to identify enhancer-like signatures and gene regulatory networks.

Disease-associated astrocyte epigenetic memory promotes CNS pathology

This study identifies an epigenetically controlled memory astrocyte subset that exacerbates CNS pathology in EAE and MS by promoting pro-inflammatory responses.

Genomic dissection and mutation-specific target discovery for breast cancer PIK3CA hotspot mutations

The paper identifies mutation-specific targets for PIK3CA hotspot mutations using a multi-modal genomics approach and isogenic cell lines.

Computational Analysis of Maize Enhancer Regulatory Elements Using ATAC-STARR-seq

The paper describes a computational framework for analyzing ATAC-STARR-seq data from maize to assess cis-regulatory element activity.

Predmoter - Cross-species prediction of plant promoter and enhancer regions

Predmoter predicts ATAC-seq and ChIP-seq read coverage in plant genomes using DNA sequences, improving efficiency in identifying cis-regulatory elements.

Distribution and dynamics of chromatin states in the C. elegans germ line

The paper defines chromatin states in C. elegans germ nuclei using histone modification and chromatin accessibility data, showing dynamic changes during germ cell differentiation.

HEMU: an integrated Andropogoneae comparative genomics database and analysis platform

HEMU provides a multi-omics database and analysis platform for the Andropogoneae tribe, enabling comparative genomics across species and omics layers.

Decoding mutational hotspots in human disease through the gene modules governing thymic regulatory T cells

The paper identifies gene regulatory modules in thymic regulatory T cells to prioritize variants in complex diseases and uncover mutational hotspots.

Genetically encoded tool for manipulation of Δ{Psi}m identifies the latter as the driver of integrative stress response induced by ATP Synthase dysfunction

The paper develops a genetically encoded tool to manipulate mitochondrial membrane potential and shows it drives the integrated stress response from ATP synthase dysfunction.

GametesOmics: A Comprehensive Multi-Omics Database for Exploring the Gametogenesis in Humans and Mice

GametesOmics integrates multi-omics data from human and mouse gametogenesis to provide tools for analyzing gene expression, DNA methylation, and chromatin accessibility.

Computational identification of key transcription factors for embryonic and postnatal Sox2+ dental epithelial stem cell

The paper identifies key transcription factors in Sox2+ dental epithelial stem cells from embryonic and postnatal stages using single-cell RNA-seq and ATAC-seq.

Common and divergent gene regulatory networks control injury-induced and developmental neurogenesis in zebrafish retina.

The paper compares gene regulatory networks in zebrafish retinal regeneration and development after different neuronal subtype losses, finding both similarities and differences.

Homeostatic mitophagy scales mitochondrial networks

The paper shows homeostatic mitophagy regulates mitochondrial network size during starvation in yeast.

Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation

The paper performs population-scale single-nucleus multi-omic profiling of skeletal muscle to identify genetic regulation across cell types and traits.

Single-cell Sequencing Highlights Heterogeneity and Malignant Progression in Actinic Keratosis and Cutaneous Squamous Cell Carcinoma

This study uses single-cell RNA-seq to analyze the progression from actinic keratosis to cutaneous squamous cell carcinoma, identifying key driver genes and tumor microenvironment interactions.

Mitotic chromosomes harbor cell type and species-specific structural features within a universal looping architecture

The paper investigates mitotic chromosome architecture across species and cell types, finding species-specific loop sizes but no cell type differences, and links loop size to chromosome arm compaction.

Integrative omics analysis reveals gene regulatory mechanisms distinguishing organoid-derived hepatocytes from primary human hepatocytes

The paper identifies gene regulatory differences between primary human hepatocytes and organoid-derived hepatocytes using integrative omics analysis.

Benchmarking computational methods to identify spatially variable genes and peaks

This study benchmarks 14 computational methods for identifying spatially variable genes and peaks using simulated and real-world spatial transcriptomics and ATAC-seq data, finding spatialDE2 performs best and highlighting the need for specialized algorithms for peaks.

Single Cell Multimodal Analyses Reveal Epigenomic and Transcriptomic Basis for Birth Defects in Maternal Diabetes

The paper uses single-cell multimodal analyses to show how maternal diabetes alters epigenomic and transcriptomic states in cardiac and craniofacial progenitors, leading to developmental defects.

Adaptation to ARF6-depletion in KRAS-driven PDAC is abolished by targeting TLR2

This study identifies TLR2 as a target to counteract adaptation to ARF6 depletion in KRAS-driven PDAC, reducing proliferation, migration, and invasion.

Novel mouse model of Weaver syndrome displays overgrowth and excess osteogenesis reversible with KDM6A/6B inhibition

The paper creates a mouse model of Weaver syndrome and shows that inhibiting KDM6A/6B can reverse excessive osteogenesis caused by an EZH2 mutation.

ROCCO: A Robust Method for Detection of Open Chromatin via Convex Optimization

ROCCO identifies consensus open chromatin regions across multiple samples using convex optimization, improving upon existing peak calling methods.

Epigenetic Small-Molecule Screen for Inhibition and Reversal of Acinar Ductal Metaplasia in Mouse Pancreatic Organoids

The paper screens epigenetic small molecules to inhibit and reverse acinar ductal metaplasia in mouse pancreatic organoids, identifying several effective compounds with improved activity over TSA.

Integration of ATAC-seq and RNA-seq identifies novel candidate genes associated with drought tolerance in Zoysia japonica Steud.

This study integrates ATAC-seq and RNA-seq to identify 63 drought-related genes and 6 regulatory motifs in Zoysia japonica, showing a positive correlation between chromatin accessibility and gene expression.

The contributions of DNA accessibility and transcription factor occupancy to enhancer activity during cellular differentiation

This study investigates how DNA accessibility and transcription factor occupancy influence enhancer activity during macrophage-neutrophil differentiation, showing that TF binding, not total accessibility, drives enhancer upregulation.

EMO: Predicting Non-coding Mutation-induced Up- and Down-regulation of Risk Gene Expression using Deep Learning

EMO predicts non-coding mutation-induced up- and down-regulation of gene expression using deep learning, achieving high performance across variant distances and cell types.

Improved Quality Metrics for Association and Reproducibility in Chromatin Accessibility Data Using Mutual Information

The paper evaluates correlation and association statistics for ATAC-seq data, finding that mutual information performs best in predicting replicate relationships after removing co-zeros.

The unique function of Runx1 in skeletal muscle differentiation and regeneration is mediated by an ETS interaction domain

This study identifies the unique role of Runx1 in skeletal muscle differentiation and regeneration through its ETS interaction domain, distinguishing it from Runx2.

Epigenomic mapping in B-cell acute lymphoblastic leukemia identifies transcriptional regulators and noncoding variants promoting distinct chromatin architectures

The paper maps chromatin accessibility in B-ALL subtypes using ATAC-seq, identifies TFs and genetic variants influencing chromatin architecture and gene regulation.

Cellular zinc status alters chromatin accessibility and binding of transcription factor TP53 to genomic sites

The paper shows that changes in labile zinc levels affect chromatin accessibility and TP53 binding to DNA.