scATAC-seq

Single-cell chromatin and gene-regulatory dynamics of mouse nephron progenitors

The paper uses single-cell chromatin accessibility and gene expression data to study regulatory dynamics in mouse nephron progenitors, identifying cell-type-specific cis-regulatory elements and transcription factors involved in fate decisions.

epiAneufinder: identifying copy number variations from single-cell ATAC-seq data

epiAneufinder identifies copy number variations from scATAC-seq data to explore single-cell CNV heterogeneity in cancer samples.

SEACells: Inference of transcriptional and epigenomic cellular states from single-cell genomics data

SEACells identifies metacells from single-cell data, improving gene-peak associations and revealing chromatin dynamics in hematopoiesis and COVID-19.

Integrated single-cell transcriptomic and epigenetic analyses of cell-state transition and lineage commitment in the embryonic mouse cerebellum

The paper integrates single-cell RNA and ATAC sequencing to analyze cell-state transitions and lineage commitment in the embryonic mouse cerebellum, identifying regulatory elements and validating gene regulatory networks.

Longitudinal single cell transcriptional and epigenetic mapping of effector, memory, and exhausted CD8 T cells reveals shared biological circuits across distinct cell fates

This study maps transcriptional and epigenetic changes in CD8 T cell differentiation using scRNA-seq and scATAC-seq, revealing shared biological circuits across effector, memory, and exhausted cell fates.

Characterizing cellular heterogeneity in chromatin state with scCUT&Tag-pro

The paper introduces scCUT&Tag-pro and scChromHMM to analyze chromatin states in single cells, showing their ability to characterize dynamic changes and regulatory priming across immune cell types.

Simultaneous profiling of spatial gene expression and chromatin accessibility for mouse brain development

This study introduces MISAR-seq to jointly profile spatial gene expression and chromatin accessibility in developing mouse brains, revealing spatiotemporal regulatory principles.

Dynamic intestinal stem cell plasticity and lineage remodeling 1 by a nutritional environment relevant to human risk for tumorigenesis

This study shows that a nutrient-rich diet reprograms intestinal stem cells and lineages, promoting tumorigenesis by altering stem cell function and inducing chronic inflammation.

Integrated single-cell profiling dissects cell-state-specific enhancer landscapes of human tumor-infiltrating T cells.

The paper integrates single-cell chromatin accessibility and RNA-seq to analyze enhancer landscapes in human tumor-infiltrating T cells, identifying key regulatory elements and their role in TIL dysfunction.

Resolving clonal substructure from single cell genomic data using CopyKit

CopyKit is a computational tool that resolves clonal substructure and reconstructs genetic lineages in tumors using single cell copy number data.

MQuad enables clonal substructure discovery using single cell mitochondrial variants

MQuad identifies clonally informative mitochondrial variants from single-cell sequencing data with high sensitivity and specificity, outperforming existing methods.

CellWalkR: An R Package for integrating single-cell and bulk data to resolve regulatory elements

CellWalkR integrates scATAC-seq with bulk epigenetic data to improve identification of cell type-specific regulatory regions by using a network-based random walk model.

PeakVI: A Deep Generative Model for Single Cell Chromatin Accessibility Analysis

PeakVI is a deep generative model for scATAC-seq data analysis that corrects batch effects, preserves biological heterogeneity, and identifies differential accessibility.

Multi-omic Analysis of Developing Human Retina and Organoids Reveals Cell-Specific Cis-Regulatory Elements and Mechanisms of Non-Coding Genetic Disease Risk.

The paper identifies cell-class-specific cis-regulatory elements in human retina and organoids, showing their correlation and function in development and disease.

The chromatin landscape of Th17 cells reveals mechanisms of diversification of regulatory and pro-inflammatory states

The paper analyzes chromatin landscapes of Th17 cell subsets to uncover regulatory mechanisms driving their heterogeneity and identifies BACH2 as a novel regulator of pathogenicity.

Simultaneous dimensionality reduction and integration for single-cell ATAC-seq data using deep learning

This paper introduces a variational auto-encoder for single-cell ATAC-seq data that performs dimensionality reduction and batch correction simultaneously.

HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads

HyDrop is a droplet microfluidic platform for scATAC-seq and scRNA-seq that improves throughput and sensitivity while reducing cost.

Optimal Transport improves cell-cell similarity inference in single-cell omics data

This paper introduces Optimal Transport as a cell-cell similarity metric for single-cell omics data, showing improved clustering performance across multiple datasets.

scJoint: transfer learning for data integration of atlas-scale single-cell RNA-seq and ATAC-seq

scJoint integrates atlas-scale scRNA-seq and scATAC-seq data using transfer learning, achieving higher cell type accuracy and joint visualizations than existing methods.

MOJITOO: a fast and universal method for integration of multimodal single cell data

MOJITOO integrates multimodal single cell data using canonical correlation analysis, outperforming existing methods in computational efficiency and clustering.

Stable Flow-induced Expression of KLK10 Inhibits Endothelial Inflammation and Atherosclerosis

This study identifies KLK10 as a flow-sensitive endothelial protein that inhibits inflammation and atherosclerosis through a PAR1/2-dependent mechanism involving HTRA1 regulation.

scDALI: Modelling allelic heterogeneity of DNA accessibility in single-cells reveals context-specific genetic regulation

scDALI models allelic heterogeneity in single-cell chromatin accessibility to identify context-specific genetic regulation.

Accurate and fast cell marker gene identification with COSG

COSG identifies marker genes for cell type distinction in single-cell and spatial transcriptome data with high accuracy and efficiency.

Single-cell multi-omics analyses reveal EZH2 as a main driver of retinoic acid resistance in PLZF-RARA leukemia.

This study identifies EZH2 as a driver of retinoic acid resistance in PLZF-RARA leukemia using single-cell multi-omics analyses and shows targeting pan-EZH2 activities can eliminate resistant cells.

IReNA: integrated regulatory network analysis of single-cell transcriptomes

IReNA integrates scRNA-seq and scATAC-seq data to infer regulatory networks, outperforming existing methods in identifying known regulators.

GAGAM: a genomic annotation-based enrichment of scATAC-seq data for Gene Activity Matrix

This paper introduces GAGAM, a method to enhance scATAC-seq data interpretation by linking peaks to genes through genomic annotations, improving interpretability over traditional Gene Activity Matrices.

scMoC: Single-Cell Multi-omics clustering

scMoC integrates scRNA-seq and scATAC-seq data to identify biologically meaningful cell clusters through RNA-guided imputation and cross-modal clustering.

Single-cell chromatin profiling reveals demethylation-dependent metabolic vulnerabilities of breast cancer epigenome

This study uses scATAC-seq to show 2HG enantiomers disrupt DNA and histone demethylation, leading to epigenetic changes in breast cancer cells.

Single-cell Chromatin Accessibility and Lipid Profiling Reveals a Metabolic Shift in Adipocytes Induced by Bariatric Surgery

This study uses single-cell ATAC sequencing and lipid profiling to show that bariatric surgery alters chromatin accessibility and fatty acid profiles in adipose tissue, suggesting a metabolic shift mediated by Scd1.

CDCP: a visualization and analyzing platform for single-cell datasets

CDCP is a platform for sharing and analyzing single-cell datasets, offering visualization and analysis tools for researchers.