scATAC-seq

SifiNet: A robust and accurate method to identify feature gene sets and annotate cells

SifiNet identifies gene sets and annotates cells without clustering, showing better performance than existing methods on multiomic data.

ScRNA-seq and scATAC-seq reveal that sertoli cell mediate spermatogenesis disorders through stage-specific communications in non-obstructive azoospermia

This study uses scRNA-seq and scATAC-seq to identify stage-specific interactions between Sertoli cell subtypes and germ cells in NOA, revealing potential molecular markers for diagnostic kits.

Massive-scale single-cell chromatin accessibility sequencing using combinatorial fluidic indexing

The paper introduces scifi-ATAC-seq, a method that increases single-cell ATAC-seq throughput by 20-fold using combinatorial fluidic indexing.

Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles

The paper develops SCENT, a method to create cell-type-specific enhancer-gene maps from single-cell multimodal data, identifying causal variants and genes for diseases.

A starting guide on multi-omic single-cell data joint analysis: basic practices and results

This paper presents a bioinformatic workflow for analyzing transcriptomic and epigenomic single-cell data separately and jointly to better understand cellular heterogeneity.

txci-ATAC-seq, a massive-scale single-cell technique to profile chromatin accessibility

The paper introduces txci-ATAC-seq, a high-throughput single-cell ATAC-seq method, and demonstrates its application across multiple tissues and genetic backgrounds.

Single-cell epigenomic dysregulation of Systemic Sclerosis fibroblasts via CREB1/EGR1 axis in self-assembled human skin equivalents

The paper characterizes single-cell transcriptomic and epigenomic features of a 3D skin-like model of systemic sclerosis, identifying fibroblast subpopulations and their interactions with macrophages.

HyGAnno: Hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data

HyGAnno transfers cell type labels from scRNA-seq to scATAC-seq using a graph neural network, improving annotation accuracy and robustness.

Molecular mechanisms reconstruction from single-cell multi-omics data with HuMMuS

HuMMuS infers regulatory mechanisms from single-cell multi-omics data, improving predictions of TF targets, binding motifs, and regulatory regions.

A longitudinal single-cell and spatial multiomic atlas of pediatric high-grade glioma

This study creates a longitudinal multiomic atlas of pediatric high-grade glioma, revealing distinct tumor cell states and therapeutic targets not seen in adult glioblastoma.

Deciphering the spatio-temporal transcriptional and chromatin accessibility of human retinal organoid development at the single cell level

This study presents the first single-cell spatio-temporal transcriptome of human retinal organoid development using single-cell RNA-Seq and spatial transcriptomics, revealing key developmental events and chromatin accessibility patterns.

Multi-condition and multi-modal temporal profile inference during mouse embryonic development

This paper introduces Sunbear, a framework for integrating multi-condition and multi-modal single-cell profiles across time to infer temporal profiles and predict dynamic relationships in mouse embryonic development.

Single cell analyses of cancer cells identified two regulatorily and functionally distinct categories in differentially expressed genes among tumor subclones

The paper identifies two distinct categories of differentially expressed genes in tumor subclones based on their regulatory and functional characteristics using single-cell transcriptomic and genomic data from colorectal cancer patients.

CDX2 dose-dependently influences the gene regulatory network underlying human extraembryonic mesoderm development

This study shows CDX2 dose-dependently regulates genes involved in tissue permeability, cell-cell adhesion, and cytoskeletal structure during extraembryonic mesoderm development using human induced pluripotent stem cells.

Single-cell multiomics reveals a gene regulatory circuit promoting leukemia cell differentiation

This study uses single-cell multiomics to identify a gene regulatory circuit involving SPI1 and CEBPE that promotes differentiation in APL leukemia cells under ATRA treatment.

TBXT dose sensitivity and the decoupling of nascent mesoderm specification from EMT progression in 2D human gastruloids

This study shows that TBXT dose affects the timing of EMT in human gastruloids without compromising mesoderm differentiation.

ScISOr-ATAC reveals convergent and divergent splicing and chromatin specificities between matched cell types across cortical regions, evolution, and in Alzheimer's disease.

The paper introduces ScISOr-ATAC to measure splicing and chromatin accessibility in frozen brain tissues, finding convergent and divergent patterns in different cell types and conditions.

SHARE-Topic: Bayesian Inerpretable Modelling of Single-Cell Multi-Omic Data

SHARE-Topic is a Bayesian model for multi-omic single-cell data that identifies interpretable patterns of co-variation between gene expression and epigenomic layers, demonstrating its utility in B-cell lymphoma analysis.

Medulloblastoma oncogene aberrations are not involved in tumor initiation, but essential for disease progression and therapy resistance

The paper uses single-cell technologies to show that large-scale chromosomal aberrations drive medulloblastoma initiation, while single-gene oncogenic events like MYC contribute to progression and therapy resistance.

Benchmarking Algorithms for Gene Set Scoring of Single-cell ATAC-seq Data

This study benchmarks gene set scoring tools for scATAC-seq, showing their comparable performance to scRNA-seq and highlighting the importance of dropout imputation.

A single-cell 3D spatiotemporal multi-omics atlas from Drosophila embryogenesis to metamorphosis

The paper constructs a 3D spatiotemporal multi-omics atlas of Drosophila development, revealing gene regulatory networks and cell type dynamics across embryogenesis to metamorphosis.

Single cell ATAC sequencing identifies sleepy macrophages during reciprocity of cytokines in L.major infection

The paper uses single cell ATAC sequencing to study cytokine reciprocity in L. major infected macrophages, identifying a transient state called sleepy macrophages regulated by NFAT5.

The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis

The paper profiles chromatin accessibility dynamics in zebrafish embryos using single-cell ATAC-seq to identify enhancers and transcription factor motifs involved in early cell fate decisions.

A Novel Therapeutic Approach using CXCR3 Blockade to Treat Immune Checkpoint Inhibitor-mediated Myocarditis

This study identifies CXCR3-CXCL9/10 axis as a therapeutic target for ICI-mediated myocarditis using mouse models and human patient data.

Analysis of Methicillin Resistance in Staphylococcus Aureus Sepsis Using TDbasedUFE

The paper uses TDbasedUFE to analyze scATAC-seq data from S. aureus sepsis patients, identifying genes with differential responses between methicillin-resistant and sensitive strains and their functional associations.

Benchmarking multi-omics integration algorithms across single-cell RNA and ATAC data

This study benchmarks 12 multi-omics integration methods on scRNA-seq and scATAC-seq data across three tasks, identifying method-specific strengths and providing selection guidelines.

Leveraging single-cell ATAC-seq to identify disease-critical fetal and adult brain cell types

The paper integrates GWAS with scATAC-seq and scRNA-seq data to identify disease-critical fetal and adult brain cell types for multiple traits.

Single nuclei multiomics reveals the drought-driven gene regulatory atlas in Arabidopsis

This study uses single-nucleus multiomics to uncover drought-driven gene regulatory mechanisms in Arabidopsis, identifying cell type-specific markers and regulatory networks.

Definition of regulatory elements and transcription factors controlling immune cell gene expression at single cell resolution using single nucleus ATAC-seq

This study uses snATAC-seq to define regulatory elements and transcription factors controlling gene expression in porcine PBMCs at single-cell resolution.

scDirect: key transcription factor identification for directing cell state transitions based on single-cell multi-omics data

scDirect identifies key transcription factors driving cell state transitions using single-cell multi-omics data, showing robust performance in benchmarking and real-world applications.