scATAC-seq

Matched single-cell chromatin, transcriptome, and surface marker profiling captures in vivo epigenomic reprogramming during basal-to-luminal transition in the mammary gland

The paper introduces OneCell CUT&Tag, a single-cell multi-omics method that captures chromatin, transcriptome, and surface marker data, revealing epigenomic reprogramming during mammary gland basal-to-luminal transition.

scAmp analyzes focal gene amplifications at single-cell resolution

scAmp detects and analyzes ecDNA at single-cell resolution, showing its impact on chromatin accessibility in cancer cells.

fastdemux: Robust SNP-based demultiplexing of single-cell population genomics data

fastdemux improves computational efficiency for SNP-based demultiplexing while maintaining accuracy in single-cell genomics data.

Ancient origin of the dorso-ventral patterning system of vertebrate paired fins

This study shows that dorso-ventral patterning genes in paired fins are conserved in median fins, supporting an ancient origin of the DV regulatory module that was redeployed during paired fin evolution.

Single-cell multiomic profiling of lung immune cells identifies novel asthma risk genes and cell-type specific functions

The paper uses single-cell multi-omics data to identify asthma risk genes and their cell-type specific functions in lung immune cells.

A Comprehensive Benchmarking Study on Computational Tools for Cross-omics Label Transfer from Single-cell RNA to ATAC Data

This study benchmarks 27 computational tools for transferring cell type labels from scRNA-seq to scATAC-seq data across human and mouse tissues, finding Bridge and GLUE as top performers.

Heterochronic transcription factor expression drives cone-dominant retina development in 13-lined ground squirrels.

Decomposing multi-scale dynamic regulation from single-cell multiomics with scMagnify

scMagnify decomposes multi-scale gene regulatory networks from single-cell multiomics data, revealing regulatory logic in development and disease.

Single-Cell Multimodal Profiling Highlights Persistent Aortic Smooth Muscle Cell Changes in Diabetic Mice Despite Glycemic Control

This study uses single-cell multi-omics to show that diabetic mice show persistent aortic smooth muscle cell dysfunction and phenotypic changes despite glycemic control, with partial reversal by dapagliflozin.

Glycosylated GM-CSF expands B-1b cells and B-1b plasma cells and programs them for immunosuppression

This study shows glycosylated GM-CSF expands immunosuppressive B-1b plasma cells and promotes regulatory functions, while non-glycosylated GM-CSF drives pro-inflammatory responses.

coelsch: Platform-agnostic single-cell analysis of meiotic recombination events

The paper benchmarks single-cell methods for meiotic recombination mapping in Arabidopsis thaliana and introduces tools to detect crossovers and haplotypes from sparse sequencing data.

Single-cell Multiome Analysis of Chromatin State and Transcriptome in the Human Basal Ganglia

This paper presents a single-cell multiome atlas of the human basal ganglia, linking chromatin states and transcriptomes to cell-type identity and disease-associated variants.

BiCLUM: Bilateral Contrastive Learning for Unpaired Single-Cell Multi-Omics Integration

BiCLUM integrates unpaired single-cell multi-omics data by aligning cell and feature spaces through bilateral contrastive learning, outperforming existing methods in visualization and quantitative metrics.

An Integrated Single-Cell and Epigenomic Resource for Comparative Analysis of the Basal Ganglia

The paper presents an integrated single-cell and epigenomic resource for exploring basal ganglia datasets across species, enabling multi-omics and comparative analysis.

Epigenetic Programming of Macrophage Phenotypes by STING-IRF3 Drives Inflammation in Ascending Thoracic Aortic Dissection

This study identifies STING-IRF3-mediated epigenetic programming of macrophages as a driver of inflammation in aortic dissection, showing its role in pro-inflammatory bias and therapeutic potential.

HyDrop v2: Scalable atlas construction for training sequence-to-function models

The paper introduces HyDrop v2, a microfluidic system for generating large scATAC-seq atlases, and shows its data is comparable to commercial platforms for training sequence-to-function models.

System-wide extraction of cis-regulatory rules from sequence-to-function models in human neural development

The paper extracts cis-regulatory rules from sequence-to-function models in human neural development using new single-cell multiome data and a computational tool called TF-MINDI.

Single-Cell Multi-Omics Insights into BMI-Mediated Immune-Related Disease Risk

This study uses single-cell multi-omics data from the CIMA cohort to identify BMI-associated immune cell features and molecular mechanisms linked to immune-related diseases.

Multimodal integration of single cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations

MAAS integrates multimodal scATAC-seq data to identify clinically relevant tumor subpopulations and improve prognostic prediction.

EBF1 regulates sensory establishment in the cochlea by positioning the medial boundary of the prosensory domain and restricting proliferation of the sensory progenitor population

The paper uses multiome sequencing to show EBF1 regulates sensory cell development in the cochlea by setting the prosensory domain boundary and limiting progenitor proliferation.

Hierarchical bounds on RNA chromatin statistical dependence across cellular states in paired single-cell multiome data

The paper quantifies RNA-chromatin statistical dependence across cellular states using paired single-cell RNA-seq and ATAC-seq data, finding that most dependence is due to cell-type composition rather than regulatory coordination.

A Latent Activated Olfactory Stem Cell State Revealed by Single Cell Transcriptomic and Epigenomic Profiling

This study identifies a latent activated stem cell state in olfactory epithelium using single-cell transcriptomic and epigenomic profiling during injury-induced regeneration.

Gsx2 Regulates Oligodendrocyte Precursor Formation in the Zebrafish Spinal Cord

This study identifies Gsx2 as a regulator of oligodendrocyte precursor cell formation in zebrafish spinal cord through single-cell and single-nuclei multi-omics analyses.

Integrative Comparison of GeneHancer and Single-Cell Co-accessibility Reveals Active Enhancer-Gene Interactions

This paper integrates GeneHancer annotations with single-cell chromatin accessibility data to identify high-confidence enhancer-gene interactions specific to a human PBMC dataset.

cellSTAAR: Incorporating single-cell-sequencing-based functional data to boost power in rare variant association testing of non-coding regions

cellSTAAR integrates single-cell ATAC-seq with whole-genome sequencing to enhance power and interpretation of rare variant association tests in non-coding regions.

Two distinct chromatin modules regulate proinflammatory gene expression

The paper identifies two chromatin modules, ACs and DCs, that regulate proinflammatory gene expression through distinct mechanisms in human endothelial cells.

scCotag: Diagonal integration of single-cell multi-omics data via prior-informed co-optimal transport and regularized barycentric mapping

scCotag improves single-cell multi-omics integration by using co-optimal transport and regularized barycentric mapping, outperforming existing methods in alignment and embedding accuracy.

MOH: a novel multilayer multi-omics heterogeneous graph for single-cell clustering

MOH improves single-cell clustering by integrating three omics types into a multilayer heterogeneous graph, achieving better performance than existing methods.

Regulatory element modules as universal features for single-cell chromatin analysis

The paper introduces REMO, a set of DNA regulatory element modules for single-cell chromatin analysis, improving cell state separation and annotation.

Integrative Single-Cell RNA and ATAC Sequencing Reveals the Impact of Chronic Cigarette Smoking on Lung Epithelial Responses to Influenza and Hyperoxia

This study uses scRNA-seq and scATAC-seq to show chronic cigarette smoke exposure enhances inflammatory and survival pathways in lung epithelial responses to influenza and hyperoxia.