scATAC-seq

scAI-SNP: a method for inferring ancestry from single-cell data

scAI-SNP infers ancestry from single-cell data using ancestry-informative SNPs, showing robustness across diverse tissues and modalities.

Hi-Compass resolves cell-type chromatin interactions by single-cell and spatial ATAC-seq data across biological scales

Hi-Compass predicts chromatin organization from single-cell and spatial ATAC-seq data, outperforming existing methods and enabling analysis across biological scales.

A genome-wide, machine learning-guided exploration of the cis-regulatory code involved in neuronal differentiation

The paper develops a machine learning method to identify cis-regulatory element profiles and their sequence features during neuronal differentiation using single-cell ATAC-seq and RNA-seq data.

Single cell multiomics reveals drivers of metabolic dysfunction-associated steatohepatitis

This study uses single-cell multi-omics to identify cell type-specific regulatory networks and novel therapeutic targets in MASLD.

Single cell multiomics and 3D genome architecture reveal novel pathways of human heart failure

The paper integrates single-cell multi-omics and 3D genome data from human hearts to identify gene regulatory changes and causal genetic contributors in heart failure.

Multiomic profiling of hypoxic glioblastoma stem cells reveals expansion of subpopulations with distinct epigenetic and CNV profiles

This study profiles hypoxic glioblastoma stem cells using multi-omics to reveal distinct subpopulations with unique epigenetic and CNV profiles.

A single cell ATAC-seq atlas uncovers dynamic changes in chromatin accessibility during cell fate specification at the neural plate border

The paper uses scATAC-seq to study chromatin accessibility changes during neural plate border cell fate specification, identifying new regulatory mechanisms involving Foxk2.

Dissecting regulatory syntax in human development with scalable multiomics and deep learning

The paper presents a single-cell multi-omics atlas of human development and uses deep learning to analyze regulatory DNA motifs and their impact on chromatin accessibility and gene expression.

Tri-omic mapping revealed concerted dynamics of 3D epigenome and transcriptome in brain cells

The paper introduces a tri-omic method to study 3D epigenome and transcriptome dynamics in brain cells across mouse lifespan, revealing distinct genomic mechanisms in neurons and non-neuronal cells.

iSHARC: Integrating scMultiome data for heterogeneity and regulatory analysis in cancer

iSHARC is a pipeline for analyzing scMultiome data, enabling quality control, integration, clustering, annotation, and regulatory analysis in cancer studies.

Chromosomal Instability in Human Trophoblast Stem Cells and Placentas

This study reveals chromosomal instability as an inherent feature of trophoblast lineage, showing high prevalence of aneuploidy in human placentas and TSCs despite maintaining proliferative capacity.

Deep dynamical models of single-cell multiomic velocities predict loss-of-function and rescue perturbations in B cells

Charting the transition from in vitro gliogenesis to the in vivo maturation of transplanted human glial progenitor cells

This study tracks the in vitro generation and in vivo differentiation of human glial progenitor cells using single-cell RNA and ATAC-seq, revealing how the host environment influences their maturation into astrocytes and oligodendrocytes.

Single cell resolution of an epigenetic signature of persister tumor cell

The paper identifies an epigenetic signature associated with persister tumor cells in ovarian cancer that correlates with chemotherapy resistance and defines the persister state.

Deciphering of single-cell chromatin accessibility and transcriptome reveals the discrepancy for ex vivo human erythropoiesis

The paper analyzes ex vivo human erythropoiesis at single-cell chromatin accessibility and transcriptome levels to identify discrepancies and constraints in erythrocyte regeneration.

Cell type-specific associations with Alzheimer's Disease conserved across racial and ethnic groups

The paper identifies cell-type-specific and continuous gene programs associated with Alzheimer's Disease across multiple racial and ethnic groups using single-nucleus RNA-seq and ATAC-seq.

Global and cross-omics feature aggregation improves single-cell multi-omics integration and clustering

scCODI improves single-cell multi-omics integration and clustering by aggregating cross-omics features and using contrastive learning, outperforming existing methods across nine datasets.

Mammalian olfactory cortex neurons retain molecular signatures of ancestral cell types

This study identifies molecular signatures of ancestral cell types in mammalian olfactory cortex neurons by comparing transcriptomes across species and cortical layers.

SCARF: Single Cell ATAC-seq and RNA-seq Foundation model

SCARF is a foundation model for integrating single-cell ATAC-seq and RNA-seq data, achieving state-of-the-art performance in cell representation and cross-omics tasks.

CHOIR improves significance-based detection of cell types and states from single-cell data

CHOIR improves cell type and state detection in single-cell data by using statistical inference to assess clustering results, outperforming existing methods across multiple data types.

Learning the cellular origins of cancer using single-cell chromatin landscapes

This study uses single-cell chromatin accessibility data and machine learning to predict cancer cell origins, revealing new insights into tumor development and challenging existing views on cancer origins.

Transcription factor networks disproportionately enrich for heritability of blood cell phenotypes

The paper identifies TF-sensitive chromatin regions as highly enriched for heritability of blood cell phenotypes, using a novel single-cell multi-omics approach.

Single-Cell Multiomic Analysis of Circadian Rhythmicity in Mouse Liver

This study uses single-nucleus multiomics to analyze circadian rhythms in mouse liver, revealing gene expression and chromatin accessibility patterns across the day.

G-quadruplex profiling in complex tissues using single-cell CUT&Tag

This study uses G4 scCUT&Tag to profile G-quadruplexes in mouse brain cells, showing lineage-specific G4s and enabling integrative analysis with scRNA-Seq data.

Defining effective strategies to integrate multi-sample single-nucleus ATAC-seq datasets via a multimodal-guided approach

The paper benchmarks snATAC-seq integration pipelines using multimodal datasets and recommends SnapATAC2 + Harmony with ENCODE cCRE features for effective integration.

Latent Epigenetic Programs in Muller Glia Contribute to Stress, Injury, and Disease Response in the Retina

The paper identifies 'pliancy genes' in Muller glia that enable rapid response to retinal stress, injury, and disease, showing species-specific differences in their activation between zebrafish and mammals.

Ocelli: an open-source tool for the visualization of developmental multimodal single-cell data

Ocelli is a Python tool for visualizing developmental multimodal single-cell data using diffusion-based modeling, improving computational efficiency and low-dimensional representation quality.

Scalable high-performance single cell data analysis with BPCells

BPCells enables scalable single-cell RNA-seq and ATAC-seq analysis on modest hardware by using disk-backed streaming algorithms and compressed formats.

CTCF-anchored chromatin loop dynamics during human meiosis

This study uses machine learning on ATAC-seq and RNA-seq data to predict CTCF-anchored chromatin loops during human meiosis, revealing dynamic changes in loop structure and function across meiotic stages.

Single-cell multiomics reveals disrupted glial gene regulatory programs in Alzheimer's disease via interpretable machine learning

This study uses single-cell multi-omics data to identify disrupted glial gene regulatory programs in Alzheimer's disease using interpretable machine learning.