scATAC-seq

Clonal lineage tracing of innate immune cells in human cancer

The paper uses mtDNA mutations to trace clonal relationships of innate immune cells in cancer, showing myeloid clones are linked to monocytes and have distinct epigenetic profiles.

Multiome Profiling Reveals Astrocyte and Neuroendocrine Targets of Prenatal Acoustic Programming in Zebra Finch Embryos

The paper uses multiome sequencing to show prenatal heat call exposure in zebra finch embryos alters astrocyte and neuroendocrine gene regulation in the hypothalamus.

Deciphering context-dependent epigenetic program by network-based prediction of clustered open regulatory elements from single-cell chromatin accessibility

The paper introduces enCORE, a framework to identify clustered open regulatory elements from single-cell ATAC-seq data, revealing regulatory programs and potential therapeutic targets in colorectal cancer.

Alignment-free integration of single-nucleus ATAC-seq across species with sPYce

sPYce integrates single-nucleus ATAC-seq data across species using k-mer histograms, revealing conserved and divergent regulatory programs without requiring genome alignments.

Epigenetic Profiling of Human Insulinomas Reveals AP-1 Family as Critical Regulators of Beta Cell Maturation

The paper identifies AP-1 family transcription factors as critical regulators of beta cell maturation by analyzing epigenomic and transcriptomic profiles of human insulinomas.

UcTCRp: a TCRβ-based framework for quantitative MAIT- and iNKT-associated repertoire-state profiling

UcTCRp profiles MAIT- and iNKT-associated immune states using TCRβ sequences without requiring single-cell data or antigen-specific markers.

scDynOmics: An Optimized Transformer Model for Representation Learning from Single-Cell Multiomics

scDynOmics is a transformer model for single-cell multiomics data that outperforms existing models and provides interpretable insights into cellular dynamics.

Chromatin landscape and epigenetic heterogeneity of acute myeloid leukemia

This study identifies 16 AML subgroups based on chromatin accessibility profiles using ATAC-seq in 1,563 cases, revealing epigenetic heterogeneity and its clinical and therapeutic implications.

Decoding Immune Reconstitution Failure in People Living with HIV through Single-cell Genomics

This study uses single-cell multi-omics to analyze immune reconstitution failure in HIV patients, identifying genetic and epigenetic factors and developing a predictive model.

Echo characterizes the desynchronization of gene expression and chromatin accessibility during cell-state transitions

Echo identifies desynchronized cell states and their drivers from paired single-cell RNA and ATAC data, revealing structured desynchronization in human fetal retina and hematopoiesis.

A weak-interaction model defines the cell-autonomous function of DNA methylation in gastrulation

The paper introduces a weak-interaction model showing DNA methylation moderates, but does not block, trans-acting regulatory machineries during mouse gastrulation.

Reprogramming Dedifferentiation Regulatory Networks Preserves Human Chondrocyte Phenotypes

This study identifies chromatin stability as critical for preserving chondrocyte function during expansion and shows that Fludarabine maintains phenotype by stabilizing chromatin and reducing STAT1 activity.

Disagreement between demultiplexing methods reveals structured cell quality gradients in multiplexed single-cell data

This paper introduces Split-flow, a pipeline that uses concordance between demultiplexing methods to classify cell quality in multiplexed single-cell data, revealing structured quality gradients.

Quantifying Cross-Modal Association Confidence for Single-Cell RNA-ATAC Integration

The paper introduces CLIC scores to quantify confidence in gene-peak associations for single-cell RNA-ATAC integration, improving integration accuracy and biological interpretability.

Predicting gene-specific regulation with transcriptomic andepigenetic single-cell data

The paper introduces MetaFR, a method that links scATAC-seq open-chromatin variation to scRNA-seq gene expression, showing improved performance over existing methods.

Dependencies in heterogeneous, lineage plastic patient-derived prostate cancer organoids revealed through integrated single-cell multiomics and CRISPR screening

The paper integrates single-cell multiomics and CRISPR screening in prostate cancer organoids to reveal lineage-specific dependencies and heterogeneity effects on gene essentiality.

Chronic alcohol exposure drives inflammaging and transposon derepression in hematopoietic stem and progenitor cells

This study shows chronic alcohol exposure leads to inflammation, DNA damage, and transposon activation in hematopoietic stem and progenitor cells, with lasting effects on myeloid bias and immune responses.

In vivo measurement and prediction of cell-type-resolved non-coding variant effects in human immunity

The paper measures and predicts non-coding variant effects in human immune cells using single-cell ATAC-seq and whole-genome sequencing, revealing regulatory mechanisms and applications in systemic lupus erythematosus.

PEPR-GNN: Perturbation-Enhancer-Promoter-RNA Graph Neural Networks for Multiome Perturb-Seq modeling of regulomes

The paper introduces PEPR-GNN, a graph neural network framework to model regulome responses during genetic perturbations using Multiome Perturb-Seq data.

Toward a probabilistic definition of chromatin accessible regions at the single-cell level

The paper introduces a probabilistic framework to define chromatin accessibility in single-cell snATAC-seq data, avoiding arbitrary thresholds and providing a dynamic understanding of accessible regions.

CSFeatures improves identification of cell type-specific differential features in single-cell and spatial omics data

CSFeatures identifies cell type-specific differential features in single-cell and spatial omics data by considering expression levels, smoothness, and proportion across cell populations.

Conservation of transcriptional regulatory networks in zebrafish and human periderm facilitates identification of GRHL1 as an orofacial cleft risk gene

The paper identifies GRHL1 as an orofacial cleft risk gene by analyzing conserved transcriptional regulatory networks between zebrafish and human periderm using single-cell multiome sequencing and functional validation.

CHAMPOLLION: Robust Multi-Omics Integration via Inverse Optimal Transport Using Paired Cells

CHAMPOLLION improves multi-omics integration by using regularized optimal transport to align unpaired cells and reveal cross-modal relationships, outperforming existing methods with fewer paired cells.

Connecting polygenic disease risk to cell states and regulatory programs through single-cell chromatin accessibility

SCADS integrates GWAS data with scATAC-seq to identify disease-relevant cell states and regulatory programs, showing heterogeneity in immune cell types for inflammatory bowel disease.

Single-nucleus multiome sequencing identifies candidate regulators of mouse gastric epithelial homeostasis

Geometry aware graph attention networks to explain single-cell chromatin state and gene expression

SEAGALL uses geometry-aware graph attention networks to extract biologically relevant features from single-cell data, revealing cell identity drivers beyond marker genes.

Predicting enhancer-gene links from single-cell multi-omics data by integrating prior Hi-C information

This paper introduces SCEG-HiC, a machine learning method that predicts enhancer-gene links using single-cell multi-omics data and Hi-C prior knowledge, showing improved performance over existing models.

Ancient regulatory evolution shapes individual language abilities in present-day humans

Polygenic score variants in HAQERs (Human Ancestor Quickly Evolved Regions, <0.1% of the genome) predict spoken language but not nonverbal IQ; language associations replicate in SPARK, ABCD and UK Biobank.

Nuclear Factor I genes drive chondrogenic cell-fate commitment

The paper maps chondrogenic cell-fate trajectories in hiPSCs using scRNA-seq and scATAC-seq, identifying NFIA and NFIB as key regulators driving chondrogenic commitment.

Epigenetically constrained astrocyte states underlie prefrontal cortex vulnerability in Down syndrome associated Alzheimer disease

The paper identifies a vulnerable astrocyte state in the prefrontal cortex of Down syndrome-associated Alzheimer's disease through integrated single-nucleus RNA-seq and ATAC-seq analysis.