scATAC-seq

Integrative single-nucleus multi-omics profiling identifies candidate regulators and signaling axes in Alzheimer's disease lipid-processing microglia

The paper identifies candidate regulators and signaling axes in Alzheimer's disease lipid-processing microglia through multi-omics analysis across multiple cohorts.

High-resolution reconstruction of cell-type specific transcriptional regulatory processes from bulk sequencing samples

This paper introduces DeepDETAILS, a method to reconstruct cell-type-specific genomic signals from bulk data, outperforming traditional methods and providing insights into disease mechanisms.

Semantic fragment representations for coordinate-free analysis of genomics data

The paper introduces LEAF-1, a fragment-level foundation model for genomics data analysis, showing it can classify cell types and detect cancer from sparse datasets and cell-free DNA.

Pre-existing chromatin accessibility primes δ-cells for injury-induced endocrine plasticity

This study shows that pre-existing chromatin accessibility in δ-cells enables their conversion into hybrid cells after β-cell loss in zebrafish, facilitating endocrine plasticity.

The developing midbrain hindbrain boundary contains molecularly distinct cell populations

The paper identifies molecularly distinct cell populations in the zebrafish isthmic region using scMultiome and validates findings in vivo.

TMO: ASYMMETRIC CROSS-MODAL ATTENTION FOR LEARNING CELL-STATE-DEPENDENT REGULATORY LAGS FROM SINGLE-CELL MULTIOMIC DATA

TMO learns cell-state-dependent regulatory lags between chromatin accessibility and gene expression using asymmetric cross-modal attention, achieving high Lag Concordance Scores on multi-omic datasets.

Early cell autonomous and niche-mediated alveolar epithelial response to influenza infection in primary lung organoids

This study models early IAV infection in alveolar organoids, revealing conserved AT2 cell responses and uninfected cell state transitions driven by inflammation.

Multiregional single-cell profiling reveals shared and specialized cellular vulnerability in Alzheimer's disease

This study uses single-nucleus RNA-seq, ATAC-seq, and Multiome to analyze Alzheimer's disease across multiple brain regions, revealing shared and region-specific cellular vulnerabilities.

MintCNA: A Unified Framework for Integrative Copy Number Profiling with Single-Cell Multi-Omics Data

MintCNA improves CNA detection in single-cell multi-omics data by integrating deep learning and multivariate change-point detection, outperforming existing methods in simulations and showing strong correlation with bulk sequencing.

Single cell analysis of HIV expression and integration sites reveals robust viral expression across diverse chromatin environments

The paper analyzes HIV integration sites and expression in CD4 T cells, finding no significant variation in viral expression based on integration site features but identifying insertional activation of host genes in some cells.

A Simple, Cost-Effective, High-Throughput Method for Measuring Chromatin Accessibility and Gene Expression in Single Nuclei

The paper introduces and benchmarks two droplet-based single-nucleus assays for chromatin accessibility and gene expression, showing they are cost-effective and produce high-quality data.

ATAClone: Cancer Clone Identification and Copy Number Estimation from Single-cell ATAC-seq

ATAClone identifies cancer clones and estimates copy numbers from scATAC-seq data, improving accuracy over existing methods.

HoloCell: A Generative Foundation Model for Holistic Cellular Modeling

HoloCell is a generative foundation model that integrates epigenomics, transcriptomics, and proteomics data across single-cell multi-omics modalities, demonstrating superior performance in representation learning and cross-modal generation.

A Multimodal Single-Cell Epigenomic and 3D Genome Atlas of the Human Basal Ganglia

This paper creates a multimodal single-cell atlas of the human basal ganglia, revealing epigenomic and 3D genome features across cell types and linking them to disease-associated genetic risk.

ATLAS: a scverse-compatible package for multi-omic single-cell trajectory inference integration

ATLAS integrates single-cell RNA-seq and ATAC-seq data to improve trajectory inference by jointly analyzing transcriptomic and chromatin accessibility information.

Cross-species chromatin accessibility pinpoints HIVEP3 as a driver of thymic epithelial maturation and self-antigen expression, preventing chronic inflammation

This study identifies HIVEP3 as a critical regulator of thymic epithelial maturation and self-antigen expression, with its deficiency causing chronic inflammation.

Single-cell multiomic approaches define a gradual, spatially-regulated epigenetic and transcriptional transition from embryonic to adult neural stem cells

Disentangling covariate effects on single cell-resolved epigenomes with DeepDive

DeepDive disentangles covariate effects on single-cell epigenomes, enabling counter-factual analyses and identifying diabetes-linked beta cell subtypes.

Single-cell chromatin tracing reveals multimodal molecular programs during memory formation

The paper develops ChromTRAP to identify recently activated neuronal ensembles and reveals brain-region- and cell-type-specific regulatory programs during learning.

Foxf1 is required for the specification and maintenance of pulmonary capillary identity

This study identifies Foxf1 as essential for maintaining pulmonary capillary identity in mice, with implications for human disease.

PRC2 complex subunit JARID2 regulates embryonic pituitary stem cell differentiation to the POMC lineage

The paper shows that JARID2 promotes pituitary stem cell differentiation to the POMC lineage by regulating chromatin landscapes and gene expression.

Somatic variant detection in normal tissues from single-cell sequencing data

This study evaluates somatic variant calling in normal tissues using single-cell RNA and ATAC sequencing, showing Monopogen outperforms other tools in accuracy and sensitivity.

A multi-omics map of diabetic nephropathy links c-Jun activation to tubular injury and metabolic stress

This study integrates multi-omics data to identify c-Jun as a key driver of tubular injury and fibrosis in diabetic nephropathy.

Conserved Cell Type Signatures Across the Brainstem and Spinal Cord in the Mouse Central Nervous System

The paper maps conserved cell type signatures in the adult mouse brainstem and spinal cord using multi-omics data, revealing shared and region-specific features.

Robust footprinting with sample-specific Tn5 bias correction for bulk and single cell ATAC-seq

This paper introduces TraceBIND, a method to correct Tn5 bias in ATAC-seq data, improving TF footprint detection and revealing age-related regulatory changes in scATAC-seq.

Single-nucleus multiomics unveils malignant cellular states, regulatory architectures and microenvironmental reorganization across the G-CIMP epigenomic transition in IDH-mutant glioma

The paper integrates single-nucleus RNA and ATAC sequencing to identify cellular states and regulatory networks associated with the G-CIMP epigenomic transition in IDH-mutant gliomas.

Single-Cell Multi-Omics Dissection of Malignant Evolutionary Mechanisms and Construction of a Prognostic Model for Clear Cell Renal Cell Carcinoma

The paper integrates single-cell multi-omics data to identify prognostic markers and mechanisms of progression in clear cell renal cell carcinoma.

Chromap Suite: an open-source single-binary platform for agentic multiomic RNA + ATAC profiling

Chromap Suite provides an open-source, single-binary platform for RNA + ATAC multiomic profiling with improved speed and memory efficiency compared to proprietary tools.

ArchVelo: Archetypal Velocity Modeling for Single-cell Multi-omic Trajectories

ArchVelo models gene regulation and infers cell trajectories using scATAC-seq and scRNA-seq data, improving accuracy and identifying new differentiation trajectories in immune cells.

Architectural fragility of gene regulatory networks underlies hematopoietic stem cell aging

The paper analyzes single-cell multiome data from human HSPCs to show aging-related rewiring of gene regulatory networks, leading to stress hyperactivation, myeloid bias, and identity loss.