scATAC-seq

gcat, its_a_scam: modular tools for single cell data processing and per-cellquality control

The paper introduces gcat and its_a_scam, modular tools for single cell genomic data processing and quality control, showing they produce results comparable to proprietary pipelines.

CloneVI: A deep generative model for deciphering the relationships between cell state and mitochondrial genotype

CloneVI infers clonal structure from cell states in single-cell RNA-seq and ATAC-seq data, linking mitochondrial DNA mutations to specific cell states.

VIGAT: VLM-guided gene activity quantification from single-cell ATAC-seq

VIGAT uses a vision-language model to quantify gene activity from single-cell ATAC-seq by analyzing accessibility patterns and genomic annotations across marker genes.

A single-cell multimodal foundation model enables cross modality analysis between transcriptome and chromatin

MUTUAL enables cross-modality analysis between transcriptome and chromatin by learning a shared RNA-ATAC space from multiome data without refitting.

Impact of Rare and Common Genetic Variation on Cell Type-Specific Gene Expression

Single-cell eQTL mapping in 5.4 million PBMCs from 1,925 individuals with matched WGS finds common-variant eQTLs for 83% and rare-variant signals for 47% of 21,404 genes.

Genetic integration with cell-specific nucleosome positioning resolves causal relationships underlying chromatin accessibility profiles

The paper maps cell type-specific genetic effects on nucleosome-free regions and nucleosome occupancy using snATAC-seq data from human muscle biopsies, showing causal relationships between these elements and GWAS traits.

Perinatal Elimination of Genetically Aberrant Neurons from Human Cerebral Cortex

The paper investigates somatic copy number variants (CNVs) in human neurons across development, finding that perinatal elimination of neurons with aberrant genomes reduces CNV prevalence and targets dosage-sensitive genes.

Single-cell multiomics reveals archetypal regulatory programs shared across CD4 and CD8 T cell subsets in viral infection

Single-Cell Sequencing in Pediatric Acute Leukemia: A Systematic Review of Biologic Insights and Translational Potential

This review evaluates single-cell sequencing findings in pediatric acute leukemia, highlighting insights into clonal evolution, chemoresistance, and immune dynamics, while noting limitations in study design and bias.

Denoising single-cell ATAC-seq data with Shannon entropy

This paper introduces a Shannon entropy-based method to filter high-quality nuclei in scATAC-seq data, improving signal-to-noise ratio and downstream analysis reliability.

multiomeR: a pipeline for reproducible analysis of large-scale single-nucleus Epi Multiome datasets

multiomeR provides a reproducible R pipeline for analyzing large-scale single-nucleus Epi Multiome datasets, improving efficiency and reducing memory usage compared to existing workflows.

Single-nucleus chromatin accessibility time course of excisional wound repair in rat skin

The paper presents a time-course single-nucleus ATAC-seq dataset from rat skin wounds, revealing chromatin accessibility changes across repair phases.

MOFI reveals dynamic multi-omics coordination during cell fate progression

MOFI reconstructs continuous cell fate transitions from paired multi-omics snapshots across time, revealing coordinated changes in transcriptomic, chromatin, and protein layers.

Same-cell mapping of epigenetic regulatory state to functional proteomic output

Proteo-Seq links chromatin accessibility and proteomic output in the same cell, revealing new protein-defined states in breast cancer cells.

Cyclic Hypoxia drives Wnt5a-ROR1 stroma-tumor crosstalk promoting breast cancer growth

This study shows cyclic hypoxia promotes breast cancer growth through WNT5A-ROR1 signaling between stromal and tumor cells in a co-culture model.

Autonomous Dampening of Wnt Signaling Selects Zebrafish Spinal Cord Progenitors for an Oligodendrocyte Fate

The paper identifies pre-OPCs in zebrafish spinal cord and shows that Wnt signaling modulation influences oligodendrocyte fate through gene expression and chromatin accessibility.

Single-Cell Multimodal Profiling Reveals Maternal Diabetes-Nkx2-5 Interaction in Congenital Heart Disease in a Genetic Model Recapitulating Human Embryopathies

The paper shows that maternal diabetes and Nkx2-5 haploinsufficiency together cause severe cardiac defects in mice, with single-cell multiomic data revealing transcriptional and chromatin changes.

A surviving beta cell subpopulation enriched in patients with T1D

Regulon-based clustering of islet scRNA-seq finds an IRF1-high, cytokine-driven beta cell state with reduced identity and autoantigen genes, enriched in type 1 diabetes donors.