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.

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.

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 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.

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.

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.

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.

Quantifying distribution shifts in single-cell data with scXMatch

scXMatch quantifies distribution shifts between single-cell data from different conditions using a non-parametric graph-based test, showing robust performance across gene expression, chromatin accessibility, and morphology data.

Epigenetic progression of pancreatic cancer to aggressive subtypes involves alternate routes of lineage reprogramming in subtype-intermediate progenitor cells

The paper identifies subtype-intermediate progenitor cells in pancreatic cancer with distinct epigenetic profiles linked to clinical outcomes and lineage reprogramming.

AtlasOT - The Fused Unbalanced Gromov-Wasserstein for Multimodal Integration of Disease Atlases

AtlasOT improves multimodal integration of disease atlases by addressing unpaired data constraints through a novel optimal transport framework.

MoTRUST: adaptive semantic protection for mosaic single-cell integration and molecular recovery

MoTRUST integrates mosaic single-cell multi-omics data and recovers missing molecular information, achieving top performance in integration and recovery tasks.

Mapping heterogeneity drivers in human PSC-derived limbal stem cell differentiation through single-cell multi-modal analysis

The paper uses single-cell multi-modal analysis to identify molecular drivers of limbal stem cell differentiation from human PSCs, revealing key transcription factors and enhancers involved in lineage specification.

Multi-Omics Integration Predicts Cell-Specific Gene Regulatory Response and Rhizosphere Dynamics in Maize Root Fertilizer Treatment

This study integrates multi-omics data to predict cell-specific gene regulatory responses and rhizosphere dynamics in maize roots under fertilizer treatments.

DeepSCENIC: transfer learning from sequence-to-function models enables causal gene regulatory network inference

DeepSCENIC uses transfer learning from sequence-to-function models to infer causal gene regulatory networks from single-cell multiome data.

Single-cell multiomic QTL mapping reveals state-dependent genetic regulation and associated gene during cellular senescence

The paper uses single-cell multiome data to identify QTLs regulating gene expression and chromatin accessibility during cellular senescence, revealing new causal variants and regulatory mechanisms.

Mammalian spermatogenesis at single-cell resolution downstream of genetic perturbations in meiotic double-strand break repair

Single-nucleus RNA+ATAC profiling of 32 mice shows asymmetric PRDM9 binding drives asynapsis, pachytene cell loss, aneuploidy and multi-megabase crossover redistribution, tuned by a chromosome 15 locus.

Single-Cell Indel Detection Enhances Genetic Ancestry and Cellular Lineage Analysis

Monopogen-Indel calls germline indels from single-cell and single-nucleus RNA data at 73.0% (retina) and ~87% (ovarian cancer) WGS-validated precision, though no single-cell somatic indel matched a WGS somatic indel.

A single-nucleus regulatory atlas links transposable elements to adult hippocampal neurogenesis

This study uses snATAC-seq and snRNA-seq to identify TE-derived regulatory elements involved in adult hippocampal neurogenesis in response to rhEPO stimulation.

NAE1-Dependent Protein Neddylation Preserves Endothelial Identity and Vascular Integrity

This study shows that NAE1-dependent neddylation maintains endothelial identity and vascular integrity by preventing pyroptosis and inflammation.

BatchRefiner: fast, significant improvement in batch integration of single-cell embeddings with ensemble refinement

BatchRefiner improves batch integration of scRNA-seq and scATAC-seq embeddings by ensemble refinement, showing significant performance gains across datasets and metrics.

MultiFlow: coupled flow matching for predicting single-cell multiomic perturbation responses in unseen cellular contexts

MultiFlow predicts single-cell multiomic perturbation responses by jointly modeling gene expression and chromatin accessibility across cellular contexts.

Regulatory logic of neuronal differentiation in the Drosophila visual system

The paper identifies cell-type-specific enhancers and regulatory codes for neuronal differentiation in Drosophila using single-cell RNA and ATAC sequencing.

Divergent malignant evolution converges on shared immunosuppressive ecosystems through tumor-intrinsic TMED2-ADAR1-dependent complement signalling in multifocal hepatocellular carcinoma

This study identifies shared immunosuppressive mechanisms in multifocal hepatocellular carcinoma despite divergent tumor evolution, highlighting a TMED2-ADAR1-C3/C5 complement axis as a potential therapeutic target.

A single-cell map of hypertension

This study maps the molecular landscape of hypertension using single-cell data from multiple organs and models, linking genetic variants to disease mechanisms.

Move BeTween modAlities (MBTA) employs flow matching to predict single cell data modalities

MBTA uses flow matching to address structural mismatch between molecular modalities, improving cross-modal translation and enabling multimodal analysis in single-cell data.

Molecular Disease Stages of Oligodendrocytic and Neuronal Tau Burden in Progressive Supranuclear Palsy

This paper identifies molecular progression trajectories in PSP by integrating snATACseq and snRNAseq data with tau pathology, revealing cell-type-specific transcriptional changes and glial reactivity.