scATAC-seq

Empirical Estimation of Ambient Contamination in Combinatorial Single-Cell Methods Using Multi-Reference Mapping

The paper introduces methods to estimate and remove ambient contamination in scifi-ATAC data, improving the accuracy of chromatin profiles and biological discovery.

Explainable Machine Learning and Epigenomic Profiling Decipher the Topological Determinants of Lentiviral Integration and Longitudinal Persistence in SCID-X1 Gene Therapy

The paper uses machine learning and epigenomic profiling to identify determinants of lentiviral integration and persistence in SCID-X1 gene therapy, finding significant depletion of persistent clones near proto-oncogenes.

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.

Cell type-resolved chromatin accessibility clocks for brain aging

The paper develops cell type-specific chromatin accessibility clocks using snATAC-seq data to predict age and detect aging-related changes in the brain.

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.

High-Specificity Detection of Chromosomal Mosaicism Reveals Cell-Type-Specific Genomic Alteration Patterns in Aging Tissues

CHASM detects chromosomal copy number alterations in single-cell data, revealing age-related genomic instability in specific cell types and states.

BRD4 represses developmental and neuronal genes through interaction with PRC1.6

Acute BRD4 degradation and BD2 mutations de-repress bivalent developmental and neuronal genes in human stem cells and organoids, consistent with BRD4 recruitment by H3K14ac/H3K23ac and interaction with PRC1.6.

GAMETE maps the genetic architecture of chromatin accessibility in rice pollen at single-nucleus resolution

GAMETE maps chromatin accessibility genetic architecture in rice pollen using single-nucleus ATAC-seq and genotype inference, revealing cell-type-specific caQTLs and chromatin dynamics.

Epithelial-Intrinsic Alterations and Maladaptation to Luminal Metabolites Underlie Persistent Crohn's Disease Pathogenesis

The paper investigates whether persistent inflammation in Crohn's disease is due to environmental triggers or intrinsic epithelial changes by comparing organoid and tissue data from patients in remission.

Chromatin Accessibility Shapes Developmental-Specific Lineage Plasticity in Hematopoiesis

The paper shows fetal hematopoietic stem and progenitor cells (HSPCs) have greater lineage plasticity than adult HSPCs, linked to chromatin accessibility differences.

Single-cell lineage tracing of human neuromesoderm organoids reveals TBX6-mediated posterior mesoderm fate diversification

The paper uses single-cell lineage tracing and multiomics profiling to map human neuromesoderm differentiation, revealing TBX6's role in posterior mesoderm fate diversification.

simPIC: flexible simulation of single-cell ATAC-seq paired-insertion counts from individuals to populations

simPIC simulates single-cell ATAC-seq count data across individuals and populations to enable controlled evaluation of chromatin accessibility QTL mapping methods.

Deep learning enables cross-species annotation and attribution of ageing states in haematopoietic stem and immune cells

The paper develops a cross-species deep learning framework to annotate and attribute ageing states in haematopoietic stem and immune cells, achieving high AUROC scores in human data.

Single-cell multimodal profiling of pan-cancer cell lines uncovers gene regulatory principles underlying intrinsic cell states and environmental features

This study constructs a pan-cancer single-cell multi-omic atlas to uncover gene regulatory principles in cancer cell states and environmental features across diverse cancer types.

An Integrative Single-Cell Epigenomic Atlas Annotates the Regulatory Genome of the Adult Mouse Brain

The paper constructs an integrative single-cell epigenomic atlas of the adult mouse brain, mapping chromatin states and gene regulatory programs across 100 cell subclasses.

Easy-Multiome enables joint profiling of gene expression and chromatin accessibility in single cells

Easy-Multiome enables joint profiling of gene expression and chromatin accessibility in plant single cells with high efficiency and minimal workflow changes.

Flexible and high-throughput simultaneous profiling of gene expression and chromatin accessibility in single cells

The paper introduces easySHARE-seq, a method for simultaneous single-cell ATAC-seq and RNA-seq, showing improved transcript recovery and scalability in murine liver nuclei.

Large-scale single-cell mapping of concealed mitochondrial ageing

The paper maps concealed mitochondrial DNA mutations across 2.7 million cells from 311 individuals, finding that low-prevalence mutations accumulate with age and predict human age.

Single-cell analysis of chromatin accessibility and gene expression in Drosophila melanogaster embryos following hypoxia treatment

This study examines hypoxia's effects on Drosophila embryos by analyzing chromatin accessibility and gene expression, identifying dose-dependent changes and a critical role for the tramtrack gene in germ cell development.

scWeave: A deep learning model that bidirectionally translates between gene expression and chromatin structure at single cell resolution

scWeave translates between gene expression and chromatin structure at single-cell resolution using deep learning, improving cross-modality inference across multiple datasets.

Single-cell multi-omic analyses resolve the cellular diversity of ALK/ROS1/MET/NTRK-fused gliomas in infants and older children

The paper uses single-cell and spatial multi-omic analyses to characterize cellular diversity in RTK-fused gliomas across pediatric age groups, identifying distinct cancer cell states and myeloid subgroups.