Single-cell chromatin state analysis with Signac.
paper
Cited
Public
- Authors
- Stuart, Tim; Srivastava, Avi; Madad, Shaista; Lareau, Caleb A; Satija, Rahul
- Year
- 2021
- Journal
- Nature methods
- PMID
- 34725479
- DOI
- 10.1038/s41592-021-01282-5
- PMCID
- PMC9255697
The recent development of experimental methods for measuring chromatin state at single-cell resolution has created a need for computational tools capable of analyzing these datasets. Here we developed Signac, a comprehensive toolkit for the analysis of single-cell chromatin data. Signac enables an end-to-end analysis of single-cell chromatin data, including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis and interactive visualization. Through its seamless compatibility with the Seurat package, Signac facilitates the analysis of diverse multimodal single-cell chromatin data, including datasets that co-assay DNA accessibility with gene expression, protein abundance and mitochondrial genotype. We demonstrate scaling of the Signac framework to analyze datasets containing over 700,000 cells.
Single-cell chromatin analysis workflow with Signac.a, Overview of key steps comprising analysis of single-cell chromatin data with Signac. All analysis tasks can be completed with one or multiple fragment files as input. b, Design of a custom Assay for single-cell chromatin data. We designed a specialized ChromatinAssay class with the capacity to store data required for analysis of single-cell chromatin datasets. c, ChromatinAssay objects can be stored side by side with standard Assay objects in a Seurat object to enable analysis of multimodal single-cell data.
Integrative single-cell analysis of gene expression and DNA accessibility in human PBMCs.a, Nucleosome signal QC metric distribution and DNA fragment length distribution for the DNA accessibility assay. b, TSS enrichment score distribution and Tn5 insertion frequency at TSS sites for the DNA accessibility assay. c, UMAP representation of the multimodal human PBMC dataset, with cells annotated by predicted cell type. UMAP was constructed from the DNA accessibility assay. Treg, regulatory T cell; TEM, effector memory T cell; cDC, conventional dendritic cell; pDC, plasmacytoid dendritic cell; HSPC, hematopoietic stem and progenitor cell; MAIT, mucosal-associated invariant T cell. d, Multimodal label transfer accuracy. Multimodal single-cell data were split into DNA accessibility and gene expression assays and multimodal label transfer performed between pseudo-scRNA-seq and pseudo-scATAC-seq datasets. e, DNA sequence motifs for top overrepresented TF motifs between CD8+ effector and naive T cells. f, chromVAR32 deviations for top enriched DNA sequence motifs (EOMES, TBX21, TBX2) for CD8+ effector (CD8 TEM) and naive CD8+ (CD8 naive) T cells. g, RNA expression for EOMES, TBX21 and TBX2 genes in CD8+ effector and naive T cells. h, TF footprinting analysis for EOMES and TBX21 motifs sites. i, Distribution of peak-to-gene link P values for all reported links. P values were determined by a one-sided z-test without multiple testing correction. j, Distances from peak to linked gene TSSs, for positive- and negative-coefficient peakβgene links. k, Total number of positive-coefficient and negative-coefficient peakβgene links for each linked gene (top) and peak (bottom). l, Representative example peakβgene links for key immune genes.
Evaluation of dimension reduction methods for single-cell chromatin data.a, UMAP representations of reduced-dimension single-cell DNA accessibility data for LSI (Signac), SCALE and SnapATAC for the full dataset and with the total number of counts per cell downsampled to 20% of the total counts. b, Runtimes for each of the dimension reduction methods profiled. CisTopic CGS, cisTopic collapsed Gibbs sampling; cisTopic Warp: cisTopic Warp-LDA. c, Mean k-NN cell type purity (k = 100) and (d) mean Silhouette score for each cell type in the dataset, for each dimension reduction method and downsampling level. For each box-plot, n = 20 points (cell types). For each box-plot, n = 6 points (cell types). Box-plot lower and upper hinges represent first and third quartiles. Upper/lower whiskers extend to the largest/smallest value no further than 1.5Γ the interquartile range. Data beyond the whiskers are plotted as single points.
Joint analysis of mitochondrial genotypes and DNA accessibility in single cells.a, UMAP plot for cells from a tumor from a patient with CRC profiled by scATAC-seq, with the major cell types annotated. b, Variance-to-mean ratio versus strand concordance (Pearson correlation between strand coverage) for mitochondrial genome variants. High confidence, highly variable mitochondrial genome sites are shown in red. c, Per-cell allele frequencies (fraction heteroplasmy) for two representative mitochondrial genome variants used to identify cell clones. d, Fraction of cells belonging to each clone that were assigned to each cell type, normalized for the total number of cells belonging to each cell type. e, Differentially accessible regions of the nuclear genome between epithelial cell clones.
Scalable analysis of single-cell chromatin data.a, UMAP representation of the full human PBMC scATAC-seq dataset of 26,579 nuclei. b, Runtimes for key analysis steps for ArchR and Signac, for each downsampled PBMC scATAC-seq dataset. c, Total runtime for an end-to-end analysis of the full PBMC scATAC-seq dataset for ArchR and Signac using eight cores. d, UMAP representation of the full BICCN adult mouse brain dataset of 734,000 nuclei. Cells are colored by their cell type label given by the original study authors53. e, Runtimes for key analysis steps for ArchR and Signac, for each downsampled BICCN scATAC-seq dataset. f, Total runtime for an end-to-end analysis of the full BICCN scATAC-seq dataset for ArchR and Signac using eight cores.
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| Molecular and cellular processes disrupted in the early postnatal Down syndrome prefrontal cortex. | Risgaard RD et al. | β | 2026 | β |
| Molecular and Chromatin Accessibility Programs Underlying Epithelial Injury and Impaired Regeneration in Neonatal Necrotizing Enterocolitis. | Xiong Y et al. | β | 2026 | β |
| Multimodal analyses of early, untreated systemic sclerosis skin identify a proinflammatory vascular niche of macrophage-fibroblast signaling. | Jarnagin HC et al. | β | 2026 | β |
| Multimodal-based analysis of single-cell ATAC-seq data enables highly accurate delineation of clinically relevant tumor cell subpopulations. | Xiong K et al. | β | 2026 | β |
| Multi-modal dissection of cell-type specific TDP-43 pathology in the motor cortex. | Ruf WP et al. | β | 2026 | β |
| Multiomic single-cell perturbation screens reveal critical lncRNA regulators of senescence. | Zhu S et al. | β | 2026 | β |
| Multiomic single nuclei profiling the mouse hippocampus reveals that ACSS2 confers neuronal resilience to tauopathy. | Egervari G et al. | β | 2026 | β |
| NFAT mediates pro-tumorigenic inflammation in cancer-associated fibroblasts in pancreatic ductal adenocarcinoma. | Guo C et al. | β | 2026 | β |
| Ontogeny Dictates Oncogenic Potential, Lineage Hierarchy, and Therapy Response in Pediatric Leukemia. | Wang K et al. | β | 2026 | β |
| Organ injury in systemic autoimmunity is mediated by stem-like CD8<sup>+</sup> T cells arising from tissue-draining lymph nodes. | Al Souz J et al. | β | 2026 | β |
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| p53 inactivation drives breast cancer metastasis to the brain through SCD1 upregulation and increased fatty acid metabolism. | Laue K et al. | β | 2026 | β |
| Pan-Cancer Single-Cell RNA Sequencing Analysis Refines Multi-Origin Monocyte and Macrophage Lineages. | Nguyen TDT et al. | β | 2026 | β |
| PathCLAST: pathway-augmented contrastive learning with attention for interpretable spatial transcriptomics. | Noh M et al. | β | 2026 | β |
| Rare epigenetic alterations are conserved across hematopoietic differentiation stages after mycobacterial infection. | Tran BT et al. | β | 2026 | β |
| Reconstructing human pancreatic gene networks enhances stem cell-derived Ξ² cell induction. | Yu XX et al. | β | 2026 | β |
| Reducing methylation of histone 3.3 lysine 4 in the medial ganglionic eminence and hypothalamus recapitulates neurodevelopmental disorder phenotypes. | Li J et al. | β | 2026 | β |
| scII: Dual-Threshold Adaptive Integration of Single-Cell Multiomics Data Driven by Imputation. | Zhang Y et al. | β | 2026 | β |
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| Single-cell analysis reveals cytotoxic and memory CD8<sup>+</sup> T cells associated with prolonged survival in relapsed/refractory leukaemia patients after haplo+cord haematopoietic stem cell transplantation. | Li H et al. | β | 2026 | β |
| Single-cell and multi-omics integrative modeling identifies mitochondrial gene HSPE1 as a therapeutic target in osteosarcoma. | Pan S et al. | β | 2026 | β |
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| Single-cell epigenetic profiling reveals a tumor-intrinsic interferon response program in ccRCC tied to poor prognosis and <i>BAP1</i> loss. | Camp SY et al. | β | 2026 | β |
| Single-cell eQTL mapping reveals cell-type-specific genetic regulation in lung cancer. | Fu Y et al. | β | 2026 | β |
| Single cell multiomic analysis of the impact of Delta-9-tetrahydrocannabinol on HIV infected CD4 T cells. | Ashokkumar M et al. | β | 2026 | β |
| Single cell multiomic landscape reveals gene programs driving lipid droplet heterogeneity in hepatic steatosis. | Sehrawat TS et al. | β | 2026 | β |
| Single Cell Multiomics of Hooked Potato Stolons Reveals Parallels to Shoot Apical Meristems in Arabidopsis. | Martin D et al. | β | 2026 | β |
| Single-cell polygenic risk scores dissect cellular and molecular heterogeneity of complex human diseases. | Zhang S et al. | β | 2026 | β |
| Single-cell profiling of trabecular meshwork identifies mitochondrial dysfunction in a glaucoma model that is protected by vitamin B3 treatment. | Tolman N et al. | β | 2026 | β |
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| Single-cell spatiotemporal dissection of the human maternal-fetal interface. | Wang C et al. | β | 2026 | β |
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| Single-nucleus epigenomic profiling of the adult human central nervous system unveils epigenetic memory of developmental programs. | Kabbe M et al. | β | 2026 | β |
| Single-nucleus multi-omics analysis of mouse small-intestinal Lgr5+ cell populations reveals Foxa3-induced Paneth cell-lineage differentiation. | Deng X et al. | β | 2026 | β |
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| Single-nucleus transcriptional and chromatin accessibility analyses of maturing mouse Achilles tendon uncover the molecular landscape of tendon stem/progenitor cells. | Tsutsumi H et al. | β | 2026 | β |
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| A high-resolution meiotic crossover map from single-nucleus ATAC-seq reveals insights into the recombination landscape in mammals. | Novakovic S et al. | β | 2025 | β |
| A Human Immuno-Lung Organoid Model to Study Macrophage-Mediated Lung Cell Senescence Upon SARS-CoV-2 Infection. | Han Y et al. | β | 2025 | β |
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| AS04 drives superior cross-protective antibody response by increased NOTCH signaling of dendritic cells and proliferation of memory B cells. | D'Onofrio V et al. | β | 2025 | β |
| A single-cell multi-omics atlas of rice. | Wang X et al. | β | 2025 | β |
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| A stem cell differentiation model reveals two alternative fates in CBFA2T3::GLIS2-driven acute megakaryoblastic leukemia initiation. | Shoeb MR et al. | β | 2025 | β |
| B cells modulate lung antiviral inflammatory responses via the neurotransmitter acetylcholine. | Cembellin-Prieto A et al. | β | 2025 | β |
| BCOR and ZC3H12A suppress a core stemness program in exhausted CD8+ T cells. | Xu J et al. | β | 2025 | β |
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| BIT: Bayesian Identification of Transcriptional regulators from epigenomics-based query region sets. | Lu Z et al. | β | 2025 | β |
| BLIMP-1-dependent differentiation of T follicular helper cells into Foxp3<sup>+</sup> T regulatory type 1 cells. | Garnica J et al. | β | 2025 | β |
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| C/EBPΞ² transcription factor promotes alcohol-induced liver fibrosis in males via HDL remodeling. | Schonfeld M et al. | β | 2025 | β |
| Cell states and neighborhoods in distinct clinical stages of primary and metastatic esophageal adenocarcinoma. | Yates J et al. | β | 2025 | β |
| Cell-type- and locus-specific epigenetic editing of memory expression. | Coda DM et al. | β | 2025 | β |
| Cell-type-aware regulatory landscapes governing monoterpene indole alkaloid biosynthesis in the medicinal plant Catharanthus roseus. | Li C et al. | β | 2025 | β |
| Cell type mapping of mild malformations of cortical development with oligodendroglial hyperplasia in epilepsy using single-nucleus multiomics. | GalvΓ£o IC et al. | β | 2025 | β |
| Cell type-specific multi-omics analysis of cocaine use disorder in the human caudate nucleus. | Zillich L et al. | β | 2025 | β |
| Cell type-specific purifying selection of synonymous mitochondrial DNA variation. | Lareau CA et al. | β | 2025 | β |
| CellWalker2: Multi-omic discovery using hierarchical cell type relationships. | Hu Z et al. | β | 2025 | β |
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| Chromatin accessibility landscape of mouse early embryos revealed by single-cell NanoATAC-seq2. | Li M et al. | β | 2025 | β |
| Chromatin accessibility provides a window into the genetic etiology of human brain disease. | Bendl J et al. | β | 2025 | β |
| ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning. | Saelens W et al. | β | 2025 | β |
| Chromatin landscape alteration uncovers multiple transcriptional circuits during memory CD8+ T-cell differentiation. | Liu Q et al. | β | 2025 | β |
| Chromatin landscape at cis-regulatory elements orchestrates cell fate decisions in early embryogenesis. | Cardamone F et al. | β | 2025 | β |
| Chromosomal instability in human trophoblast stem cells and placentas. | Wang D et al. | β | 2025 | β |
| Chronic exposure to glucocorticoids amplifies inhibitory neuron cell fate during human neurodevelopment in organoids. | Dony L et al. | β | 2025 | β |
| Combinatorial profiling of multiple histone modifications and transcriptome in single cells using scMTR-seq. | Wang Y et al. | β | 2025 | β |
| Combined single-cell profiling of chromatin-transcriptome and splicing across brain cell types, regions and disease state. | Hu W et al. | β | 2025 | β |
| Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution. | Chen Y et al. | β | 2025 | β |
| Comparative analysis of gene regulation in single cells using Compass. | Wan C et al. | β | 2025 | β |
| Comparative analysis of tongue cancer organoids among patients identifies the heritable nature of minimal residual disease. | Sase M et al. | β | 2025 | β |
| Comprehensive analysis of multi-omics single-cell data using the single-cell analyst. | Pan L et al. | β | 2025 | β |
| Comprehensive Characterization of Bihormonal Cells and Endocrine Cell Lineages in Mammalian Pancreatic Islets. | Yu XX et al. | β | 2025 | β |
| Comprehensive single-cell aging atlas of healthy mammary tissues reveals shared epigenomic and transcriptomic signatures of aging and cancer. | Angarola BL et al. | β | 2025 | β |
| Computational Analyses and Challenges of Single-cell ATAC-seq. | Wang C et al. | β | 2025 | β |
| Conservation of cis-regulatory codes over half a billion years of evolution. | Ogawa Y et al. | β | 2025 | β |
| Contextual regulation of T follicular helper cell expansion and differentiation into T regulatory type 1 cells by multiple transcription factors. | Garnica J et al. | β | 2025 | β |
| Continuous Activation of C/EBPΞ² Transcription Factor Prevents Fibrosis Resolution After Alcohol Cessation. | Schonfeld M et al. | β | 2025 | β |
| Control of quiescence and activation of human muscle stem cells by cytokines. | Striedinger K et al. | β | 2025 | β |
| Co-profiling of single-cell gene expression and chromatin landscapes in stickleback pituitary. | Liu L et al. | β | 2025 | β |
| CoTF-reg reveals cooperative transcription factors in oligodendrocyte gene regulation using single-cell multi-omics. | Choi JJ et al. | β | 2025 | β |
| CountASAP: a lightweight, easy to use python package for processing ASAPseq data. | Boughter CT et al. | β | 2025 | β |
| CREM is a regulatory checkpoint of CAR and IL-15 signalling in NK cells. | Rafei H et al. | β | 2025 | β |
| CTCF-anchored chromatin loop dynamics during human meiosis. | Kaiser VB et al. | β | 2025 | β |
| CXCL12 Drives Reversible Fibroimmune Remodeling in Androgenetic Alopecia Revealed by Single-Cell RNA Sequencing. | An S et al. | β | 2025 | β |
| DANSE: a pipeline for dynamic modelling of time-series multi-omics data. | Jansen Klomp LF et al. | β | 2025 | β |
| dbscATAC: a resource of single-cell super-enhancers/enhancers and gene markers derived from scATAC-seq data. | Li Y et al. | β | 2025 | β |
| Deciphering gene regulatory programs in mouse embryonic skin through single-cell multiomics analysis. | Deng Q et al. | β | 2025 | β |
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| Decoding DNA sequence-driven evolution of the human brain epigenome at cellular resolution. | Caglayan E et al. | β | 2025 | β |
| Decoding human cardiovascular development and disease through single-cell transcriptomic and epigenomic profiling. | Dunkenberger L et al. | β | 2025 | β |
| Decoding immune low-response states in sepsis: single-cell and 3D spatial transcriptomic insights into immunoparalysis. | Yang Y et al. | β | 2025 | β |
| Decoding per- and polyfluoroalkyl substances (PFAS) in hepatocellular carcinoma: a multi-omics and computational toxicology approach. | Hong Y et al. | β | 2025 | β |
| Decoding the germline genetic architecture of prostate cancer at a single cell resolution. | Wang C et al. | β | 2025 | β |
| Defining the regulatory logic of breast cancer using single-cell epigenetic and transcriptome profiling. | Regner MJ et al. | β | 2025 | β |
| Depth-corrected multi-factor dissection of chromatin accessibility for scATAC-seq data with PACS. | Miao Z et al. | β | 2025 | β |
| DiabetesOmic: A comprehensive multi-omics diabetes database. | Cai FH et al. | β | 2025 | β |
| Dietary methionine restriction started late in life promotes healthy aging in a sex-specific manner. | HernΓ‘ndez-Arciga U et al. | β | 2025 | β |
| Direct specification of lymphatic endothelium from mesenchymal progenitors. | Lupu IE et al. | β | 2025 | β |
| Discovery of oligodendrocyte enhancers that regulate Sox10 expression. | An H et al. | β | 2025 | β |
| Disrupted transcriptional networks regulated by CHD1L during neurodevelopment underlie the mirrored neuroanatomical and growth phenotypes of the 1q21.1 copy number variant. | LemΓ©e MV et al. | β | 2025 | β |
| Distinct gene regulatory dynamics drive skeletogenic cell fate convergence during vertebrate embryogenesis. | Wang M et al. | β | 2025 | β |
| Distinct mechanisms of transcriptomic habituation to repeated stress in the mouse hippocampus. | Waag R et al. | β | 2025 | β |
| Distinct transcriptomic and epigenomic responses of mature oligodendrocytes during disease progression in a mouse model of multiple sclerosis. | Zheng C et al. | β | 2025 | β |
| Distinct type I and II interferon responses direct cortical and medullary thymic epithelial cell development. | Mohammed A et al. | β | 2025 | β |
| Divergent FOXA1 mutations drive prostate tumorigenesis and therapy-resistant cellular plasticity. | Eyunni S et al. | β | 2025 | β |
| DNA hypomethylation traits define human regulatory T cells in cutaneous tissue and identify their blood recirculating counterparts. | Beumer N et al. | β | 2025 | β |
| DOGMA-seq and multimodal, single-cell analysis in acute myeloid leukemia. | Kim J et al. | β | 2025 | β |
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| Dynamics and variegation in the Treg response to Interleukin-2. | Seddu K et al. | β | 2025 | β |
| Dysfunctional KLRB1<sup>+</sup>CD8<sup>+</sup> T-cell responses are generated in chronically inflamed systemic sclerosis skin. | Gaydosik AM et al. | β | 2025 | β |
| Dysregulated RNA splicing impairs regeneration in alcohol-associated liver disease. | Chembazhi UV et al. | β | 2025 | β |
| Effective Integration of Single-Cell Multi-Omics Data Using Improved Network-Based Integrative Clustering with Multigraph Regularization. | Zhang S et al. | β | 2025 | β |
| Empowering integrative and collaborative exploration of single-cell and spatial multimodal data with SGS genome browser. | Xia T et al. | β | 2025 | β |
| Enhancing single-cell ATAC sequencing with formaldehyde fixation, cryopreservation, and multiplexing for flexible analysis. | Hohl T et al. | β | 2025 | β |
| EpiAgent: foundation model for single-cell epigenomics. | Chen X et al. | β | 2025 | β |
| Epidermal Loss of PRMT5 Leads to the Emergence of an Atypical Basal Keratinocyte-Like Cell Population and Defective Epidermal Stratification. | Recka N et al. | β | 2025 | β |
| Epithelial WNT secretion drives niche escape of developing gastric cancer. | Lee J et al. | β | 2025 | β |
| Establishment of a novel brainstem ischemic dysphagia model: single-cell sequencing reveals the molecular mechanisms underlying mPES intervention. | Tian Y et al. | β | 2025 | β |
| Evolutionary Process Underlying Receptor Gene Expansion and Cellular Divergence of Olfactory Sensory Neurons in Honeybees. | Zhang W et al. | β | 2025 | β |
| Evolving cell states and oncogenic drivers during the progression of IDH-mutant gliomas. | Wu J et al. | β | 2025 | β |
| Expression status transition ofΒ NOTCH1Β accompanies chromatin remodeling in human early retinal progenitor cells | Watabe Y et al. | β | 2025 | β |
| Facilitate integrated analysis of single cell multiomic data by binarizing gene expression values. | Misra R et al. | β | 2025 | β |
| FAP<sup>+</sup> fibroblasts orchestrate tumor microenvironment remodeling in renal cell carcinoma with tumor thrombus. | Ma J et al. | β | 2025 | β |
| Fate and state transitions during human blood vessel organoid development. | Nikolova MT et al. | β | 2025 | β |
| FOXR2 Targets LHX6+/DLX+ Neural Lineages to Drive Central Nervous System Neuroblastoma. | Jessa S et al. | β | 2025 | β |
| Frizzled5 controls murine intestinal epithelial cell plasticity through organization of chromatin accessibility. | Deng L et al. | β | 2025 | β |
| Functional characterization of eQTLs and asthma risk loci with scATAC-seq across immune cell types and contexts. | Wei J et al. | β | 2025 | β |
| Functional maps of a genomic locus reveal confinement of an enhancer by its target gene. | Eder M et al. | β | 2025 | β |
| Functional Specificity of Astrocyte Subtypes in Alzheimer's Disease: Decoding Disease Mechanisms Through Network-based Analysis of Integrated Single-Nuclei Multi-Omic Data. | Δ°lgΓΌn A et al. | β | 2025 | β |
| Functional, sustained recovery of hearing in Otoferlin-deficient mice using DB-OTO, a hair-cell-specific AAV-based gene therapy. | Chung Y et al. | β | 2025 | β |
| Galaxy single-cell & spatial omics community update: Navigating new frontiers in 2025. | Loach M et al. | β | 2025 | β |
| Generalization of the sci-L3 method to achieve high-throughput linear amplification for replication template strand sequencing, genome conformation capture, and the joint profiling of RNA and chromatin accessibility. | Chovanec P et al. | β | 2025 | β |
| Gene regulatory mechanisms guiding bifurcation of inhibitory and excitatory neuron lineages in the mouse anterior brainstem. | Kilpinen S et al. | β | 2025 | β |
| Genetic variation in IL-4 activated tissue resident macrophages determines strain-specific synergistic responses to LPS epigenetically. | Zhao M et al. | β | 2025 | β |
| GFI1-driven transcriptional and epigenetic programs maintain CD8<sup>+</sup> Tβcell stemness and persistence. | Chaudhry MZ et al. | β | 2025 | β |
| Guided co-clustering transfer across unpaired and paired single-cell multi-omics data. | Li H et al. | β | 2025 | β |
| HALO: hierarchical causal modeling for single cell multi-omics data. | Mao H et al. | β | 2025 | β |
| Heart failure-specific cardiac fibroblasts contribute to cardiac dysfunction via the MYC-CXCL1-CXCR2 axis. | Komuro J et al. | β | 2025 | β |
| Hepatic metabolic reprogramming in male mice during short-term caloric restriction involves enhanced glucocorticoid rhythms. | Makris K et al. | β | 2025 | β |
| HIF regulates multiple translated endogenous retroviruses: Implications for cancer immunotherapy. | Jiang Q et al. | β | 2025 | β |
| Histological signatures map anti-fibrotic factors in mouse and human lungs. | Guo JL et al. | β | 2025 | β |
| Human brain vascular multi-omics elucidates disease-risk associations. | Reid MM et al. | β | 2025 | β |
| Identification and characterization of human retinal stem cells capable of retinal regeneration. | Liu H et al. | β | 2025 | β |
| Identification of Crosstalk Genes Between Primary SjΓΆgren's Syndrome and Primary Biliary Cirrhosis by Transcriptome Analysis. | Tao T et al. | β | 2025 | β |
| Identification of mouse and human embryonic pancreatic cells with adult Procr<sup>+</sup> progenitor transcriptomic and epigenomic characteristics. | Heidenreich AC et al. | β | 2025 | β |
| IFN-I-mediated neutropoiesis bias drives neutrophil priming and inflammatory comorbidities. | Li Y et al. | β | 2025 | β |
| IL-27 producers in a neonatal BCG vaccination model are a heterogenous population of myeloid cells that are diverse in phenotype and function. | Divens AM et al. | β | 2025 | β |
| IMATAC imputes single-cell ATAC-seq data by deep hierarchical network with denoising autoencoder. | Li Y et al. | β | 2025 | β |
| Immune dysregulation in COVID-19 induced ARDS in kidney transplant recipients revealed by single-cell RNA sequencing. | Pang J et al. | β | 2025 | β |
| Immune microenvironment and prognostic genes of triple-negative breast cancer in the context of transcriptome and single-cell sequencing. | Huang X et al. | β | 2025 | β |
| Improving cellular fitness of human stem cell-derived islets under hypoxia. | Wang X et al. | β | 2025 | β |
| Inhibition of Glutamine Metabolism Attenuates Tumor Progression Through Remodeling of the Macrophage Immune Microenvironment. | Li T et al. | β | 2025 | β |
| Innate immune molecular landscape following controlled human influenza virus infection. | Thistlethwaite W et al. | β | 2025 | β |
| INSTINCT: Multi-sample integration of spatial chromatin accessibility sequencing data via stochastic domain translation. | Liu Y et al. | β | 2025 | β |
| Insulin signalling-associated cell fate promotes neoplastic invasiveness in non-functioning pituitary gonadotroph adenoma via cis-regulatory elements activation. | Liu H et al. | β | 2025 | β |
| Integrated omics reveals disease-associated radial glia-like cells with epigenetically dysregulated interferon response in multiple sclerosis. | Park B et al. | β | 2025 | β |
| Integrated single-cell multiome analysis reveals muscle fiber-type gene regulatory circuitry modulated by endurance exercise. | Rubenstein AB et al. | β | 2025 | β |
| Integrated single-cell multiomic profiling of caudate nucleus suggests key mechanisms in alcohol use disorder. | Green NC et al. | β | 2025 | β |
| Integration of scRNA-Seq and scATAC-Seq Reveals Malignant Characteristics of Sarcomatoid Clear Cell Renal Cell Carcinoma. | Lu W et al. | β | 2025 | β |
| Integrative analysis of molecular mechanisms in prostate cancer via single-cell RNA sequencing and weighted gene co-expression network analysis. | Zhai J et al. | β | 2025 | β |
| Integrative single-cell RNA and ATAC sequencing reveals the impact of chronic cigarette smoking on lung epithelial responses to influenza and hyperoxia. | Cha PC et al. | β | 2025 | β |
| Interneuron Loss and Microglia Activation by Transcriptome Analyses in the Basal Ganglia of Tourette Disorder. | Wang Y et al. | β | 2025 | β |
| Interpretable and integrative analysis of single-cell multiomics with scMKL. | Kupp SD et al. | β | 2025 | β |
| Interrogating the regulatory epigenome of cellular senescence. | Thanos DF et al. | β | 2025 | β |
| Intestinal secretory differentiation reflects niche-driven phenotypic and epigenetic plasticity of a common signal-responsive terminal cell. | Bhattacharya S et al. | β | 2025 | β |
| Intragenic viral silencer element regulates HTLV-1 latency via RUNX complex recruitment. | Sugata K et al. | β | 2025 | β |
| IT-scC&T-seq streamlines scalable, parallel profiling of protein-DNA interactions in single cells. | Ma J et al. | β | 2025 | β |
| Jund orchestrates <i>cis</i>-regulatory element dynamics to facilitate endothelial-to-hematopoietic transition. | Guo J et al. | β | 2025 | β |
| Kidney multiome-based genetic scorecard reveals convergent coding and regulatory variants. | Liu H et al. | β | 2025 | β |
| Large B cell lymphoma microenvironment archetype profiles. | Li X et al. | β | 2025 | β |
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| Lifting regenerative barriers promotes epithelial cell fate plasticity supporting lineage conversion. | Bejar MT et al. | β | 2025 | β |
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| Complementation testing identifies genes mediating effects at quantitative trait loci underlying fear-related behavior. | Chen PB et al. | β | 2024 | β |
| Computational tools for plant genomics and breeding. | Wang H et al. | β | 2024 | β |
| Concepts and new developments in droplet-based single cell multi-omics. | Chow A et al. | β | 2024 | β |
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| Deciphering MΓΌller cell heterogeneity signatures in diabetic retinopathy across species: an integrative single-cell analysis. | Deng X et al. | β | 2024 | β |
| Decoding aging in the heart via single cell dual omics of non-cardiomyocytes. | Song Y et al. | β | 2024 | β |
| Deconvolution of spatial transcriptomics data via graph contrastive learning and partial least square regression. | Mo Y et al. | β | 2024 | β |
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| Descart: a method for detecting spatial chromatin accessibility patterns with inter-cellular correlations. | Chen X et al. | β | 2024 | β |
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| Direct neuronal reprogramming of mouse astrocytes is associated with multiscale epigenome remodeling and requires Yy1. | Pereira A et al. | β | 2024 | β |
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| Disruption of the <i>Uty</i> epigenetic regulator locus in hematopoietic cells phenocopies the profibrotic attributes of Y chromosome loss in heart failure. | Horitani K et al. | β | 2024 | β |
| Distinct melanocyte subpopulations defined by stochastic expression of proliferation or maturation programs enable a rapid and sustainable pigmentation response. | Aggarwal A et al. | β | 2024 | β |
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| Elucidating allergic reaction mechanisms in response to SARS-CoV-2 mRNA vaccination in adults. | Shah MM et al. | β | 2024 | β |
| Enhancer-driven gene regulatory networks inference from single-cell RNA-seq and ATAC-seq data. | Li Y et al. | β | 2024 | β |
| Enhlink infers distal and context-specific enhancer-promoter linkages. | Poirion OB et al. | β | 2024 | β |
| Epigenetic Dynamics in Reprogramming to Dopaminergic Neurons for Parkinson's Disease. | Cho B et al. | β | 2024 | β |
| Epigenetic dysregulation in Alzheimer's disease peripheral immunity. | Ramakrishnan A et al. | β | 2024 | β |
| Epigenetic memory of radiotherapy in dermal fibroblasts impairs wound repair capacity in cancer survivors. | Bian X et al. | β | 2024 | β |
| Epigenetic reprogramming driving successful and failed repair in acute kidney injury. | Muto Y et al. | β | 2024 | β |
| Epigenetic reprogramming shapes the cellular landscape of schwannoma. | Liu SJ et al. | β | 2024 | β |
| Exaptation of ancestral cell-identity networks enables C<sub>4</sub> photosynthesis. | Swift J et al. | β | 2024 | β |
| Ex vivo expansion potential of murine hematopoietic stem cells is a rare property only partially predicted by phenotype. | Zhang Q et al. | β | 2024 | β |
| ezSingleCell: an integrated one-stop single-cell and spatial omics analysis platform for bench scientists. | Sethi R et al. | β | 2024 | β |
| Flexible modeling of regulatory networks improves transcription factor activity estimation. | Chen C et al. | β | 2024 | β |
| Forskolin-driven conversion of human somatic cells into induced neurons through regulation of the cAMP-CREB1-JNK signaling. | Wang G et al. | β | 2024 | β |
| From Omics to Multi-Omics: A Review of Advantages and Tradeoffs. | Hayes CN et al. | β | 2024 | β |
| GATA2 heterozygosity causes an epigenetic feedback mechanism resulting in myeloid and erythroid dysplasia. | Gioacchino E et al. | β | 2024 | β |
| GEEES: inferring cell-specific gene-enhancer interactions from multi-modal single-cell data. | Chen S et al. | β | 2024 | β |
| Glioblastoma evolution and heterogeneity from a 3D whole-tumor perspective. | Mathur R et al. | β | 2024 | β |
| Hematopoietic cells emerging from hemogenic endothelium exhibit lineage-specific oxidative stress responses. | Biezeman H et al. | β | 2024 | β |
| Hepatocyte Period 1 dictates oxidative substrate selection independent of the core circadian clock. | Sun J et al. | β | 2024 | β |
| Histone lactylation-related genes correlate with the molecular patterns and functions of cancer-associated fibroblasts and have significant clinical implications in clear cell renal cell carcinoma. | Kong W et al. | β | 2024 | β |
| HOXD12 defines an age-related aggressive subtype of oligodendroglioma. | Nuechterlein N et al. | β | 2024 | β |
| Human vascularized macrophage-islet organoids to model immune-mediated pancreatic Ξ² cell pyroptosis upon viral infection. | Yang L et al. | β | 2024 | β |
| HyGAnno: hybrid graph neural network-based cell type annotation for single-cell ATAC sequencing data. | Zhang W et al. | β | 2024 | β |
| Identification of a distal enhancer regulating hedgehog interacting protein gene in human lung epithelial cells. | Guo F et al. | β | 2024 | β |
| Identification of endothelial and mesenchymal FOXF1 enhancers involved in alveolar capillary dysplasia. | Wang G et al. | β | 2024 | β |
| ID factors regulate the ability of MΓΌller glia to become proliferating neurogenic progenitor-like cells. | Taylor OB et al. | β | 2024 | β |
| IL-4-induced SOX9 confers lineage plasticity to aged adult lung stem cells. | Cai XT et al. | β | 2024 | β |
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| Innate immune memory after brain injury drives inflammatory cardiac dysfunction. | Simats A et al. | β | 2024 | β |
| Integrated single-cell analysis reveals distinct epigenetic-regulated cancer cell states and a heterogeneity-guided core signature in tamoxifen-resistant breast cancer. | Fang K et al. | β | 2024 | β |
| Integrated Single-cell Multiomic Analysis of HIV Latency Reversal Reveals Novel Regulators of Viral Reactivation. | Ashokkumar M et al. | β | 2024 | β |
| Integrated single-cell multiomics uncovers foundational regulatory mechanisms of lens development and pathology. | Tangeman JA et al. | β | 2024 | β |
| Integrating single-cell multimodal epigenomic data using 1D convolutional neural networks. | Gao C et al. | β | 2024 | β |
| Integrating Single-Cell RNA-Seq and ATAC-Seq Analysis Reveals Uterine Cell Heterogeneity and Regulatory Networks Linked to Pimpled Eggs in Chickens. | Li W et al. | β | 2024 | β |
| Integration of multi-modal single-cell data. | Lee MYY et al. | β | 2024 | β |
| Integration of single-cell transcriptome and chromatin accessibility and its application on tumor investigation. | Yang C et al. | β | 2024 | β |
| Integrative single-cell characterization of a frugivorous and an insectivorous bat kidney and pancreas. | Gordon WE et al. | β | 2024 | β |
| Interleukin-21 engineering enhances NK cell activity against glioblastoma via CEBPD. | Shanley M et al. | β | 2024 | β |
| In vivo interaction screening reveals liver-derived constraints to metastasis. | Borrelli C et al. | β | 2024 | β |
| In vivo perturb-seq of cancer and microenvironment cells dissects oncologic drivers and radiotherapy responses in glioblastoma. | Liu SJ et al. | β | 2024 | β |
| Kmt2c restricts G-CSF-driven HSC mobilization and granulocyte production in a methyltransferase-independent manner. | Wang HC et al. | β | 2024 | β |
| KMT2D deficiency leads to cellular developmental disorders and enhancer dysregulation in neural-crest-containing brain organoids. | Shan Z et al. | β | 2024 | β |
| Longitudinal analysis of genetic and epigenetic changes in human pluripotent stem cells in the landscape of culture-induced abnormality. | Kim YJ et al. | β | 2024 | β |
| Long-range <i>Atoh1</i> enhancers maintain competency for hair cell regeneration in the inner ear. | Shi T et al. | β | 2024 | β |
| Loss of Ezh2 in the medial ganglionic eminence alters interneuron fate, cell morphology and gene expression profiles. | Rhodes CT et al. | β | 2024 | β |
| Mapping enhancer and chromatin accessibility landscapes charts the regulatory network of Alzheimer's disease. | Xu D et al. | β | 2024 | β |
| Mapping genotypes to chromatin accessibility profiles in single cells. | Izzo F et al. | β | 2024 | β |
| Massively parallel inΒ vivo Perturb-seq reveals cell-type-specific transcriptional networks in cortical development. | Zheng X et al. | β | 2024 | β |
| Maternal inflammation regulates fetal emergency myelopoiesis. | Collins A et al. | β | 2024 | β |
| Mechanisms of action and resistance in histone methylation-targeted therapy. | Yamagishi M et al. | β | 2024 | β |
| Midkine as a driver of age-related changes and increase in mammary tumorigenesis. | Yan P et al. | β | 2024 | β |
| Mitochondrial dysfunction and increased reactive oxygen species production in MECP2 mutant astrocytes and their impact on neurons. | Tomasello DL et al. | β | 2024 | β |
| MitoSort: Robust Demultiplexing of Pooled Single-cell Genomic Data Using Endogenous Mitochondrial Variants. | Tang Z et al. | β | 2024 | β |
| MOCHA's advanced statistical modeling of scATAC-seq data enables functional genomic inference in large human cohorts. | Rachid Zaim S et al. | β | 2024 | β |
| Modeling fragment counts improves single-cell ATAC-seq analysis. | Martens LD et al. | β | 2024 | β |
| MoNETA: MultiOmics Network Embedding for SubType Analysis. | Scala G et al. | β | 2024 | β |
| Mosaic integration and knowledge transfer of single-cell multimodal data with MIDAS. | He Z et al. | β | 2024 | β |
| Multidimensional profiling of human TΒ cells reveals high CD38 expression, marking recent thymic emigrants and age-related naive TΒ cell remodeling. | Bohacova P et al. | β | 2024 | β |
| Multimodal profiling reveals site-specific adaptation and tissue residency hallmarks of Ξ³Ξ΄ T cells across organs in mice. | du Halgouet A et al. | β | 2024 | β |
| Multimodal single-cell analyses reveal mechanisms of perianal fistula in diverse patients with Crohn's disease. | Levantovsky RM et al. | β | 2024 | β |
| Multimodal single-cell profiling reveals neuronal vulnerability and pathological cell states in focal cortical dysplasia. | GalvΓ£o IC et al. | β | 2024 | β |
| Multiome in the Same Cell Reveals the Impact of Osmotic Stress on Arabidopsis Root Tip Development at Single-Cell Level. | Liu Q et al. | β | 2024 | β |
| Multiomic-based immune response profiling in migraine, vestibular migraine and Meniere's disease. | Cruz-Granados P et al. | β | 2024 | β |
| Multi-omic lineage tracing predicts the transcriptional, epigenetic and genetic determinants of cancer evolution. | Nadalin F et al. | β | 2024 | β |
| Multi-Omics Integration in Nephrology: Advances, Challenges, and Future Directions. | Saliba A et al. | β | 2024 | β |
| Multiplexed single-cell characterization of alternative polyadenylation regulators. | Kowalski MH et al. | β | 2024 | β |
| MultiSC: a deep learning pipeline for analyzing multiomics single-cell data. | Lin X et al. | β | 2024 | β |
| Nano-CUT&Tag for multimodal chromatin profiling at single-cell resolution. | BΓ‘rcenas-Walls JR et al. | β | 2024 | β |
| Neuronal MAPT expression is mediated by long-range interactions with cis-regulatory elements. | Rogers BB et al. | β | 2024 | β |
| Non-stem cell lineages as an alternative origin of intestinal tumorigenesis in the context of inflammation. | Verhagen MP et al. | β | 2024 | β |
| NR4a1/2 deletion promotes accumulation of TCF1<sup>+</sup> stem-like precursors of exhausted CD8<sup>+</sup> T cells in the tumor microenvironment. | Srirat T et al. | β | 2024 | β |
| OpenAnnotateApi: Python and R packages to efficiently annotate and analyze chromatin accessibility of genomic regions. | Gao Z et al. | β | 2024 | β |
| Opportunities and challenges of single-cell and spatially resolved genomics methods for neuroscience discovery. | Bonev B et al. | β | 2024 | β |
| Pan-cancer single-cell dissection reveals phenotypically distinct B cell subtypes. | Yang Y et al. | β | 2024 | β |
| Peak-agnostic high-resolution cis-regulatory circuitry mapping using single cell multiome data. | Zhang Z et al. | β | 2024 | β |
| Podocyte-specific KLF6 primes proximal tubule CaMK1D signaling to attenuate diabetic kidney disease. | Gujarati NA et al. | β | 2024 | β |
| Probabilistic association of differentially expressed genes with <i>cis</i>-regulatory elements. | Roberts BS et al. | β | 2024 | β |
| Progenitors of distinct lineages shape the diversity of mature type 2 conventional dendritic cells. | Rodrigues PF et al. | β | 2024 | β |
| Progress in multifactorial single-cell chromatin profiling methods. | Stuart T | β | 2024 | β |
| Protocol for the isolation and single-nuclei multiomic analyses of the human fetal epicardium. | Travisano SI et al. | β | 2024 | β |
| Quantification of escape from X chromosome inactivation with single-cell omics data reveals heterogeneity across cell types and tissues. | Tomofuji Y et al. | β | 2024 | β |
| Recruitment of homodimeric proneural factors by conserved CAT-CAT E-boxes drives major epigenetic reconfiguration in cortical neurogenesis. | de Martin X et al. | β | 2024 | β |
| Regulatory mechanisms orchestrating cellular diversity of Cd36+ olfactory sensory neurons revealed by scRNA-seq and scATAC-seq analysis. | Yang J et al. | β | 2024 | β |
| Representing and extracting knowledge from single-cell data. | Mihai IS et al. | β | 2024 | β |
| REUNION: transcription factor binding prediction and regulatory association inference from single-cell multi-omics data. | Yang Y et al. | β | 2024 | β |
| RNA-mediated symmetry breaking enables singular olfactory receptor choice. | Pourmorady AD et al. | β | 2024 | β |
| RNA Shielding of p65 Is Required to Potentiate Oncogenic Inflammation in TET2-Mutated Clonal Hematopoiesis. | Ben-Crentsil NA et al. | β | 2024 | β |
| Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data. | Gabriel AA et al. | β | 2024 | β |
| Robust reprogramming of glia into neurons by inhibition of Notch signaling and nuclear factor I (NFI) factors in adult mammalian retina. | Le N et al. | β | 2024 | β |
| ROR2 Regulates Cellular Plasticity in Pancreatic Neoplasia and Adenocarcinoma. | Benitz S et al. | β | 2024 | β |
| Ruxolitinib Improves Immune-Dysregulation Features but not Epigenetic Abnormality in a Patient with STAT1 GOF. | Koh JY et al. | β | 2024 | β |
| rworkflows: automating reproducible practices for the R community. | Schilder BM et al. | β | 2024 | β |
| Safety, efficacy and determinants of response of allogeneic CD19-specific CAR-NK cells in CD19<sup>+</sup> B cell tumors: a phase 1/2 trial. | Marin D et al. | β | 2024 | β |
| SARS-CoV-2 inflammation durably imprints memory CD4 T cells. | Gray-Gaillard SL et al. | β | 2024 | β |
| scaDA: A novel statistical method for differential analysis of single-cell chromatin accessibility sequencing data. | Zhao F et al. | β | 2024 | β |
| scATAcat: cell-type annotation for scATAC-seq data. | Altay A et al. | β | 2024 | β |
| scConfluence: single-cell diagonal integration with regularized Inverse Optimal Transport on weakly connected features. | Samaran J et al. | β | 2024 | β |
| scCross: a deep generative model for unifying single-cell multi-omics with seamless integration, cross-modal generation, and in silico exploration. | Yang X et al. | β | 2024 | β |
| scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data. | Gao Z et al. | β | 2024 | β |
| scGRN: a comprehensive single-cell gene regulatory network platform of human and mouse. | Huang X et al. | β | 2024 | β |
| scMaui: a widely applicable deep learning framework for single-cell multiomics integration in the presence of batch effects and missing data. | Jeong Y et al. | β | 2024 | β |
| scMitoMut for calling mitochondrial lineage-related mutations in single cells. | Sun W et al. | β | 2024 | β |
| scMoresDB: A comprehensive database of single-cell multi-omics data for human respiratory system. | Chen K et al. | β | 2024 | β |
| scMultiome analysis identifies a single caudal hindbrain compartment in the developing zebrafish nervous system. | Warns J et al. | β | 2024 | β |
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| Sequential drug treatment targeting cell cycle and cell fate regulatory programs blocks non-genetic cancer evolution in acute lymphoblastic leukemia. | Malyukova A et al. | β | 2024 | β |
| Sex-specific regulatory architecture of pancreatic islets from subjects with and without type 2 diabetes. | Qadir MMF et al. | β | 2024 | β |
| SHARE-Topic: Bayesian interpretable modeling of single-cell multi-omic data. | Kazwini NE et al. | β | 2024 | β |
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| Similarity Network Analysis of the Adaptive Immune Response in the Proximal Airway. | Clark E et al. | β | 2024 | β |
| Simultaneous Epigenetic and Gene Expression Profiling at Single Cell Resolution Uncovers Stem-Like Treg Subsets Induced With Oligonucleotide Expansion in Humans. | Nam HJ et al. | β | 2024 | β |
| Single-cell CAR T atlas reveals type 2 function in 8-year leukaemia remission. | Bai Z et al. | β | 2024 | β |
| Single cell dual-omic atlas of the human developing retina. | Zuo Z et al. | β | 2024 | β |
| Single-cell EpiChem jointly measures drug-chromatin binding and multimodal epigenome. | Dong C et al. | β | 2024 | β |
| Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems. | Zenk F et al. | β | 2024 | β |
| Single-cell genomics and regulatory networks for 388 human brains. | Emani PS et al. | β | 2024 | β |
| Single-cell genomics details the maturation block in BCP-ALL and identifies therapeutic vulnerabilities in DUX4-r cases. | Thorsson H et al. | β | 2024 | β |
| Single-cell insights: pioneering an integrated atlas of chromatin accessibility and transcriptomic landscapes in diabetic cardiomyopathy. | Su Q et al. | β | 2024 | β |
| Single-cell joint profiling of multiple epigenetic proteins and gene transcription. | Xiong H et al. | β | 2024 | β |
| Single-cell mitochondrial sequencing reveals low-frequency mitochondrial mutations in naturally aging mice. | Liu F et al. | β | 2024 | β |
| Single-cell m<sup>6</sup>A profiling in the mouse brain uncovers cell type-specific RNA methylomes and age-dependent differential methylation. | Tegowski M et al. | β | 2024 | β |
| Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis. | Mitra S et al. | β | 2024 | β |
| Single-cell multi-omics analysis reveals candidate therapeutic drugs and key transcription factor specifically for the mesenchymal subtype of glioblastoma. | Yang Y et al. | β | 2024 | β |
| Single-cell multiomics decodes regulatory programs for mouse secondary palate development. | Yan F et al. | β | 2024 | β |
| Single-cell multiomics guided mechanistic understanding of Fontan-associated liver disease. | Hu P et al. | β | 2024 | β |
| Single-Cell Multi-Omics Map of Cell Type-Specific Mechanistic Drivers of Multiple Sclerosis Lesions. | Elkjaer ML et al. | β | 2024 | β |
| Single-cell multi-omics map of human fetal blood in Down syndrome. | Marderstein AR et al. | β | 2024 | β |
| Single-cell multiomics reveals ENL mutation perturbs kidney developmental trajectory by rewiring gene regulatory landscape. | Song L et al. | β | 2024 | β |
| Single-cell multiomics reveals the interplay of clonal evolution and cellular plasticity in hepatoblastoma. | Roehrig A et al. | β | 2024 | β |
| Single-cell 'omic profiles of human aortic endothelial cells in vitro and human atherosclerotic lesions ex vivo reveal heterogeneity of endothelial subtype and response to activating perturbations. | Adelus ML et al. | β | 2024 | β |
| Single-Cell Sequencing Technology in Ruminant Livestock: Challenges and Opportunities. | Lyons A et al. | β | 2024 | β |
| Single-cell spatial multi-omics and deep learning dissect enhancer-driven gene regulatory networks in liver zonation. | Bravo GonzΓ‘lez-Blas C et al. | β | 2024 | β |
| Single-cell systems pharmacology identifies development-driven drug response and combination therapy in B cell acute lymphoblastic leukemia. | Huang X et al. | β | 2024 | β |
| Single-nucleotide variant calling in single-cell sequencing data with Monopogen. | Dou J et al. | β | 2024 | β |
| Single-nucleus chromatin accessibility and transcriptomic map of breast tissues of women of diverse genetic ancestry. | Bhat-Nakshatri P et al. | β | 2024 | β |
| Single-nucleus multi-omics analyses reveal cellular and molecular innovations in the anterior cingulate cortex during primate evolution. | Yuan J et al. | β | 2024 | β |
| Single-nucleus multi-omics of Parkinson's disease reveals a glutamatergic neuronal subtype susceptible to gene dysregulation via alteration of transcriptional networks. | Shwab EK et al. | β | 2024 | β |
| Single-nucleus multiomics unravels the genetic mechanisms underlying musk secretion in Chinese forest musk deer (Moschus berezovskii). | Liu C et al. | β | 2024 | β |
| Single-nucleus RNA and ATAC sequencing analyses provide molecular insights into early pod development of peanut fruit. | Cui Y et al. | β | 2024 | β |
| Slide-tags enables single-nucleus barcoding for multimodal spatial genomics. | Russell AJC et al. | β | 2024 | β |
| Small data methods in omics: the power of one. | Johnston KG et al. | β | 2024 | β |
| SMARCA4 is a haploinsufficient B cell lymphoma tumor suppressor that fine-tunes centrocyte cell fate decisions. | Deng Q et al. | β | 2024 | β |
| SMARCA5-mediated chromatin remodeling is required for germinal center formation. | Stoler-Barak L et al. | β | 2024 | β |
| Spatial Transcriptomics and Single-Nucleus Multi-Omics Analysis Revealing the Impact of High Maternal Folic Acid Supplementation on Offspring Brain Development. | Xu X et al. | β | 2024 | β |
| STAT3-Mediated Ferroptosis is Involved in Sepsis-Associated Acute Respiratory Distress Syndrome. | Lin S et al. | β | 2024 | β |
| Systematic single-cell analysis reveals dynamic control of transposable element activity orchestrating the endothelial-to-hematopoietic transition. | Feng C et al. | β | 2024 | β |
| Targeting pro-inflammatory TΒ cells as a novel therapeutic approach to potentially resolve atherosclerosis in humans. | Fan L et al. | β | 2024 | β |
| TFAP2 paralogs regulate midfacial development in part through a conserved ALX genetic pathway. | Nguyen TT et al. | β | 2024 | β |
| T-follicular helper cells are epigenetically poised to transdifferentiate into T-regulatory type 1 cells. | Garnica J et al. | β | 2024 | β |
| Thalamocortical organoids enable inΒ vitro modeling of 22q11.2 microdeletion associated with neuropsychiatric disorders. | Shin D et al. | β | 2024 | β |
| The activity of early-life gene regulatory elements is hijacked in aging through pervasive AP-1-linked chromatin opening. | Patrick R et al. | β | 2024 | β |
| The chromatin accessibility dynamics during cell fate specifications in zebrafish early embryogenesis. | Xu Q et al. | β | 2024 | β |
| The chromatin landscape of healthy and injured cell types in the human kidney. | Gisch DL et al. | β | 2024 | β |
| The evolution of ovarian somatic cells characterized by transcriptome and chromatin accessibility across rodents, monkeys, and humans. | Zhang Q et al. | β | 2024 | β |
| The G4 resolvase Dhx36 modulates cardiomyocyte differentiation and ventricular conduction system development. | GΓ³mez-Del Arco P et al. | β | 2024 | β |
| The transcription factor NF-ΞΊB orchestrates nucleosome remodeling during the primary response to Toll-like receptor 4 signaling. | Feng AC et al. | β | 2024 | β |
| The type 2 cytokine Fc-IL-4 revitalizes exhausted CD8<sup>+</sup> T cells against cancer. | Feng B et al. | β | 2024 | β |
| TIM-3<sup>+</sup> CD8 T cells with a terminally exhausted phenotype retain functional capacity in hematological malignancies. | Minnie SA et al. | β | 2024 | β |
| Tissue-specific enhancer-gene maps from multimodal single-cell data identify causal disease alleles. | Sakaue S et al. | β | 2024 | β |
| Transcriptional re-programming of liver-resident iNKT cells into T-regulatory type-1-like liver iNKT cells involves extensive gene de-methylation. | MontaΓ±o J et al. | β | 2024 | β |
| Transcription Factor Activity Regulating Macrophage Heterogeneity during Skin Wound Healing. | Zandigohar M et al. | β | 2024 | β |
| Transcription factor dynamics, oscillation, and functions in human enteroendocrine cell differentiation. | Singh PNP et al. | β | 2024 | β |
| Transcription factor Tox2 is required for metabolic adaptation and tissue residency of ILC3 in the gut. | Das A et al. | β | 2024 | β |
| Transcriptomic, epigenomic, and spatial metabolomic cell profiling redefines regional human kidney anatomy. | Li H et al. | β | 2024 | β |
| Transient chromatin decompaction at the start of <i>D. melanogaster</i> male embryonic germline development. | Li YR et al. | β | 2024 | β |
| TriTan: an efficient triple nonnegative matrix factorization method for integrative analysis of single-cell multiomics data. | Ma X et al. | β | 2024 | β |
| txci-ATAC-seq: a massive-scale single-cell technique to profile chromatin accessibility. | Zhang H et al. | β | 2024 | β |
| Type I interferons induce an epigenetically distinct memory B cell subset in chronic viral infection. | Cooper L et al. | β | 2024 | β |
| Uncovering functional lncRNAs by scRNA-seq with ELATUS. | GoΓ±i E et al. | β | 2024 | β |
| Understanding isoform expression by pairing long-read sequencing with single-cell and spatial transcriptomics. | Belchikov N et al. | β | 2024 | β |
| Uniform quantification of single-nucleus ATAC-seq data with Paired-Insertion Counting (PIC) and a model-based insertion rate estimator. | Miao Z et al. | β | 2024 | β |
| Unraveling the epigenetic code: human kidney DNA methylation and chromatin dynamics in renal disease development. | Yan Y et al. | β | 2024 | β |
| Variant-to-function analysis of the childhood obesity chr12q13 locus implicates rs7132908 as a causal variant within the 3' UTR of FAIM2. | Littleton SH et al. | β | 2024 | β |
| YY1 knockout in pro-B cells impairs lineage commitment, enabling unusual hematopoietic lineage plasticity. | Banerjee S et al. | β | 2024 | β |
| A benchmark of computational pipelines for single-cell histone modification data. | Raimundo F et al. | β | 2023 | β |
| A global view of aging and Alzheimer's pathogenesis-associated cell population dynamics and molecular signatures in human and mouse brains. | Sziraki A et al. | β | 2023 | β |
| A marmoset brain cell census reveals regional specialization of cellular identities. | Krienen FM et al. | β | 2023 | β |
| An atlas of healthy and injured cell states and niches in the human kidney. | Lake BB et al. | β | 2023 | β |
| AP-1 signaling modulates cardiac fibroblast stress responses. | Whitehead AJ et al. | β | 2023 | β |
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| A single-cell atlas of in vitro multiculture systems uncovers the in vivo lineage trajectory and cell state in the human lung. | Lee W et al. | β | 2023 | β |
| A single cell genomics atlas of the Drosophila larval eye reveals distinct photoreceptor developmental timelines. | Bollepogu Raja KK et al. | β | 2023 | β |
| AtacAnnoR: a reference-based annotation tool for single cell ATAC-seq data. | Tian L et al. | β | 2023 | β |
| A universal tool for predicting differentially active features in single-cell and spatial genomics data. | Vandenbon A et al. | β | 2023 | β |
| Automatic cell-type harmonization and integration across Human Cell Atlas datasets. | Xu C et al. | β | 2023 | β |
| Benchmarking algorithms for joint integration of unpaired and paired single-cell RNA-seq and ATAC-seq data. | Lee MYY et al. | β | 2023 | β |
| Bile acid-dependent transcription factors and chromatin accessibility determine regional heterogeneity of intestinal antimicrobial peptides. | Wang Y et al. | β | 2023 | β |
| CD38-Specific CAR Integrated into CD38 Locus Driven by Different Promoters Causes Distinct Antitumor Activities of T and NK Cells. | Liao C et al. | β | 2023 | β |
| Characterization and Optimization of Multiomic Single-Cell Epigenomic Profiling. | Sandoval L et al. | β | 2023 | β |
| Characterizing control of memory CD8 T cell differentiation by BTB-ZF transcription factor Zbtb20. | Preiss NK et al. | β | 2023 | β |
| Chromatin accessibility analysis suggested vascular induction of the biliary epithelium via the Notch signaling pathway in the human liver. | Yoshihara M et al. | β | 2023 | β |
| Chromosome-level organization of the regulatory genome in the Drosophila nervous system. | Mohana G et al. | β | 2023 | β |
| Clustering single-cell multimodal omics data with jrSiCKLSNMF. | Ellis D et al. | β | 2023 | β |
| Cofea: correlation-based feature selection for single-cell chromatin accessibility data. | Li K et al. | β | 2023 | β |
| Control of nutrient uptake by IRF4 orchestrates innate immune memory. | Santosa EK et al. | β | 2023 | β |
| Craniofacial developmental biology in the single-cell era. | Tseng KC et al. | β | 2023 | β |
| Deciphering early human pancreas development at the single-cell level. | Ma Z et al. | β | 2023 | β |
| Decoding Human Biology and Disease Using Single-cell Omics Technologies. | Shi Q et al. | β | 2023 | β |
| Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney. | Xiong L et al. | β | 2023 | β |
| Droplet-based single-cell joint profiling of histone modifications and transcriptomes. | Xie Y et al. | β | 2023 | β |
| Dynamic chromatin remodeling in cycling human endometrium at single-cell level. | Vrljicak P et al. | β | 2023 | β |
| Dynamic regulatory elements in single-cell multimodal data implicate key immune cell states enriched for autoimmune disease heritability. | Gupta A et al. | β | 2023 | β |
| Dynamic single-cell regulomes characterize human peripheral blood innate lymphoid cell subpopulations. | Falquet M et al. | β | 2023 | β |
| Epigenetic memory of coronavirus infection in innate immune cells and their progenitors. | Cheong JG et al. | β | 2023 | β |
| Epigenetic regulation during cancer transitions across 11 tumour types. | Terekhanova NV et al. | β | 2023 | β |
| Epigenomic landscape exhibits interferon signaling suppression in the patient of myocarditis after BNT162b2 vaccination. | Kim H et al. | β | 2023 | β |
| Epstein-Barr virus evades restrictive host chromatin closure by subverting B cell activation and germinal center regulatory loci. | SoRelle ED et al. | β | 2023 | β |
| Exposure to lung-migrating helminth protects against murine SARS-CoV-2 infection through macrophage-dependent T cell activation. | Oyesola OO et al. | β | 2023 | β |
| Expression of the transcription factor Klf6 by thymic epithelial cells is required for thymus development. | Malin J et al. | β | 2023 | β |
| Gene regulatory network inference in the era of single-cell multi-omics. | Badia-I-Mompel P et al. | β | 2023 | β |
| Genome-wide profiling of transcription factor activity in primary liver cancer using single-cell ATAC sequencing. | Craig AJ et al. | β | 2023 | β |
| GoM DE: interpreting structure in sequence count data with differential expression analysis allowing for grades of membership. | Carbonetto P et al. | β | 2023 | β |
| hdWGCNA identifies co-expression networks in high-dimensional transcriptomics data. | Morabito S et al. | β | 2023 | β |
| Integrating single-cell transcriptomes, chromatin accessibility, and multiomics analysis of mesoderm-induced embryonic stem cells. | Ko KD et al. | β | 2023 | β |
| Integration site-dependent HIV-1 promoter activity shapes host chromatin conformation. | Collora JA et al. | β | 2023 | β |
| Integrative single-nucleus multi-omics analysis prioritizes candidate cis and trans regulatory networks and their target genes in Alzheimer's disease brains. | Gamache J et al. | β | 2023 | β |
| Joint epigenome profiling reveals cell-type-specific gene regulatory programmes in human cortical organoids. | Noack F et al. | β | 2023 | β |
| KDM6A epigenetically regulates subtype plasticity in small cell lung cancer. | Duplaquet L et al. | β | 2023 | β |
| Lifelong restructuring of 3D genome architecture in cerebellar granule cells. | Tan L et al. | β | 2023 | β |
| Lineage commitment of dermal fibroblast progenitors is controlled by Kdm6b-mediated chromatin demethylation. | Phan QM et al. | β | 2023 | β |
| Lineage Plasticity and Stemness Phenotypes in Prostate Cancer: Harnessing the Power of Integrated "Omics" Approaches to Explore Measurable Metrics. | Logotheti S et al. | β | 2023 | β |
| Longitudinal scRNA-seq analysis in mouse and human informs optimization of rapid mouse astrocyte differentiation protocols. | Frazel PW et al. | β | 2023 | β |
| Loss of PBAF promotes expansion and effector differentiation of CD8<sup>+</sup> TΒ cells during chronic viral infection and cancer. | Kharel A et al. | β | 2023 | β |
| macroH2A2 antagonizes epigenetic programs of stemness in glioblastoma. | Nikolic A et al. | β | 2023 | β |
| Mild dehydration effects on the murine kidney single-nucleus transcriptome and chromatin accessibility. | Huynh NV et al. | β | 2023 | β |
| Mixed model-based deconvolution of cell-state abundances (MeDuSA) along a one-dimensional trajectory. | Song L et al. | β | 2023 | β |
| Molecular features driving cellular complexity of human brain evolution. | Caglayan E et al. | β | 2023 | β |
| MSL2 ensures biallelic gene expression in mammals. | Sun Y et al. | β | 2023 | β |
| Multimodal single cell analysis infers widespread enhancer co-activity in a lymphoblastoid cell line. | Ziyani C et al. | β | 2023 | β |
| Multimodal single-cell datasets characterize antigen-specific CD8<sup>+</sup> T cells across SARS-CoV-2 vaccination and infection. | Zhang B et al. | β | 2023 | β |
| Multi-omic profiling of the developing human cerebral cortex at the single-cell level. | Zhu K et al. | β | 2023 | β |
| Multi-omics approach reveals dysregulated genes during hESCs neuronal differentiation exposure to paracetamol. | Spildrejorde M et al. | β | 2023 | β |
| Multi-omics computational analysis unveils the involvement of AP-1 and CTCF in hysteresis of chromatin states during macrophage polarization. | Zhang Y et al. | β | 2023 | β |
| Muscle denervation promotes functional interactions between glial and mesenchymal cells through NGFR and NGF. | Nicoletti C et al. | β | 2023 | β |
| Mutations from patients with IPEX ported to mice reveal different patterns of FoxP3 and Treg dysfunction. | Leon J et al. | β | 2023 | β |
| Neural cell diversity in the light of single-cell transcriptomics. | FernΓ‘ndez-Moya SM et al. | β | 2023 | β |
| Noncoding variants alter GATA2 expression in rhombomere 4 motor neurons and cause dominant hereditary congenital facial paresis. | Tenney AP et al. | β | 2023 | β |
| Opposing gene regulatory programs governing myofiber development and maturation revealed at single nucleus resolution. | Dos Santos M et al. | β | 2023 | β |
| Osteogenic Differentiation Potential of Mesenchymal Stem Cells Using Single Cell Multiomic Analysis. | Chen D et al. | β | 2023 | β |
| Paired single-cell multi-omics data integration with Mowgli. | Huizing GJ et al. | β | 2023 | β |
| Pluripotent stem cell-derived model of the post-implantation human embryo. | Weatherbee BAT et al. | β | 2023 | β |
| Probabilistic tensor decomposition extracts better latent embeddings from single-cell multiomic data. | Wang RH et al. | β | 2023 | β |
| Quantitative control of Ets1 dosage by a multi-enhancer hub promotes Th1 cell differentiation and protects from allergic inflammation. | Chandra A et al. | β | 2023 | β |
| Revealing spatial multimodal heterogeneity in tissues with SpaTrio. | Yang P et al. | β | 2023 | β |
| Robust enhancer-gene regulation identified by single-cell transcriptomes and epigenomes. | Xie F et al. | β | 2023 | β |
| RORΞ³t<sup>+</sup> c-Maf<sup>+</sup> VΞ³4<sup>+</sup> Ξ³Ξ΄ TΒ cells are generated in the adult thymus but do not reach the periphery. | Yang T et al. | β | 2023 | β |
| SCALA: A complete solution for multimodal analysis of single-cell Next Generation Sequencing data. | Tzaferis C et al. | β | 2023 | β |
| scBridge embraces cell heterogeneity in single-cell RNA-seq and ATAC-seq data integration. | Li Y et al. | β | 2023 | β |
| SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks. | Bravo GonzΓ‘lez-Blas C et al. | β | 2023 | β |
| scIBD: a self-supervised iterative-optimizing model for boosting the detection of heterotypic doublets in single-cell chromatin accessibility data. | Zhang W et al. | β | 2023 | β |
| scMHNN: a novel hypergraph neural network for integrative analysis of single-cell epigenomic, transcriptomic and proteomic data. | Li W et al. | β | 2023 | β |
| scMultiome analysis identifies embryonic hindbrain progenitors with mixed rhombomere identities. | Kim YI et al. | β | 2023 | β |
| scNCL: transferring labels from scRNA-seq to scATAC-seq data with neighborhood contrastive regularization. | Yan X et al. | β | 2023 | β |
| scTour: a deep learning architecture for robust inference and accurate prediction of cellular dynamics. | Li Q | β | 2023 | β |
| Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development. | Jiang F et al. | β | 2023 | β |
| Single cell analysis of transcriptome and open chromatin reveals the dynamics of hair follicle stem cell aging. | Zhang C et al. | β | 2023 | β |
| Single-cell brain organoid screening identifies developmental defects in autism. | Li C et al. | β | 2023 | β |
| Single-cell chromatin accessibility and transcriptomic characterization of Behcet's disease. | Shi W et al. | β | 2023 | β |
| Single-cell chromatin accessibility profiling of cell-state-specific gene regulatory programs during mouse organogenesis. | Deng Q et al. | β | 2023 | β |
| Single-cell DNA methylome and 3D multi-omic atlas of the adult mouse brain. | Liu H et al. | β | 2023 | β |
| Single-cell epigenetic, transcriptional, and protein profiling of latent and active HIV-1 reservoir revealed that IKZF3 promotes HIV-1 persistence. | Wei Y et al. | β | 2023 | β |
| Single-cell landscape of primary central nervous system diffuse large B-cell lymphoma. | Liu N et al. | β | 2023 | β |
| Single-cell mapping identifies MSI<sup>+</sup> cells as a common origin for diverse subtypes of pancreatic cancer. | Rajbhandari N et al. | β | 2023 | β |
| Single-cell methylation analysis of brain tissue prioritizes mutations that alter transcription. | Flint J et al. | β | 2023 | β |
| Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells. | Lareau CA et al. | β | 2023 | β |
| Single-cell multiomic understanding of HIV-1 reservoir at epigenetic, transcriptional, and protein levels. | Wong M et al. | β | 2023 | β |
| Single-cell transcriptomics and epigenomics unravel the role of monocytes in neuroblastoma bone marrow metastasis. | Fetahu IS et al. | β | 2023 | β |
| Single-cell transcriptomics identifies prothymosin Ξ± restriction of HIV-1 in vivo. | Geretz A et al. | β | 2023 | β |
| Single-nuclei multiomic analyses identify human cardiac lymphatic endothelial cells associated with coronary arteries in the epicardium. | Travisano SI et al. | β | 2023 | β |
| Single-nucleus genomics in outbred rats with divergent cocaine addiction-like behaviors reveals changes in amygdala GABAergic inhibition. | Zhou JL et al. | β | 2023 | β |
| Single-nucleus multiomic mapping of m<sup>6</sup>A methylomes and transcriptomes in native populations of cells with sn-m6A-CT. | Hamashima K et al. | β | 2023 | β |
| Single-Nucleus Profiling Identifies Accelerated Oligodendrocyte Precursor Cell Senescence in a Mouse Model of Down Syndrome. | Rusu B et al. | β | 2023 | β |
| SMARCB1 loss activates patient-specific distal oncogenic enhancers in malignant rhabdoid tumors. | Liu NQ et al. | β | 2023 | β |
| SOCS3 deletion in effector TΒ cells confers an anti-tumorigenic role of IL-6 to the pro-tumorigenic cytokine. | Mise-Omata S et al. | β | 2023 | β |
| Tbx5 maintains atrial identity in post-natal cardiomyocytes by regulating an atrial-specific enhancer network. | Sweat ME et al. | β | 2023 | β |
| Temporally specific gene expression and chromatin remodeling programs regulate a conserved <i>Pdyn</i> enhancer. | Phillips RA et al. | β | 2023 | β |
| TET2 and TET3 loss disrupts small intestine differentiation and homeostasis. | Ansari I et al. | β | 2023 | β |
| The impact of the Hedgehog signal pathway on the tumor immune microenvironment of gastric adenocarcinoma by integrated analysis of scRNA-seq and RNA-seq datasets. | Zhong J et al. | β | 2023 | β |
| Therapeutic Effects of Upadacitinib on Experimental Autoimmune Uveitis: Insights From Single-Cell Analysis. | Huang Z et al. | β | 2023 | β |
| The single-cell landscape of alternative transcription start sites of diabetic retina. | Mao P et al. | β | 2023 | β |
| The SWI/SNF chromatin remodeling complexes BAF and PBAF differentially regulate epigenetic transitions in exhausted CD8<sup>+</sup> TΒ cells. | Baxter AE et al. | β | 2023 | β |
| Thymic mimetic cells function beyond self-tolerance. | Givony T et al. | β | 2023 | β |
| Transcription factor NFYa controls cardiomyocyte metabolism and proliferation during mouse fetal heart development. | Cui M et al. | β | 2023 | β |
| Tumor heterogeneity and tumor-microglia interactions in primary and recurrent IDH1-mutant gliomas. | Blanco-Carmona E et al. | β | 2023 | β |
| Uncovering a mammalian neural-specific poly(A) binding protein with unique properties. | Sharma S et al. | β | 2023 | β |
| Uncovering oligodendrocyte enhancers that control Cnp expression. | Fan C et al. | β | 2023 | β |
| Universal DNA methylation age across mammalian tissues. | Lu AT et al. | β | 2023 | β |
| Ursa: A Comprehensive Multiomics Toolbox for High-Throughput Single-Cell Analysis. | Pan L et al. | β | 2023 | β |
| Using single-cell chromatin accessibility sequencing to characterize CD4+ T cells from murine tissues. | Braband KL et al. | β | 2023 | β |
| VarID2 quantifies gene expression noise dynamics and unveils functional heterogeneity of ageing hematopoietic stem cells. | Rosales-Alvarez RE et al. | β | 2023 | β |