ArticleGenome biology2020
Single-cell ATAC-seq signal extraction and enhancement with SCATE.
Article in Genome biology, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
33 citing papers in PubMed.
- Epigenetics in forest trees- key driver to phenotypic plasticity and adaptation under stress.Functional & integrative genomics · 2025Review
- Advancing biological understanding of cellular senescence with computational multiomics.Nature genetics · 2025Review
- EpiFoundation: A Foundation Model for Single-Cell ATAC-seq via Peak-to-Gene Alignment.bioRxiv : the preprint server for biology · 2025Article
- Recent advances in omics and the integration of multi-omics in osteoarthritis research.Arthritis research & therapy · 2025Review
- Capturing cell-type-specific activities of cis-regulatory elements from peak-based single-cell ATAC-seq.Cell genomics · 2025Article
- Single-cell omics: experimental workflow, data analyses and applications.Science China. Life sciences · 2025Review
- Review
- Tissue characterization at an enhanced resolution across spatial omics platforms with deep generative model.Nature communications · 2024Article
- A Cell Cycle-Aware Network for Data Integration and Label Transferring of Single-Cell RNA-Seq and ATAC-Seq.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- CloudATAC: a cloud-based framework for ATAC-Seq data analysis.Briefings in bioinformatics · 2024Article
- TFvelo: gene regulation inspired RNA velocity estimation.Nature communications · 2024Article
- A review of single-cell transcriptomics and epigenomics studies in maternal and child health.Epigenomics · 2024Review
- Modeling fragment counts improves single-cell ATAC-seq analysis.Nature methods · 2024Article
- Epigenetic modifications and miRNAs determine the transition of somatic cells into somatic embryos.Plant cell reports · 2023Review
- Integrative approaches based on genomic techniques in the functional studies on enhancers.Briefings in bioinformatics · 2023Review
- A novel prognostic related lncRNA signature associated with amino acid metabolism in glioma.Frontiers in immunology · 2023Article
- Single-cell transcriptome analysis for cancer and biology of the pancreas: A review on recent progress.Frontiers in genetics · 2023Review
- ATAC-seq exposes differences in chromatin accessibility leading to distinct leaf shapes in mulberry.Plant direct · 2022Article
- Artificial intelligence and machine learning approaches using gene expression and variant data for personalized medicine.Briefings in bioinformatics · 2022Review
- Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Single-cell sequencing assay for transposase-accessible chromatin (scATAC-seq) is the state-of-the-art technology for analyzing genome-wide regulatory landscapes in single cells. Single-cell ATAC-seq data are sparse and noisy, and analyzing such data is challenging. Existing computational methods cannot accurately reconstruct activities of individual cis-regulatory elements (CREs) in individual cells or rare cell subpopulations. We present a new statistical framework, SCATE, that adaptively integrates information from co-activated CREs, similar cells, and publicly available regulome data to substantially increase the accuracy for estimating activities of individual CREs. We demonstrate that SCATE can be used to better reconstruct the regulatory landscape of a heterogeneous sample.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.