ArticleNature biotechnology2021
Scalable, multimodal profiling of chromatin accessibility, gene expression and protein levels in single cells.
Article in Nature biotechnology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 326 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
326 citing papers in PubMed, 522 citations in OpenAlex.
- Immunophenotyping by Single-Cell CITE-Seq.Methods in molecular biology (Clifton, N.J.) · 2027Article
- Regulatory-prior-guided attention preserves biological structure during unpaired single-cell RNA-ATAC integration.Bioinformatics (Oxford, England) · 2026Article
- Quantifying distribution shifts in single-cell data with scXMatch.Bioinformatics (Oxford, England) · 2026Article
- The dual-enhanced graph learning framework DePass allows paired data integration in single-cell and spatial multiomics.Nature cell biology · 2026Article
- Unifying multimodal single-cell data with a mixture-of-experts β-variational autoencoder framework.Genome research · 2026Article
- DUET-seq: An Open-Source Droplet Platform for High-Fidelity Joint Chromatin and Transcriptome Profiling Reveals Temporal Regulatory Decoupling in Single Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Clonal selection of somatic mutations shapes NK cell memory.bioRxiv : the preprint server for biology · 2026Article
- Review
- Continual integration of single-cell multimodal data with MIRACLE.Nature computational science · 2026Article
- Topology-guided dual-masked contrastive learning for weakly supervised cell-type annotation in single-cell multi-omics.Briefings in bioinformatics · 2026Article
- mmVelo: a deep generative model for estimating cell state-dependent dynamics across multiple modalities.Bioinformatics (Oxford, England) · 2026Article
- Unique CD8bioRxiv : the preprint server for biology · 2026Article
- Unifying multimodal single-cell data with a mixture-of-expertsbioRxiv : the preprint server for biology · 2026Article
- A map of intra- and intercellular immune responses across diverse in vitro stimuli and inflammatory disease.Genome medicine · 2026Article
- Multiome-based identification of molecular markers for prospective identification of platelet-biased HSCs.Stem cell reports · 2026Article
- Post-vaccination expansion of extrafollicular Th10 and regulatory Tfr cells distinguishes strong from weak influenza vaccine responses in older adults.medRxiv : the preprint server for health sciences · 2026Article
- UDEC-MO: an uncertainty-guided deep embedded clustering framework for bulk and single-cell multi-omics data.Briefings in bioinformatics · 2026Article
- Establishing human immune system mice: application, opportunity, and challenges.Experimental & molecular medicine · 2026Review
- Single-nucleus chromatin accessibility and gene expression co-profiling by ISSAAC-seq.Nature protocols · 2026Review
- Single-cell Omics Assessment of Mitochondrial Function: Current Status and Future Perspectives.Genomics, proteomics & bioinformatics · 2026Review
266 more citing papers are in PubMed but not listed here.
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Authors and funding
21 authors at 5 institutions in 3 countries.
Funding
Abstract
Recent technological advances have enabled massively parallel chromatin profiling with scATAC-seq (single-cell assay for transposase accessible chromatin by sequencing). Here we present ATAC with select antigen profiling by sequencing (ASAP-seq), a tool to simultaneously profile accessible chromatin and protein levels. Our approach pairs sparse scATAC-seq data with robust detection of hundreds of cell surface and intracellular protein markers and optional capture of mitochondrial DNA for clonal tracking, capturing three distinct modalities in single cells. ASAP-seq uses a bridging approach that repurposes antibody:oligonucleotide conjugates designed for existing technologies that pair protein measurements with single-cell RNA sequencing. Together with DOGMA-seq, an adaptation of CITE-seq (cellular indexing of transcriptomes and epitopes by sequencing) for measuring gene activity across the central dogma of gene regulation, we demonstrate the utility of systematic multi-omic profiling by revealing coordinated and distinct changes in chromatin, RNA and surface proteins during native hematopoietic differentiation and peripheral blood mononuclear cell stimulation and as a combinatorial decoder and reporter of multiplexed perturbations in primary T cells.
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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.