ArticleNature biotechnology2017
Single-cell genome sequencing at ultra-high-throughput with microfluidic droplet barcoding.
Article in Nature biotechnology, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 194 papers, 1 of them a synthesis that pooled it.
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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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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
194 citing papers in PubMed, 1 synthesis or guideline pooled it, 455 citations in OpenAlex.
- The microbial dark matter and "wanted list" in worldwide wastewater treatment plants.Microbiome · 2023Pooled it
- Active Droplet Formation in a Microfluidic Cross-Junction Using Stacked Piezoelectric Actuators.Micromachines · 2026Article
- Intelligent label-free droplet microfluidic sorting system for single-cell encapsulation and morphology-guided screening.Microsystems & nanoengineering · 2026Article
- Effect of droplet size on the encapsulation efficiency of microparticles in passive microfluidic systems.Biomedical microdevices · 2026Article
- Single-nucleus DNA sequencing delves into the varied genomic evolution of pancreatic cancer.Nature genetics · 2026Article
- Droplet microfluidics strategies for overcoming bottlenecks in antibiotics discovery.iScience · 2026Review
- Understanding microbial ecology and evolution with single-cell genomics.Nature reviews. Genetics · 2026Article
- Advances in high-throughput mutation breeding systems integrating atmospheric and room-temperature plasma (ARTP) with droplet-based microfluidics.Microbial cell factories · 2025Review
- Intratumoral microbiome: a crucial regulating factor in development and progression of colorectal cancer.Molecular biomedicine · 2025Review
- Deterministic Co-encapsulation of Microparticles in Droplets via Synchronized Merging for Single-Cell Genomics.Analytical chemistry · 2025Article
- Single-particle genomics uncovers abundant non-canonical marine viruses from nanolitre volumes.Nature microbiology · 2025Article
- Article
- Profiling the heterogeneity of microbial populations and communities at the single-cell level.mLife · 2025Review
- Hybrid BAG-seq: DNA and RNA from the same single nucleus reveals interactions between genomic and transcriptomic landscapes in human tumor samples.Genome biology · 2025Article
- Dissection of intratumor microbiome-host interactions at the single-cell level in lung cancer.hLife · 2025Article
- A data-intelligence-intensive bioinformatics copilot system for large-scale omics research and scientific insights.Briefings in bioinformatics · 2025Article
- Barcodes based on nucleic acid sequences: Applications and challenges (Review).Molecular medicine reports · 2025Review
- Microbiome Single Cell Atlases Generated with a Commercial Instrument.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Improving engineered biological systems with electronics and microfluidics.Nature biotechnology · 2025Review
- Engineering next-generation microfluidic technologies for single-cell phenomics.Nature genetics · 2025Review
134 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The application of single-cell genome sequencing to large cell populations has been hindered by technical challenges in isolating single cells during genome preparation. Here we present single-cell genomic sequencing (SiC-seq), which uses droplet microfluidics to isolate, fragment, and barcode the genomes of single cells, followed by Illumina sequencing of pooled DNA. We demonstrate ultra-high-throughput sequencing of >50,000 cells per run in a synthetic community of Gram-negative and Gram-positive bacteria and fungi. The sequenced genomes can be sorted in silico based on characteristic sequences. We use this approach to analyze the distributions of antibiotic-resistance genes, virulence factors, and phage sequences in microbial communities from an environmental sample. The ability to routinely sequence large populations of single cells will enable the de-convolution of genetic heterogeneity in diverse cell populations.
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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.