ArticleNature methods2015
Interactive analysis and assessment of single-cell copy-number variations.
Article in Nature methods, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 170 papers.
What it found
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Who cites it
170 citing papers in PubMed.
- Somatic mosaicism in the brain: linking development, ageing and neurodegeneration.Nature reviews. Neurology · 2026Review
- NICE: A Two-Step Non-Invasive Framework for Embryo cfDNA Read Enrichment and Quality Assessment.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A medium throughput approach for single cell copy number variation sequencing towards efficient application in clinics.Journal of advanced research · 2026Article
- CNVeil resolves haplotype-specific copy number and uncovers subclonal architecture hidden from total copy number profiling in single-cell cancer genomes.bioRxiv : the preprint server for biology · 2026Article
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- Single-cell genomic analysis of cancer cells from one treatment-naïve patient with metastatic prostate cancer.BMC genomic data · 2026Article
- The landscape and regulatory potential of eccDNAs in mammalian preimplantation embryos.Nature communications · 2026Article
- CNAScope: pan-cancer copy number aberration database with functional annotation and interactive visualization.Nucleic acids research · 2026Article
- Benchmarking Ploidy Estimation Methods for Bulk and Single-Cell Whole Genome Sequencing.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Single-cell aneuploidy and chromosomal arm imbalances define subclones with divergent transcriptomic phenotypes.NAR genomics and bioinformatics · 2025Article
- Single cell long read whole genome sequencing reveals somatic transposon activity in human brain.Communications biology · 2025Article
- The Somatic Aneuploidy Landscape of Adult Glia Reveals 16p as a Hotspot and Differentiates Mosaicism in Normal Glia from Chromosomal Instability in Glioblastoma.Research square · 2025Article
- Advances in single-cell DNA sequencing enable insights into human somatic mosaicism.Nature reviews. Genetics · 2025Review
- Large-scale single-cell phylogenetic mapping of clonal evolution in the human aging esophagus.bioRxiv : the preprint server for biology · 2025Article
- A personalized multi-platform assessment of somatic mosaicism in the human frontal cortex.bioRxiv : the preprint server for biology · 2025Article
- The dual role of whole-genome duplication: biological mechanisms, functional consequences, and detection advances.Acta biochimica et biophysica Sinica · 2025Review
- SoMaCX: a complex generative genome modeling framework.BMC genomics · 2025Article
- Article
- Genetic Deconvolution of Embryonic and Maternal Cell-Free DNA in Spent Culture Medium of Human Preimplantation Embryo Through Deep Learning.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
110 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
We present Ginkgo (http://qb.cshl.edu/ginkgo), a user-friendly, open-source web platform for the analysis of single-cell copy-number variations (CNVs). Ginkgo automatically constructs copy-number profiles of cells from mapped reads and constructs phylogenetic trees of related cells. We validated Ginkgo by reproducing the results of five major studies. After comparing three commonly used single-cell amplification techniques, we concluded that degenerate oligonucleotide-primed PCR is the most consistent for CNV analysis.
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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.