ArticleGenome biology2020
CSS: cluster similarity spectrum integration of single-cell genomics data.
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 36 papers.
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Who cites it
36 citing papers in PubMed.
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- Classification of indeterminate and off-target cell types within human kidney organoid differentiation.iScience · 2026Article
- Systematic scRNA-seq screens profile neural organoid response to morphogens.Nature methods · 2026Article
- Immunoregulatory Roles of Tumor-Originated Pericytes Identified by Single-Cell Analysis in Glioblastoma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Multi-omics unravel heterogeneity of glucose metabolism reprogramming in gastric cancer.Clinical and experimental medicine · 2025Article
- The transcription factor NFIL3 drives innate lymphoid cell specification from lymphoid progenitors.Immunity · 2025Article
- Murine vascular organoids are responsive and adaptable 3D systems with cellular heterogeneity and dynamic plasticity.Science advances · 2025Article
- Establishment of human gastrulating stem cells with the capacity of stable differentiation into multiple gastrulating cell types.Cell research · 2025Article
- Single-cell transcriptomics redefines focal neuroendocrine differentiation as a distinct prostate cancer pathology.Molecular oncology · 2025Article
- Targeting ribosomes reprograms the tumour microenvironment and augments cancer immunotherapy.British journal of cancer · 2025Article
- Recent evolution of the developing human intestine affects metabolic and barrier functions.Science (New York, N.Y.) · 2025Article
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- Metabotissugenic citrate biomaterials orchestrate bone regeneration via citrate-mediated signaling pathways.Science advances · 2025Article
- Early developmental origins of cortical disorders modeled in human neural stem cells.Nature communications · 2025Article
- HumanTestisDB: A Comprehensive Atlas of Testicular Transcriptomes and Cellular Interactions.Genomics, proteomics & bioinformatics · 2025Article
- The Hypoxia-Associated High-Risk Cell Subpopulation Distinctly Enhances the Progression of Glioma.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- An integrated transcriptomic cell atlas of human endoderm-derived organoids.Nature genetics · 2025Article
- Mitochondrial dysfunction and increased reactive oxygen species production in MECP2 mutant astrocytes and their impact on neurons.Scientific reports · 2024Article
Corrections and comments
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
It is a major challenge to integrate single-cell sequencing data across experiments, conditions, batches, time points, and other technical considerations. New computational methods are required that can integrate samples while simultaneously preserving biological information. Here, we propose an unsupervised reference-free data representation, cluster similarity spectrum (CSS), where each cell is represented by its similarities to clusters independently identified across samples. We show that CSS can be used to assess cellular heterogeneity and enable reconstruction of differentiation trajectories from cerebral organoid and other single-cell transcriptomic data, and to integrate data across experimental conditions and human individuals.
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