ArticleNature biotechnology2021
Robust integration of multiple single-cell RNA sequencing datasets using a single reference space.
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 30 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
30 citing papers in PubMed.
- IntegrateRigor: annotation-free integration optimization for cell identity recovery reveals cancer-immune interface niches.bioRxiv : the preprint server for biology · 2026Article
- Disruption of CSF-1 receptor-mediated metal ion homeostasis in the murine brain promotes neurodegenerative disease.The Journal of clinical investigation · 2026Article
- Single-Cell RNA Analysis of Murine Osteosarcoma Uncovers Skp2 Function in Metastasis, Genomic Instability, and Immune Activation and Reveals Additional Target Pathways.Cancer research communications · 2026Article
- Single-cell RNA-sequencing of circulating tumour cells: A practical guide to workflow and translational applications.Cancer metastasis reviews · 2025Review
- A pluripotent stem cell atlas of multilineage differentiation.Scientific data · 2025Article
- A Single-Cell RNA Sequencing Atlas of the Chronic Obstructive Pulmonary Disease Distal Lung to Predict Cell-Cell Communication.American journal of respiratory cell and molecular biology · 2025Article
- Machine learning-based prediction reveals kinase MAP4K4 regulates neutrophil differentiation through phosphorylating apoptosis-related proteins.PLoS computational biology · 2025Article
- Atlas of multilineage stem cell differentiation reveals TMEM88 as a developmental regulator of blood pressure.Nature communications · 2025Article
- Macrophages in the infarcted heart acquire a fibrogenic phenotype, expressing matricellular proteins, but do not undergo fibroblast conversion.Journal of molecular and cellular cardiology · 2024Article
- scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison.NAR genomics and bioinformatics · 2024Article
- Deep Batch Integration and Denoise of Single-Cell RNA-Seq Data.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Molecular and network disruptions in neurodevelopment uncovered by single cell transcriptomics analysis ofHeliyon · 2024Article
- Beaconet: A Reference-Free Method for Integrating Multiple Batches of Single-Cell Transcriptomic Data in Original Molecular Space.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Integration mapping of cardiac fibroblast single-cell transcriptomes elucidates cellular principles of fibrosis in diverse pathologies.Science advances · 2024Article
- scDAPP: a comprehensive single-cell transcriptomics analysis pipeline optimized for cross-group comparison.bioRxiv : the preprint server for biology · 2024Article
- Comprehensive integration of single-cell transcriptomic data illuminates the regulatory network architecture of plant cell fate specification.Plant diversity · 2024Article
- SKP2 Knockout in Rb1/p53-Deficient Mouse Models of Osteosarcoma Induces Immune Infiltration and Drives a Transcriptional Program with a Favorable Prognosis.Molecular cancer therapeutics · 2024Article
- Semi-supervised integration of single-cell transcriptomics data.Nature communications · 2024Article
- Protective effects of macrophage-specific integrin α5 in myocardial infarction are associated with accentuated angiogenesis.Nature communications · 2023Article
- Cardiac Pericytes Acquire a Fibrogenic Phenotype and Contribute to Vascular Maturation After Myocardial Infarction.Circulation · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
In many biological applications of single-cell RNA sequencing (scRNA-seq), an integrated analysis of data from multiple batches or studies is necessary. Current methods typically achieve integration using shared cell types or covariance correlation between datasets, which can distort biological signals. Here we introduce an algorithm that uses the gene eigenvectors from a reference dataset to establish a global frame for integration. Using simulated and real datasets, we demonstrate that this approach, called Reference Principal Component Integration (RPCI), consistently outperforms other methods by multiple metrics, with clear advantages in preserving genuine cross-sample gene expression differences in matching cell types, such as those present in cells at distinct developmental stages or in perturbated versus control studies. Moreover, RPCI maintains this robust performance when multiple datasets are integrated. Finally, we applied RPCI to scRNA-seq data for mouse gut endoderm development and revealed temporal emergence of genetic programs helping establish the anterior-posterior axis in visceral endoderm.
Indexed as
Identifiers
What OpenQuestion holds
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.