ArticleNature methods2017
Single-cell mRNA quantification and differential analysis with Census.
Article in Nature methods, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,186 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.
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.
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Who cites it
1,186 citing papers in PubMed, 2,084 citations in OpenAlex.
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- Integrated single-cell and metabolomic profiling identifies ovarian metabolic differences and endothelial heterogeneity associated with litter-size variation in Hu sheep.Journal of animal science and biotechnology · 2026Article
- Single-Nucleus Atlas of Spinal Sarcopenia Patients Reveals Disruption of Quiescent and Regenerative Satellite Cell Niches in Fatty-Infiltrated Muscle.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- A single-cell census of pulmonary endarterectomies tissue across different anatomical regions in chronic thromboembolic pulmonary hypertension.Clinical and translational medicine · 2026Article
- Nonexpansive biodegradable matrix promotes blood vessel organoid development for neurovascular repair and functional recovery in ischaemic stroke.Nature biomedical engineering · 2026Article
- Article
- Betulinic acid alleviates ankylosing spondylitis and remodels Th17/Treg-associated immune landscapes revealed by single-cell transcriptomics.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Single-cell RNA sequencing reveals chondrocyte heterogeneity and fibrocartilage transition in osteonecrosis of the femoral head.iScience · 2026Article
- Multi-Omics Analysis Identifies Fibroblast-Associated Stromal-Immune Networks Linked to Pregnancy-Associated Attenuation of Imiquimod-Induced Psoriatic Dermatitis.Biomedicines · 2026Article
- The development of single-cell lineage tracing technology and its application in immunotherapy.Molecular therapy. Advances · 2026Review
- HIF1AJournal for immunotherapy of cancer · 2026Article
- The long noncoding RNA Peanut (Gm11454) biases progenitors towards neurogenesis and rod photoreceptor differentiation during postnatal retinal development.Developmental biology · 2026Article
- Integrated analysis of single-cell and transcriptome data reveals temporal dynamics of microglial phagocytic reprogramming in neuropathic pain progression.Scientific reports · 2026Article
- Lineage-Specific CagA Binding Mechanics and Microenvironmental Rewiring in East Asian Gastric Carcinogenesis.Molecules (Basel, Switzerland) · 2026Article
- Single-cell and machine learning-based neural regulation signature for prognosis prediction and immunotherapy response in lung adenocarcinoma.Translational oncology · 2026Article
- Article
1,126 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
6 authors at 2 institutions in 1 country.
Funding
Abstract
Single-cell gene expression studies promise to reveal rare cell types and cryptic states, but the high variability of single-cell RNA-seq measurements frustrates efforts to assay transcriptional differences between cells. We introduce the Census algorithm to convert relative RNA-seq expression levels into relative transcript counts without the need for experimental spike-in controls. Analyzing changes in relative transcript counts led to dramatic improvements in accuracy compared to normalized read counts and enabled new statistical tests for identifying developmentally regulated genes. Census counts can be analyzed with widely used regression techniques to reveal changes in cell-fate-dependent gene expression, splicing patterns and allelic imbalances. We reanalyzed single-cell data from several developmental and disease studies, and demonstrate that Census enabled robust analysis at multiple layers of gene regulation. Census is freely available through our updated single-cell analysis toolkit, Monocle 2.
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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.