ArticleNature methods2023
Recovery of missing single-cell RNA-sequencing data with optimized transcriptomic references.
Article in Nature methods, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 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
37 citing papers in PubMed, 46 citations in OpenAlex.
- A hybrid transcriptome assembly reveals coding and noncoding landscapes in Drosophila hemocytes.Genetics · 2026Article
- Gravlax: an annotation-independent molecular evidence archive for single-cell RNA-seq.bioRxiv : the preprint server for biology · 2026Article
- Increasing usable reads in RNA-seq protocols.iScience · 2026Article
- WTAP-Mediated mAdvanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- StringTie3 improves total RNA-seq assembly by resolving nascent and mature transcripts.Nature methods · 2026Article
- Article
- Survodutide acts through circumventricular organs in the brain and activates neuronal regions associated with appetite regulation.Molecular metabolism · 2026Article
- YAP/TAZ-VGLL3 governs adipocyte fate via epigenetic reprogramming of PPARγ and its target enhancers.Science advances · 2026Article
- Article
- Distinct mechanisms of transcriptomic habituation to repeated stress in the mouse hippocampus.Nature communications · 2025Article
- A transcriptomic atlas of astrocyte heterogeneity across space and time in mouse and marmoset.Neuron · 2025Article
- MedakaBase as a unified genomic resource platform for medaka fish biology.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Article
- Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability.bioRxiv : the preprint server for biology · 2025Article
- Multi-omic identification of perineurial hyperplasia and lipid-associated nerve macrophages in human polyneuropathies.Nature communications · 2025Article
- A nociceptive amygdala-striatal pathway modulating affective-motivational pain.Science advances · 2025Article
- Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons.Nature communications · 2025Article
- Astrocyte regional specialization is shaped by postnatal development.bioRxiv : the preprint server for biology · 2025Article
- Projection-TAGs enable multiplex projection tracing and multi-modal profiling of projection neurons.bioRxiv : the preprint server for biology · 2025Article
- Mimicking opioid analgesia in cortical pain circuits.bioRxiv : the preprint server for biology · 2025Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
Single-cell RNA-sequencing (scRNA-seq) is an indispensable tool for characterizing cellular diversity and generating hypotheses throughout biology. Droplet-based scRNA-seq datasets often lack expression data for genes that can be detected with other methods. Here we show that the observed sensitivity deficits stem from three sources: (1) poor annotation of 3' gene ends; (2) issues with intronic read incorporation; and (3) gene overlap-derived read loss. We show that missing gene expression data can be recovered by optimizing the reference transcriptome for scRNA-seq through recovering false intergenic reads, implementing a hybrid pre-mRNA mapping strategy and resolving gene overlaps. We demonstrate, with a diverse collection of mouse and human tissue data, that reference optimization can substantially improve cellular profiling resolution and reveal missing cell types and marker genes. Our findings argue that transcriptomic references need to be optimized for scRNA-seq analysis and warrant a reanalysis of previously published datasets and cell atlases.
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.