ReviewGenome biology2022
Statistics or biology: the zero-inflation controversy about scRNA-seq data.
Review in Genome biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 156 papers, 1 of them a synthesis that pooled it.
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
156 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Comparative transcriptomic meta-analysis reveals elevated TCL1A expression in human circulating immune cells across chronic pain conditions.British journal of anaesthesia · 2026Pooled it
- Restricted TCR Diversity and Expansion of CD177MedComm · 2026Article
- Reduced expression of Brain Expressed X-linked genes in Alzheimer's disease.Journal of Alzheimer's disease : JAD · 2026Article
- Canon enables causal inference of downstream genes in single-cell CRISPR studies via instrumental variable analysis.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- IAGRN: An Interleaved-Attention Graph Neural Network for Gene Regulatory Network Inference.International journal of molecular sciences · 2026Article
- Evaluating statistical models for overdispersed multiomics data: a multiplex immunofluorescence case study.American journal of epidemiology · 2026Article
- Data-intensive immune network modelling for One Health.Briefings in bioinformatics · 2026Review
- PLNFGL: joint estimation of multi-condition gene networks from single-cell RNA-seq data.Bioinformatics (Oxford, England) · 2026Article
- Cross-Modal Denoising and Integration of Spatial Multi-Omics Data with CANDIES.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Loss of chromosome Y in hematopoietic cells: mechanisms and implications for human disease.MedScience · 2026Review
- Highly Constrained Kinetic Models for Single-Cell Gene Expression Analysis.bioRxiv : the preprint server for biology · 2026Article
- Differential expression analysis in single-cell and spatial RNA-seq without model assumptions.Cell reports methods · 2026Article
- Inferring absolute counts from proportions by constraining multivariate normal distributions.NPJ systems biology and applications · 2026Article
- A unified framework for selecting and evaluating cell-type-specific gene co-expressions in single-cell data.Briefings in bioinformatics · 2026Article
- Immune cell annotation in the single-cell studies: technologies, challenges, and integrative solutions.Immunologic research · 2026Review
- scDEBGCL: a deep embedding approach based on bipartite graph contrastive learning for single-cell RNA-seq data.BMC biology · 2026Article
- Hypergraph representations of single-cell RNA sequencing data for improved cell clustering.Bioinformatics (Oxford, England) · 2026Article
- MetaScreener: a robust dual-mode framework for directional prioritization of actionable signatures through multi-dataset and multi-approach integration.Journal of translational medicine · 2026Article
- From noise to models to numbers: Evaluating negative binomial models and parameter estimations in single-cell RNA-seq.PLoS computational biology · 2026Article
- scDesignPop generates realistic population-scale single-cell RNA-seq for power analysis, benchmarking, and privacy protection.bioRxiv : the preprint server for biology · 2026Article
96 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
4 authors.
Funding
Abstract
Researchers view vast zeros in single-cell RNA-seq data differently: some regard zeros as biological signals representing no or low gene expression, while others regard zeros as missing data to be corrected. To help address the controversy, here we discuss the sources of biological and non-biological zeros; introduce five mechanisms of adding non-biological zeros in computational benchmarking; evaluate the impacts of non-biological zeros on data analysis; benchmark three input data types: observed counts, imputed counts, and binarized counts; discuss the open questions regarding non-biological zeros; and advocate the importance of transparent analysis.
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.