ReviewBriefings in bioinformatics2025
The current landscape and emerging challenges of benchmarking single-cell methods.
Review in Briefings in bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
6 citing papers in PubMed.
- Benchmark pitfalls expose need for expert-guided spatial clustering.Nature methods · 2026Article
- Single-Cell and Spatial Omics: Methods and Applications.MedComm · 2026Review
- Building a continuous benchmarking ecosystem in bioinformatics.PLoS computational biology · 2025Article
- Insights, opportunities, and challenges provided by large cell atlases.Genome biology · 2025Review
- scMetaIntegrator: a meta-analysis approach to paired single-cell differential expression analysis.bioRxiv : the preprint server for biology · 2025Article
- Defining and benchmarking open problems in single-cell analysis.Research square · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors.
Funding
Abstract
With the rapid development of computational methods for single-cell sequencing data, benchmarking serves as a valuable resource. As the number of benchmarking studies surges, it is timely to assess the current state of the field. We conducted a systematic literature search and assessed 282 papers, including all 130 benchmark-only papers from the search and an additional 152 method development papers containing benchmarking. This collective effort provides the most comprehensive quantitative summary of the current landscape of single-cell benchmarking studies. We examine performances across nine broad categories, including often ignored aspects such as role of datasets, robustness of methods and downstream evaluation. Our analysis highlights challenges such as how to effectively combine knowledge across multiple benchmarking studies and in what ways can the community recognize the risk and prevent benchmarking fatigue. This paper highlights the importance of adopting a community-led research paradigm to tackle these challenges and establish best practice standards.
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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.