SynthesisGenome biology2023
Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.
Synthesis in Genome biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers, 2 of them syntheses that pooled it.
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
11 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- Deciphering cell-type-and temporally specific matrisome expression signatures in human cortical development and neurodevelopmental disorders via scRNA-seq meta-analysis.Nature communications · 2025Pooled it
- Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.Genome biology · 2023Pooled it
- Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments.Genome research · 2026Article
- Building a continuous benchmarking ecosystem in bioinformatics.PLoS computational biology · 2025Article
- Moderated designs can balance between batch-effect mitigation and cell loss due to hashtag-assisted pooling in single-cell experiments.bioRxiv : the preprint server for biology · 2025Article
- The current landscape and emerging challenges of benchmarking single-cell methods.Briefings in bioinformatics · 2025Review
- Defining and benchmarking open problems in single-cell analysis.Nature biotechnology · 2025Article
- Assessing the impact of transcriptomics data analysis pipelines on downstream functional enrichment results.Nucleic acids research · 2024Article
- Challenges and best practices in omics benchmarking.Nature reviews. Genetics · 2024Review
- Defining and benchmarking open problems in single-cell analysis.Research square · 2024Article
- The Quartet Data Portal: integration of community-wide resources for multiomics quality control.Genome biology · 2023Article
Corrections and comments
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Authors and funding
20 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computational methods represent the lifeblood of modern molecular biology. Benchmarking is important for all methods, but with a focus here on computational methods, benchmarking is critical to dissect important steps of analysis pipelines, formally assess performance across common situations as well as edge cases, and ultimately guide users on what tools to use. Benchmarking can also be important for community building and advancing methods in a principled way. We conducted a meta-analysis of recent single-cell benchmarks to summarize the scope, extensibility, and neutrality, as well as technical features and whether best practices in open data and reproducible research were followed. The results highlight that while benchmarks often make code available and are in principle reproducible, they remain difficult to extend, for example, as new methods and new ways to assess methods emerge. In addition, embracing containerization and workflow systems would enhance reusability of intermediate benchmarking results, thus also driving wider adoption.
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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.