ReviewNature communications2019
Systematic benchmarking of omics computational tools.
Review in Nature communications, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 3 of them syntheses 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
79 citing papers in PubMed, 3 syntheses or guidelines pooled it.
- Packaging and containerization of computational methods.Nature protocols · 2024Pooled it
- Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.Genome biology · 2023Pooled it
- Guidelines for benchmarking of optimization-based approaches for fitting mathematical models.Genome biology · 2019Guideline
- NeuroMetBench: patient-aware evidence bounds for transcript-derived metabolic representations across cancer proteogenomic contexts.Functional & integrative genomics · 2026Article
- Benchmarking of Reference-Based Tools for Strain-Level Resolution of Plant Microbiome.Molecular ecology resources · 2026Article
- The dark genome in cardiovascular medicine.European heart journal · 2026Review
- A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.NAR genomics and bioinformatics · 2026Article
- Multi-omics technologies: Novel tools and methods for assessing nerve injury and regeneration.Neural regeneration research · 2026Article
- Benchmarking RNA-seq with the Quartet and MAQC reference materials to establish best practices for accurate alternative splicing analysis.Nature communications · 2026Article
- Trends in Computational Metabolomics: A Perspective on Five Years of Software Development, Challenges, and Opportunities (2021-2025).Analytical chemistry · 2026Review
- Evidence standards for multi-ancestry polygenic prediction.Genome biology · 2026Review
- TADShop: systematic benchmarking and identification of topologically associating domains.Nature methods · 2026Article
- LEMMIv2: benchmarking framework for metagenomic and 16S amplicon profilers with a catalogue of evaluated tools.Genome biology · 2026Article
- A multi-agent platform for assessment and improvement of bioinformatics software documentation.bioRxiv : the preprint server for biology · 2026Article
- TaxaScope: a container-native, visualization-centric workstation for genome-based bacterial taxonomy.Frontiers in microbiology · 2026Article
- LungMicroHostR: an R package for integrated host-microbiome analysis of bronchoalveolar lavage fluid metagenomic sequencing data.Frontiers in bioinformatics · 2026Article
- Emerging trends and clinical challenges in AI-enhanced emotion diagnosis using physiological data.Medical & biological engineering & computing · 2026Review
- The current landscape and emerging challenges of benchmarking single-cell methods.Briefings in bioinformatics · 2025Review
- A Novel Spectral Barcoding and Classification Approach for Complex Biological Samples Using Multiexcitation Raman Spectroscopy (MX-Raman).Analytical chemistry · 2025Article
- Analysis of metagenomic data.Nature reviews. Methods primers · 2025Article
19 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
8 authors.
Funding
Abstract
Computational omics methods packaged as software have become essential to modern biological research. The increasing dependence of scientists on these powerful software tools creates a need for systematic assessment of these methods, known as benchmarking. Adopting a standardized benchmarking practice could help researchers who use omics data to better leverage recent technological innovations. Our review summarizes benchmarking practices from 25 recent studies and discusses the challenges, advantages, and limitations of benchmarking across various domains of biology. We also propose principles that can make computational biology benchmarking studies more sustainable and reproducible, ultimately increasing the transparency of biomedical data and results.
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.