ReviewGenome biology2019
Essential guidelines for computational method benchmarking.
Review in Genome biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers, 2 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
86 citing papers in PubMed, 2 syntheses or guidelines pooled it, 21 citations in OpenAlex.
- 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
- Comparison of the Cox Proportional Hazards Model and Random Survival Forest Algorithm for Predicting Patient-Specific Survival Probabilities in Clinical Trial Data.Biometrical journal. Biometrische Zeitschrift · 2026Article
- Review
- SURE-Pipe: a pipeline to compare genomes and extract shared and unique regions.NAR genomics and bioinformatics · 2026Article
- A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq nanopore long reads data.NAR genomics and bioinformatics · 2026Article
- A Framework for Benchmarking Pathway Reconstruction Algorithms.bioRxiv : the preprint server for biology · 2026Article
- Introducing openESM: A database of openly available experience sampling datasets.Behavior research methods · 2026Article
- Evidence standards for multi-ancestry polygenic prediction.Genome biology · 2026Review
- A systematic benchmarking framework and dual-view optimization strategy for single-cell DNA methylation imputation.Briefings in bioinformatics · 2026Article
- Robust Metabolomics Data Normalization across Scales and Experimental Designs.Analytical chemistry · 2026Article
- Ten simple rules for executing an inherited research plan in computational biology.PLoS computational biology · 2026Article
- A benchmarking framework for comparative evaluation of low-complexity region detection tools in the human proteome.Scientific reports · 2026Article
- LungMicroHostR: an R package for integrated host-microbiome analysis of bronchoalveolar lavage fluid metagenomic sequencing data.Frontiers in bioinformatics · 2026Article
- How benchmarking of bioinformatics tools is essential for informed workflow selection: a case study on SARS-CoV-2 subgenomic RNA detection.Frontiers in bioinformatics · 2026Article
- A comparison of computational methods for expression forecasting.Genome biology · 2025Article
- Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms.Bioinformatics (Oxford, England) · 2025Article
- Building a continuous benchmarking ecosystem in bioinformatics.PLoS computational biology · 2025Article
- GHIST 2024: The First Genomic History Inference Strategies Tournament.Molecular biology and evolution · 2025Article
- No Reproducibility, No Progress: Rethinking CT Benchmarking.Journal of imaging · 2025Article
26 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
9 authors at 6 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
In computational biology and other sciences, researchers are frequently faced with a choice between several computational methods for performing data analyses. Benchmarking studies aim to rigorously compare the performance of different methods using well-characterized benchmark datasets, to determine the strengths of each method or to provide recommendations regarding suitable choices of methods for an analysis. However, benchmarking studies must be carefully designed and implemented to provide accurate, unbiased, and informative results. Here, we summarize key practical guidelines and recommendations for performing high-quality benchmarking analyses, based on our experiences in computational biology.
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.