ArticleGenome biology2021
On the optimistic performance evaluation of newly introduced bioinformatic methods.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers, 1 of them a synthesis that pooled it.
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Who cites it
16 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis of (single-cell method) benchmarks reveals the need for extensibility and interoperability.Genome biology · 2023Pooled it
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- ganon2: up-to-date and scalable metagenomics analysis.NAR genomics and bioinformatics · 2025Article
- Evaluating computational tools for protein-coding sequence detection: Are they up to the task?RNA (New York, N.Y.) · 2025Article
- Defining and benchmarking open problems in single-cell analysis.Nature biotechnology · 2025Article
- A bioinformatician, computer scientist, and geneticist lead bioinformatic tool development-which one is better?Bioinformatics advances · 2025Article
- Challenges and best practices in omics benchmarking.Nature reviews. Genetics · 2024Review
- Defining and benchmarking open problems in single-cell analysis.Research square · 2024Article
- Seqpac: a framework for sRNA-seq analysis in R using sequence-based counts.Bioinformatics (Oxford, England) · 2023Article
- The shaky foundations of simulating single-cell RNA sequencing data.Genome biology · 2023Article
- Computational prediction of human deep intronic variation.GigaScience · 2022Review
- Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.Microbiome · 2022Article
- Critical assessment of computational tools for prokaryotic and eukaryotic promoter prediction.Briefings in bioinformatics · 2022Article
- Sustained software development, not number of citations or journal choice, is indicative of accurate bioinformatic software.Genome biology · 2022Article
- DECONbench: a benchmarking platform dedicated to deconvolution methods for tumor heterogeneity quantification.BMC bioinformatics · 2021Article
- On the optimistic performance evaluation of newly introduced bioinformatic methods.Genome biology · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most research articles presenting new data analysis methods claim that "the new method performs better than existing methods," but the veracity of such statements is questionable. Our manuscript discusses and illustrates consequences of the optimistic bias occurring during the evaluation of novel data analysis methods, that is, all biases resulting from, for example, selection of datasets or competing methods, better ability to fix bugs in a preferred method, and selective reporting of method variants. We quantitatively investigate this bias using an example from epigenetic analysis: normalization methods for data generated by the Illumina HumanMethylation450K BeadChip microarray.
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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.