ArticleBriefings in bioinformatics2023
The five pillars of computational reproducibility: bioinformatics and beyond.
Article in Briefings in bioinformatics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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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.
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Who cites it
40 citing papers in PubMed.
- A reproducible entropy-weighted Gower-CLARA-TOPSIS procedure for mixed-type MSME segmentation and prioritization.MethodsX · 2026Article
- Reproducibility in biomedical research.Nature medicine · 2026Review
- A practical guide to studying genome function using single-molecule genomics.Nature reviews. Molecular cell biology · 2026Review
- Article
- Do papers tell the whole story? A benchmark and framework for uncovering hidden implementation gaps in bioinformatics.Briefings in bioinformatics · 2026Article
- Integrating Mutation-Derived and Expression Features from Single-Cell RNA Sequencing: Pitfalls of Standard Cross-Validation in Small-Cohort Settings.International journal of molecular sciences · 2026Article
- Critical Artifacts Improve Reproducibility of Protein-Ligand Binding Affinity Prediction Models on CASF-2016.Journal of chemical information and modeling · 2026Article
- Evidence standards for multi-ancestry polygenic prediction.Genome biology · 2026Review
- SNPio: a Python interface for population genomic data processing.BMC bioinformatics · 2026Article
- Eras of bioinformatics technologies from command-line interfaces to artificial intelligence (AI) chatbots.Briefings in bioinformatics · 2026Review
- ScriptManager: a platform for scalable and reproducible high-resolution analysis of genomics datasets.bioRxiv : the preprint server for biology · 2026Article
- MetaNet: a scalable and integrated tool for reproducible omics network analysis.Bioinformatics (Oxford, England) · 2026Article
- Ten simple rules for executing an inherited research plan in computational biology.PLoS computational biology · 2026Article
- scArchon: a scalable benchmarking framework for assessing single-cell perturbation models.Genome biology · 2026Article
- Toward trustworthy artificial intelligence in multi-omics: a review of reproducibility, stability, and interpretability.Briefings in bioinformatics · 2026Review
- Artificial intelligence for antimicrobial resistance: advancing reproducibility, interpretability, and clinical deployment.Briefings in bioinformatics · 2026Review
- Progress and new challenges in image-based profiling.Molecular systems biology · 2026Review
- AutoRNAseq: Automated Bulk RNA-seq Analysis Pipeline.bioRxiv : the preprint server for biology · 2026Article
- Ten common mistakes that could ruin your enrichment analysis.PLoS computational biology · 2026Article
- Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Computational reproducibility is a simple premise in theory, but is difficult to achieve in practice. Building upon past efforts and proposals to maximize reproducibility and rigor in bioinformatics, we present a framework called the five pillars of reproducible computational research. These include (1) literate programming, (2) code version control and sharing, (3) compute environment control, (4) persistent data sharing and (5) documentation. These practices will ensure that computational research work can be reproduced quickly and easily, long into the future. This guide is designed for bioinformatics data analysts and bioinformaticians in training, but should be relevant to other domains of study.
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Registered trials
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