ArticlePLoS computational biology2023
Facilitating bioinformatics reproducibility with QIIME 2 Provenance Replay.
Article in PLoS computational biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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
12 citing papers in PubMed.
- Trustworthy Agentic AI in Bioinformatics: From Workflow Automation to Traceable and Validated Biological Inference.Biology · 2026Review
- Vaginal Microbiota and Ovarian Cancer: A New Frontier in Immunomodulation and Diagnosis.Immunology · 2026Review
- Progress and new challenges in image-based profiling.Molecular systems biology · 2026Review
- Review
- ViromeXplore: integrative workflows for complete and reproducible virome characterization.Briefings in bioinformatics · 2025Article
- Article
- Assessing microbiome engraftment extent following fecal microbiota transplant with q2-fmt.PLoS computational biology · 2025Article
- Study on characteristics of gut flora composition of pregnant women with preeclampsia.BMC pregnancy and childbirth · 2025Article
- Navigating complexities of polymorphic microbiomes in endometrial cancer.NPJ biofilms and microbiomes · 2025Article
- A bacteriophage-conditional mouse model reveals the impact of phages within a conventionally colonized gut microbiota.Cell host & microbe · 2025Article
- The Gut Microbiota Is Involved in the Regulation of Cognitive Flexibility in Adolescent BALB/c Mice Exposed to Chronic Physical Stress and a High-Fat Diet.Microorganisms · 2024Article
- Analysis of Human Milk Microbiota in Northern Greece by Comparative 16S rRNA Sequencing vs. Local Dairy Animals.Nutrients · 2024Article
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
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving many different tools. Additionally, many biologists are not trained in how to effectively record their bioinformatics analysis steps to ensure reproducibility, so critical information is often missing. Software tools used in bioinformatics can automate provenance tracking of the results they generate, removing most barriers to bioinformatics reproducibility. Here we present an implementation of that idea, Provenance Replay, a tool for generating new executable code from results generated with the QIIME 2 bioinformatics platform, and discuss considerations for bioinformatics developers who wish to implement similar functionality in their software.
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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.