ArticleBioinformatics (Oxford, England)2018
bioBakery: a meta'omic analysis environment.
Article in Bioinformatics (Oxford, England), 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 240 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
240 citing papers in PubMed, 2 syntheses or guidelines pooled it.
- A two-cohort study on the association between the gut microbiota and bone density, microarchitecture, and strength.Frontiers in endocrinology · 2023Pooled it
- Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin.Genome biology · 2022Pooled it
- Effect of Household Air Pollution on the Gut Microbiome and Virome of Adult Women Living in Uganda.Environmental health perspectives · 2026Trial
- Trial
- Altered Salivary Microbiota Following Bifidobacterium animalis Subsp. Lactis BL-11 Supplementation Are Associated with Anthropometric Growth and Social Behavior Severity in Individuals with Prader-Willi Syndrome.Probiotics and antimicrobial proteins · 2022Trial
- Gut Microbial Stability is Associated with Greater Endurance Performance in Athletes Undertaking Dietary Periodization.mSystems · 2022Trial
- Microbiome connections with host metabolism and habitual diet from 1,098 deeply phenotyped individuals.Nature medicine · 2021Trial
- Effects of a low dose of 3-nitrooxypropanol and a combination of direct-fed microbials on methane emission, oral swab bacterial community, and performance in dairy cows.Journal of animal science and biotechnology · 2026Article
- Exploring the Oral Resistome: From Metagenomics to Precision Oral Health.Microorganisms · 2026Review
- CAMEO: a CAZyme mapping engine optimized for HUMAnN.Microbiology resource announcements · 2026Article
- Microbial transmission and ecology of human and environmental microbial communities in childcare centers.Research square · 2026Article
- A geroprotective probiotic and its functional metabolite counteract inflammaging to extend healthspan.Nature aging · 2026Article
- Integrative analysis of rumen microbiota activity and host metabolism following methanogenesis inhibition in dairy cattle.Microbiology spectrum · 2026Article
- Prevalence and chronology of colibactin-associated mutational processes and their microbiome spectra in Japanese colorectal cancer.Nature genetics · 2026Article
- A protocol for the Teen Bugs study: An integrative, multi-omics approach to understanding the role of the gut microbiome and mesocorticolimbic system in adolescent mental health following early adverse caregiving.Brain, behavior, & immunity - health · 2026Article
- Tracing NADCell reports · 2026Article
- TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.Nature communications · 2026Article
- Eucommia ulmoides leaves improving growth by regulating the rumen microbiome in sheep.BMC microbiology · 2026Article
- Attenuation of Immune Senescence Markers After Intensive Cancer Therapy Through Resistance Training: A Pilot Study.Cancers · 2026Article
- Complex correlations between mitochondrial DNA variants and gut microbiome in major depressive disorder: a genome-wide association analysis.BMC psychiatry · 2026Article
180 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
Summary: bioBakery is a meta'omic analysis environment and collection of individual software tools with the capacity to process raw shotgun sequencing data into actionable microbial community feature profiles, summary reports, and publication-ready figures. It includes a collection of pre-configured analysis modules also joined into workflows for reproducibility. Availability and implementation: bioBakery (http://huttenhower.sph.harvard.edu/biobakery) is publicly available for local installation as individual modules and as a virtual machine image. Each individual module has been developed to perform a particular task (e.g. quantitative taxonomic profiling or statistical analysis), and they are provided with source code, tutorials, demonstration data, and validation results; the bioBakery virtual image includes the entire suite of modules and their dependencies pre-installed. Images are available for both Amazon EC2 and Google Compute Engine. All software is open source under the MIT license. bioBakery is actively maintained with a support group at biobakery-users@googlegroups.com and new tools being added upon their release. Contact: chuttenh@hsph.harvard.edu. Supplementary information: Supplementary data are available at Bioinformatics online.
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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.