Experiments
Searchable full-text extractions: founding hypothesis, core claims, experimental setups, key results and statistics — pulled out of each paper as structure. Search a cell line, an assay or an entity (e.g. HUH7) and find every paper that worked with it. This corpus stands on its own: most entries carry no reproduction assessment (yet).
-
Has reproduction · 59
The effect of 16S rRNA region choice on bacterial community metabarcoding results.
PMID 30720800 · PMC6362892 · Scientific data · 2019 · 8 claims · 8 setups
The V2-V3 16S rRNA fragment has higher resolution for lower-rank taxa (genera and species) than V3-V4, enabling more precise distance-based OTU clustering.
-
Has reproduction · 83
Accurate prediction of metagenome-assembled genome completeness by MAGISTA, a random forest model built on alignment-free intra-bin statistics.
PMID 35248155 · PMC8898458 · Environmental microbiome · 2022 · 7 claims · 7 setups
MAGISTA, a random forest model built on alignment-free intra-bin distance-distribution statistics, can estimate MAG completeness and purity without relying on reference marker genes.
-
Has reproduction · 85
Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens.
PMID 33103064 · PMC7568946 · One health outlook · 2020 · 8 claims · 3 setups
An open-access pathogen surveillance database (NCBI Pathogen Detection) plus contributor Best Practices enables FAIR, interoperable genomic data across human, animal, food, and environmental sources for One Health surveillance.
-
Has reproduction · 92
Draft Genome Sequences of Antimicrobial-Resistant Shigella Clinical Isolates from Pakistan.
PMID 31346012 · PMC6658682 · Microbiology resource announcements · 2019 · 6 claims · 7 setups
Draft genome sequences of three multidrug-resistant Shigella clinical isolates from Pakistan (two S. flexneri, one S. sonnei) are reported as a resource for AMR surveillance.
-
Has reproduction · 44
An OMICs-based meta-analysis to support infection state stratification.
PMID 33560295 · PMC8388022 · Bioinformatics (Oxford, England) · 2021 · 7 claims · 6 setups
Multi-class Random Forest models built from meta-analyzed blood gene expression data can predict infection state (bacterial/viral/none) with high accuracy, correctly classifying 93% of bacterial and 89% of viral samples in the best model.
-
Has reproduction · 66
RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.
PMID 36159175 · PMC9492272 · NAR genomics and bioinformatics · 2022 · 8 claims · 6 setups
RiboTaxa, combining BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2's Sklearn classifier, was built as a pipeline for SSU rRNA-based taxonomic profiling of metagenomics data.
-
Has reproduction · 50
The molecular landscape of sepsis severity in infants: enhanced coagulation, innate immunity, and T cell repression.
PMID 38817614 · PMC11137207 · Frontiers in immunology · 2024 · 8 claims · 8 setups
Only two of seven published sepsis gene signatures (derived from adult/pediatric/geriatric cohorts) showed good concordance (>80% accuracy) when applied to infant sepsis, showing limited generalizability of non-infant signatures.
-
Has reproduction · 55
Environment and Co-occurring Native Mussel Species, but Not Host Genetics, Impact the Microbiome of a Freshwater Invasive Species (Corbicula fluminea).
PMID 35444631 · PMC9014210 · Frontiers in microbiology · 2022 · 7 claims · 7 setups
The gut microbiome of C. fluminea is diverse, differs with environmental conditions, and varies spatially among rivers, but is unrelated to host genetic variation
-
Has reproduction · 86
LMAS: evaluating metagenomic short de novo assembly methods through defined communities.
PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups
LMAS (Last Metagenomic Assembler Standing) is a flexible, Nextflow-based, Docker-containerized automated workflow for benchmarking de novo metagenomic assemblers against defined mock communities, producing an interactive HTML report.
-
Has reproduction · 89
DFAST and DAGA: web-based integrated genome annotation tools and resources.
PMID 27867804 · PMC5107635 · Bioscience of microbiota, food and health · 2016 · 8 claims · 7 setups
DFAST is a web-based genome annotation pipeline with integrated quality assessment (CheckM) and taxonomic assessment (ANI) that produces DDBJ submission-ready files
-
Has reproduction · 50
MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.
PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 6 claims · 6 setups
MEDUSA is an automated, Conda-installable and Snakemake-managed pipeline performing preprocessing, assembly, alignment, taxonomic classification, and functional annotation on shotgun data.