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).
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Has reproduction · 86
The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.
PMID 37027361 · PMC10081788 · PloS one · 2023 · 7 claims · 7 setups
Obtaining an accurate species-level microbial profile using current direct-read metagenomics profiling software is still a challenging task.
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Has reproduction · 43
TransFlow: a Snakemake workflow for transmission analysis of Mycobacterium tuberculosis whole-genome sequencing data.
PMID 36469333 · PMC9825751 · Bioinformatics (Oxford, England) · 2023 · 8 claims · 8 setups
TransFlow is a Snakemake- and Conda-based workflow that combines state-of-the-art tools into a single, fast, scalable pipeline for MTBC WGS-based transmission analysis.
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Full-text index only
The global landscape of sequence diversity.
PMID 17996061 · PMC2258180 · Genome biology · 2007 · 7 claims · 5 setups
Eukaryotic sequence datasets show substantially greater genetic diversity (higher sequence/gene family discovery rates) than bacterial datasets, likely related to differences in modes of genetic inheritance.
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Full-text index only
Metagenomic study of the oral microbiota by Illumina high-throughput sequencing.
PMID 19796657 · PMC3568755 · Journal of microbiological methods · 2009 · 8 claims · 6 setups
The 16S rRNA V5 hypervariable region, amplified as a short ~82-base segment, provides reliable taxonomic identification of oral bacteria against public databases like HOMD.