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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TOFU-MAaPO: fast, scalable and reproducible analysis of large metagenome sequence data from the Sequence Read Archive.
PMID 42277027 · PMC13260335 · Nature communications · 2026 · 8 claims · 5 setups
TOFU-MAaPO yields significantly more high-quality MAGs than metaFun, nf-core/mag, and ATLAS due to integration of multiple complementary binning tools with unified MAGScoT refinement
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Has reproduction · 24
MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.
PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups
MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics
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Antimicrobial resistance dissemination via horizontal gene transfer is constrained in stratified waters.
PMID 41813906 · PMC13022341 · Communications biology · 2026 · 8 claims · 7 setups
No evidence for recent HGT-mediated dissemination of ARGs across depth layers was detected, despite genetic compatibility among co-occurring bacteria.
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metaFun: An analysis pipeline for metagenomic big data with fast and unified functional searches.
PMID 41530917 · PMC12818822 · Gut microbes · 2026 · 8 claims · 8 setups
metaFun is an open-source, end-to-end Nextflow/Apptainer pipeline integrating quality control, taxonomic profiling, functional profiling, de novo assembly, binning, genome assessment, comparative genomics, network analysis, and strain-level microdiversity analysis into a unified framework