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).

• Shifts from cooperative to individual-based predation defense determine microbial predator-prey dynamics.

  PMID 36854789 · PMC10119117 · The ISME journal · 2023 · 8 claims · 4 setups

  Has reproduction · 84

  Across all 16 replicate co-cultures of P. putida and P. lacustris, bacteria show a consistent succession of defense strategies over five weeks (~35 predator generations).

  pseudomonas filamentous axenically semi-continuous morphometric whole-genome

• Reconstruction of 2,965 Microbial Genomes from Mangrove Sediments across Guangxi, China.

  PMID 41419779 · PMC12858935 · Scientific data · 2025 · 7 claims · 8 setups

  Has reproduction · 87

  A standardized assembly, binning, and dereplication pipeline was used to reconstruct 2,965 non-redundant MAGs from 38 mangrove sediment samples across six sites in Guangxi

  mangrove sediment quality-filtered bacterial whole-genome physicochemical laser

• Large-scale quality assessment of prokaryotic genomes with metashot/prok-quality.

  PMID 35136576 · PMC8804904 · F1000Research · 2021 · 8 claims · 6 setups

  Has reproduction · 98

  metashot/prok-quality is a container-enabled Nextflow pipeline for quality assessment and dereplication of draft prokaryotic genomes

  draft filtered chimeric genome chimerism ribosomal

• LMAS: evaluating metagenomic short de novo assembly methods through defined communities.

  PMID 36576131 · PMC9795473 · GigaScience · 2022 · 8 claims · 5 setups

  Has reproduction · 86

  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.

  zymobiomics assembled assembler-generated novo reference-based contig

• polishCLR: A Nextflow Workflow for Polishing PacBio CLR Genome Assemblies.

  PMID 36792366 · PMC9985148 · Genome biology and evolution · 2023 · 8 claims · 8 setups

  Has reproduction · 71

  polishCLR is a reproducible, containerized Nextflow workflow that implements best practices for polishing PacBio CLR genome assemblies.

  helicoverpa alternate contigs assemblies long-read short-read duplicate