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).

• Comparative Genomics Provides Insight into the Function of Broad-Host Range Sponge Symbionts.

  PMID 34519538 · PMC8546597 · mBio · 2021 · 8 claims · 8 setups

  Has reproduction · 90

  Eleven new genomes were added to the Tethybacterales order and a novel family (Polydorabacteraceae) was identified

  tsitsikamma tethybacterales putative bin genome 16s multi-locus

• Graph-Based Approaches Significantly Improve the Recovery of Antibiotic Resistance Genes From Complex Metagenomic Datasets.

  PMID 34690959 · PMC8528159 · Frontiers in microbiology · 2021 · 8 claims · 6 setups

  Has reproduction · 75

  GraphAMR, a Nextflow pipeline that aligns AMR profile HMMs (or AA sequences) to metagenomic assembly graphs via PathRacer, then dereplicates and annotates hits, recovers more and more complete AMR genes than contig-based or read-based methods.

  urban soil ncbi profile metagenomic amr

• MiGPC: a comprehensive catalog of enzybiotics from environmental metagenomes.

  PMID 41888223 · PMC13172421 · Scientific reports · 2026 · 8 claims · 8 setups

  Has reproduction · 24

  MiGPC is the first genome-resolved metagenomic gene and protein catalog specifically targeted to enzybiotics

  environmental quality-filtered assembled predicted metagenomic metagenome gene

• A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.

  PMID 36333777 · PMC9636832 · Microbiome · 2022 · 7 claims · 6 setups

  Has reproduction · 64

  Genome-resolved metagenomics of separated foregut and midgut reconstructed 20 MAGs including novel lineages of Hepatoplasmataceae (foregut) and Deferribacteres (midgut).

  rimicaris foregut deferribacteres shotgun fluorescence yoyo-1

• SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes.

  PMID 36875992 · PMC9978240 · F1000Research · 2022 · 7 claims · 8 setups

  Has reproduction · 67

  SnakeMAGs is a simple, efficient, flexible and scalable Snakemake workflow that processes Illumina reads from raw data to MAG classification and relative abundance estimation

  publicly bins quality-filtered assembled workflow genome megahit

• Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.

  PMID 36192523 · PMC9529974 · Communications biology · 2022 · 8 claims · 8 setups

  Has reproduction · 68

  Built an integrated horse gut microbiome gene catalog (~25 million unique genes) and 372 metagenome-assembled genomes (MAGs) spanning 4179 genera and 95 phyla

  fecal horse dominant plasma shotgun taxonomic functional

• 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

  Has reproduction · 83

  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.

  pooled hc227 contig sets shotgun novo alignment-free

• What defines a photosynthetic microbial mat in western Antarctica?

  PMID 40043057 · PMC11882083 · PloS one · 2025 · 6 claims · 8 setups

  Has reproduction · 85

  Taxonomic composition of Antarctic microbial mat communities is characterized by similar bacterial groups across regions

  microbial quality-filtered overflowing shotgun taxonomic alpha

• Metagenomic analysis of respiratory tract DNA viral communities in cystic fibrosis and non-cystic fibrosis individuals.

  PMID 19816605 · PMC2756586 · PloS one · 2009 · 8 claims · 8 setups

  Full-text index only

  CF phage communities are highly similar to each other, whereas Non-CF individuals have more distinct, variable phage communities reflecting transient environmental sampling

  sputum phage metagenomes inferred metagenomic functional diversity