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).

• Microbial metagenomics.

  PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups

  Full-text index only

  Metagenomic sequencing of the human GI tract reveals microbial community composition (e.g., Actinobacteria and Archaea prominence) differing from prior culture-based estimates dominated by Firmicutes and Bacteroides

  gastrointestinal acid ocean group metagenomic shotgun comparative

• Improving genomic prediction accuracy for methane emission and feed efficiency in sheep: integrating rumen microbial PCA with host genomic variation using neural network GBLUP (NN-GBLUP).

  PMID 40676527 · PMC12273308 · Genetics, selection, evolution : GSE · 2025 · 6 claims · 8 setups

  Has reproduction · 85

  PCA effectively reduces the dimensionality of high-dimensional RMC data while retaining essential biological information.

  sheep rumen rmc genomic rumen snp

• MBGD update 2010: toward a comprehensive resource for exploring microbial genome diversity.

  PMID 19906735 · PMC2808943 · Nucleic acids research · 2010 · 8 claims · 6 setups

  Full-text index only

  MBGD allows users to create ortholog groups using a specified subgroup of organisms, distinguishing it from other comparative genomics resources

  complete user-submitted ortholog mbgd hierarchical automated phylogenetic

• 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

• How bacterial communities expand functional repertoires.

  PMID 17238278 · PMC1750926 · PLoS biology · 2006 · 8 claims · 7 setups

  Full-text index only

  The human microbiome contains roughly 100 times as many genes as does the human genome

  bacteroides distal interleukin-10-deficient macrophages transcriptional metagenomic microbiota

• Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.

  PMID 38491422 · PMC10943865 · Genetics, selection, evolution : GSE · 2024 · 8 claims · 5 setups

  Full-text index only

  The host genome's influence on the functional rumen microbiome contributes to temporal variation in average daily gain (ADG1-ADG4) across finishing months in beef cattle.

  rumen blood beef metagenome snp longitudinal

• Unlocking the microbial studies through computational approaches: how far have we reached?

  PMID 36920617 · PMC10016191 · Environmental science and pollution research international · 2023 · 8 claims · 8 setups

  Has reproduction

  Metagenomics enables culture-independent study of microbial communities directly from their natural environments, bypassing the need for clonal isolation.

  clinical bacteriophage vaginal hbv ngs random whole-genome

• Comparative genomics and understanding of microbial biology.

  PMID 10998382 · PMC2627966 · Emerging infectious diseases · 2000 · 8 claims · 7 setups

  Full-text index only

  GC content varies widely among prokaryotic genomes (29% in B. burgdorferi to 68% in M. tuberculosis) and shapes codon usage and amino acid composition.

  completed same sequenced mycobacterium whole-genome comparative phylogenomic

• NCBI Reference Sequences: current status, policy and new initiatives.

  PMID 18927115 · PMC2686572 · Nucleic acids research · 2009 · 7 claims · 5 setups

  Full-text index only

  RefSeq is a curated, non-redundant, explicitly linked database of nucleotide and protein sequences spanning genomes, transcripts and proteins across prokaryotes, eukaryotes and viruses

  microbial bacterial prokaryotic refseq spliced structural functional

• CONSULT: accurate contamination removal using locality-sensitive hashing.

  PMID 34377979 · PMC8340999 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

  Has reproduction · 90

  CONSULT uses locality-sensitive hashing to test whether query k-mers fall within a user-defined Hamming distance of a reference k-mer database, allowing inexact matching against tens of thousands of microbial species.

  tree gtdb kraken-ii genome k-mer genome-skim organelle

• On the holobiont 'predictome' of immunocompetence in pigs.

  PMID 37127575 · PMC10150480 · Genetics, selection, evolution : GSE · 2023 · 8 claims · 8 setups

  Has reproduction · 40

  Holobiont (combined genotype + microbiome) models performed better than partial models (genotype-only or microbiome-only) overall

  duroc fecal plasma serum snp 16s immunoglobulin

• Unraveling the role of bacteria with heritable versus non-heritable relative abundance in the gut on boar semen quality.

  PMID 41199168 · PMC12590650 · Genetics, selection, evolution : GSE · 2025 · 6 claims · 7 setups

  Has reproduction · 61

  39 heritable and 91 non-heritable bacterial genera were identified in the boar gut based on heritability of relative abundance

  fecal blood boar gut 16s snp gas