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).

Publications 1.3k Datasets 392.5k Experiments 6

System / cell line: oral ✕ Assay: functional ✕ Clear

The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

PMID 20041198 · PMC2788695 · PLoS genetics · 2009 · 8 claims · 8 setups

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The B. dentium Bd1 genome was sequenced to completion, revealing a single circular 2,636,368 bp chromosome with 2,143 predicted ORFs

dentium core whole-genome 3d-structure comparative
Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease.

PMID 34830313 · PMC8625315 · International journal of molecular sciences · 2021 · 8 claims · 2 setups

Has reproduction · 79

TCDD dose-dependently enriches Lactobacillus species, particularly L. reuteri, in the mouse cecum microbiome

cecum fecal shotgun humann
Metagenomic and Untargeted Metabolomic Analysis of the Effect of Sporisorium reilianum Polysaccharide on Improving Obesity.

PMID 37107373 · PMC10137368 · Foods (Basel, Switzerland) · 2023 · 6 claims · 6 setups

Has reproduction

SRP intervention reduces obesity, serum lipid levels, hepatic lipid accumulation, and adipocyte hypertrophy in high-fat-diet rats, especially at high dose.

rats liver fecal srp body serum histology
A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

PMID 22719821 · PMC3374610 · PloS one · 2012 · 8 claims · 7 setups

Has reproduction · 78

METAREP version 1.3.1 is an open-source, scalable tool for querying, browsing and comparing extremely large volumes of metagenomic annotations, with an extended data model, dynamic weighting, distributed searches and advanced clustering.

microbiome pooled hmp metarep genome assembly-based enzymatic
Probing the cancer genome.

PMID 18492227 · PMC2441462 · Genome biology · 2008 · 8 claims · 8 setups

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Combined Sanger and 454 pyrosequencing of MCF-7 BAC clones identified 157 PCR-confirmed translocation breakpoint junctions, including 10 in-frame junctions confirmed at the transcript level

mcf-7 tumor lung oral sanger solexa gistic
Ligilactobacillus salivarius regulating translocation of core bacteria to enrich mouse intrinsic microbiota of heart and liver in defense of heat stress.

PMID 40276518 · PMC12018310 · Frontiers in immunology · 2025 · 7 claims · 6 setups

Has reproduction

Intrinsic microbiota (chiefly genera Burkholderia and Ralstonia) reside in the heart and liver of SPF mice, with the heart having lower bacterial abundance than the liver

spf heart ileum metagenomic culturomics 16s

Experiments

The Bifidobacterium dentium Bd1 genome sequence reflects its genetic adaptation to the human oral cavity.

Aryl Hydrocarbon Receptor (AhR) Activation by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin (TCDD) Dose-Dependently Shifts the Gut Microbiome Consistent with the Progression of Non-Alcoholic Fatty Liver Disease.

Metagenomic and Untargeted Metabolomic Analysis of the Effect of Sporisorium reilianum Polysaccharide on Improving Obesity.

A case study for large-scale human microbiome analysis using JCVI's metagenomics reports (METAREP).

Probing the cancer genome.

Ligilactobacillus salivarius regulating translocation of core bacteria to enrich mouse intrinsic microbiota of heart and liver in defense of heat stress.