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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Manual annotation and analysis of the defensin gene cluster in the C57BL/6J mouse reference genome.
PMID 20003482 · PMC2807441 · BMC genomics · 2009 · 8 claims · 6 setups
Manual annotation of the mouse Chromosome 8 defensin region identifies 98 gene loci: 54 in the alpha-defensin cluster and 44 in the beta-defensin cluster
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Has reproduction · 84
Main Factors Influencing the Gut Microbiota of Datong Yaks in Mixed Group.
PMID 35883324 · PMC9312300 · Animals : an open access journal from MDPI · 2022 · 7 claims · 6 setups
Gut microbial diversity (alpha and beta) differs significantly among domestic males, domestic females, and wild male Datong yaks.
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Has reproduction · 62
Metatranscriptomics of the human oral microbiome during health and disease.
PMID 24692635 · PMC3977359 · mBio · 2014 · 8 claims · 8 setups
Disease-associated periodontal communities display conserved community-level metabolic gene expression profiles between patients, whereas the metabolic gene expression of individual species is highly variable between patients.
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Has reproduction · 99
Verrucomicrobia are prevalent in north-temperate freshwater lakes and display class-level preferences between lake habitats.
PMID 29590198 · PMC5874073 · PloS one · 2018 · 8 claims · 8 setups
Verrucomicrobia is highly prevalent in north-temperate freshwater lakes, on average the 4th most abundant phylum (range 1.7–41.7%).
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Has reproduction · 87
Machine learning reveals microbial interactions driving plastic degradation across plastisphere environments.
PMID 41657981 · PMC12876002 · Frontiers in microbiology · 2025 · 6 claims · 7 setups
Wastewater plastispheres harbor the most diverse and compositionally even microbial communities among the three habitats.
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Has reproduction · 75
Different Intestinal Microbiota with Growth Stages of Three-Breed Hybrid Pig.
PMID 35978648 · PMC9377885 · BioMed research international · 2022 · 7 claims · 5 setups
The composition and relative abundance of intestinal microbiota in three-breed hybrid pigs differ significantly across growth stages (60, 120, 180 days)
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Has reproduction · 100
Niche Modification by Sulfate-Reducing Bacteria Drives Microbial Community Assembly in Anoxic Marine Sediments.
PMID 36988509 · PMC10128000 · mBio · 2023 · 7 claims · 7 setups
SRB modify niches (e.g., pH) to affect species coexistence during organic matter degradation
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Insights into the physiology of childbirth using transcriptomics.
PMID 16752954 · PMC1475648 · PLoS medicine · 2006 · 7 claims · 4 setups
Labor results in a change in the transcriptome in each component of the uterus studied
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HaploSNPer: a web-based allele and SNP detection tool.
PMID 18307806 · PMC2288614 · BMC genetics · 2008 · 6 claims · 2 setups
HaploSNPer is a web-based tool integrating BLASTN, CAP3/PHRAP, and QualitySNP into a single pipeline for allele and SNP detection from diploid and polyploid species
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In vivo application of RNA interference: from functional genomics to therapeutics.
PMID 16096010 · PMC7112075 · Advances in genetics · 2005 · 7 claims · 7 setups
RNAi operates through two mechanistically related but distinct pathways: cytoplasmic delivery of siRNA duplexes and nuclear delivery of shRNA expression cassettes that mimic miRNA
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Has reproduction · 61
Tourmaline: A containerized workflow for rapid and iterable amplicon sequence analysis using QIIME 2 and Snakemake.
PMID 35902092 · PMC9334028 · GigaScience · 2022 · 8 claims · 1 setups
Tourmaline is a Python-based workflow that implements QIIME 2 using the Snakemake workflow management system to automate amplicon sequence analysis.
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Has reproduction · 78
Disrupted PGR-B and ESR1 signaling underlies defective decidualization linked to severe preeclampsia.
PMID 34709177 · PMC8553341 · eLife · 2021 · 8 claims · 5 setups
A 120-gene endometrial transcriptomic fingerprint encodes defective decidualization associated with severe preeclampsia.
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Has reproduction · 80
Recombination Facilitates Adaptive Evolution in Rhizobial Soil Bacteria.
PMID 34410427 · PMC8662638 · Molecular biology and evolution · 2021 · 8 claims · 7 setups
α varies from 0.07 to 0.39 across five Rhizobium species and is positively correlated with the level of recombination
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Has reproduction · 68
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
Built an integrated horse gut microbiome gene catalog (~25 million unique genes) and 372 metagenome-assembled genomes (MAGs) spanning 4179 genera and 95 phyla
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A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.
PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups
Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units
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Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.
PMID 19907653 · PMC2771352 · PloS one · 2009 · 8 claims · 7 setups
IL10 haplotype 1 (rs1800871, rs1800872, rs3024490, rs1554286) is associated with a pro-inflammatory ex vivo cytokine response (lower IL-10, higher TNF-alpha) relative to the population mean
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Threshold-dominated regulation hides genetic variation in gene expression networks.
PMID 18062810 · PMC2238762 · BMC systems biology · 2007 · 8 claims · 2 setups
Threshold robustness (insensitivity of a singular/regulating variable's equilibrium value to parameter perturbations, except threshold changes) increases with increasing response function steepness and is present even under Michaelis-Menten conditions, not just in the step-function limit.
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Has reproduction · 67
Trem2 promotes anti-inflammatory responses in microglia and is suppressed under pro-inflammatory conditions.
PMID 32959884 · PMC7689298 · Human molecular genetics · 2020 · 8 claims · 8 setups
Trem2 promotes/drives the IL-4-induced anti-inflammatory gene expression program (e.g. Arg1, Ap1b1) in microglia, and reduced Trem2 attenuates this response.
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Has reproduction · 56
Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.
PMID 35862823 · PMC9426513 · mSystems · 2022 · 8 claims · 5 setups
The vast majority of recovered gene cluster families (GCFs) in sponge microbiomes show no similarity to any characterized BGC, revealing extreme biosynthetic novelty
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Speeding disease gene discovery by sequence based candidate prioritization.
PMID 15766383 · PMC1274252 · BMC bioinformatics · 2005 · 7 claims · 8 setups
Disease genes (OMIM) differ significantly from non-disease genes in sequence-based features including gene/cDNA/protein size, exon number, homolog conservation, secretion signal, 3' UTR length, CpG islands, and distance to nearest gene.