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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Has reproduction · 79
Symbiosis genes show a unique pattern of introgression and selection within a Rhizobium leguminosarum species complex.
PMID 32176601 · PMC7276703 · Microbial genomics · 2020 · 8 claims · 8 setups
The 196 R. leguminosarum sv. trifolii strains constitute a five-species complex (genospecies gsA-gsE) that occur in sympatry but show little recent between-species gene transfer in core or accessory genomes, except for a few highly mobile regions.
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Has reproduction · 93
Population genomics of the Wolbachia endosymbiont in Drosophila melanogaster.
PMID 23284297 · PMC3527207 · PLoS genetics · 2012 · 8 claims · 8 setups
Wolbachia infection status can be accurately predicted in silico from whole-genome shotgun sequence of individual host strains, showing 99% concordance with diagnostic PCR.
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Phylogenetic variation and polymorphism at the toll-like receptor 4 locus (TLR4).
PMID 11104518 · PMC31919 · Genome biology · 2000 · 7 claims · 7 setups
The Tlr4 extracellular domain is far more variable than the cytoplasmic domain, both among mouse strains and among species
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Comparative genomics of multidrug resistance in Acinetobacter baumannii.
PMID 16415984 · PMC1326220 · PLoS genetics · 2006 · 7 claims · 5 setups
A. baumannii strain AYE contains an 86-kb genomic resistance island (AbaR1) clustering 45 of its 52 resistance genes, the largest resistance island described to date
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Has reproduction · 83
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
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.
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Has reproduction · 90
Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes.
PMID 35547116 · PMC9084900 · Frontiers in microbiology · 2022 · 8 claims · 8 setups
A novel early-branching Wolbachia strain (wTex), one of the earliest supergroup L strains, was discovered in a plant-parasitic nematode community from 1 of 16 sampled sites.
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Proteomic solutions for analytical challenges associated with alcohol research.
PMID 23584870 · PMC3860482 · Alcohol research & health : the journal of the National Institute on Alcohol Abuse and Alcoholism · 2008 · 7 claims · 4 setups
Protein-level meta-analyses analogous to the transcriptome meta-analysis by Mulligan et al. (2006) are not yet possible because proteins lack a uniform sample preparation/analysis method and span up to 8 orders of magnitude in abundance.
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Has reproduction · 89
Gut-derived Lactobacillus from exceptional responders mitigates chemoradiotherapy-induced intestinal injury through methionine-driven epigenetic modulation.
PMID 40469520 · PMC12130557 · iMeta · 2025 · 8 claims · 8 setups
High pretreatment gut abundance of Lactobacillus (and Bifidobacterium) is strongly associated with the absence of ACRIII in rectal cancer patients undergoing neoadjuvant chemoradiotherapy.
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More biology from the sequence.
PMID 11532209 · PMC138951 · Genome biology · 2001 · 8 claims · 8 setups
The Schizosaccharomyces pombe genome has been sequenced to completion with no gaps, telomere to telomere.
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Versatile and open software for comparing large genomes.
PMID 14759262 · PMC395750 · Genome biology · 2004 · 8 claims · 8 setups
MUMmer 3.0 efficiently handles comparisons of large eukaryotic genomes at varying evolutionary distances
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Of rats and men.
PMID 15003114 · PMC395761 · Genome biology · 2004 · 8 claims · 10 setups
The rat genome has been sequenced to draft level, with over 90% of the genome sampled using more than 36 million sequence reads (assembly version 3.1)
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Rats go genomic.
PMID 16522223 · PMC1431730 · Genome biology · 2006 · 7 claims · 8 setups
A systems biology approach combining genome-wide expression profiling with expression QTL (eQTL) mapping can identify candidate genes underlying complex-disease QTLs
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SNPdetector: a software tool for sensitive and accurate SNP detection.
PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups
SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection
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Microbial metagenomics.
PMID 16207365 · PMC1257460 · Genome biology · 2005 · 8 claims · 8 setups
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
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Complete genome sequence and comparative analysis of the wild-type commensal Escherichia coli strain SE11 isolated from a healthy adult.
PMID 18931093 · PMC2608844 · DNA research : an international journal for rapid publication of reports on genes and genomes · 2008 · 8 claims · 6 setups
The SE11 genome comprises a 4.8 Mb chromosome encoding 4679 protein-coding genes and six plasmids encoding 323 protein-coding genes
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The hemolytic and cytolytic activities of Serratia marcescens phospholipase A (PhlA) depend on lysophospholipid production by PhlA.
PMID 20003541 · PMC2800117 · BMC microbiology · 2009 · 8 claims · 8 setups
S. marcescens possesses a hemolytic factor independent of ShlA, revealed because an shlAB deletion mutant loses contact hemolysis but retains hemolysis on blood agar plates.
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Has reproduction · 52
Thermophilic and mesophilic sulfate reduction by rare biosphere bacteria in acidic metal-bearing mine wastes from the temperate climate zone.
PMID 41345487 · PMC12739157 · Scientific reports · 2025 · 8 claims · 8 setups
High in-situ sulfate reduction rates occur in acidic Bom-Gorkhon tailings sediments (up to 9.86 µmol SO4 cm-3 day-1 at 20 °C)
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Has reproduction · 95
Comparative Genome Analysis of 16SrXII-A 'Candidatus Phytoplasma solani' POT Transmitted by Hyalesthes obsoletus.
PMID 41597744 · PMC12843639 · Microorganisms · 2026 · 7 claims · 8 setups
The complete 832,614 bp circular chromosome of the H. obsoletus-transmissible 'Ca. P. solani' 16SrXII-A strain POT was assembled and functionally reconstructed.
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Has reproduction · 98
Diminutive, degraded but dissimilar: Wolbachia genomes from filarial nematodes do not conform to a single paradigm.
PMID 33295865 · PMC8116671 · Microbial genomics · 2020 · 8 claims · 4 setups
wCtub and wDcau (863 988 bp and 863 427 bp) are the smallest Wolbachia genomes sequenced to date and are the first genomes representing supergroup J.
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Kinetoplastid genomics: the thin end of the wedge.
PMID 18675383 · PMC2676795 · Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases · 2008 · 8 claims · 8 setups
Completion of the T. brucei, T. cruzi, and L. major genome sequencing projects enabled numerous studies that would otherwise have been difficult or impossible.