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 · 50
Grad-seq identifies KhpB as a global RNA-binding protein in Clostridioides difficile that regulates toxin production.
PMID 37223250 · PMC10117727 · microLife · 2021 · 8 claims · 9 setups
Grad-seq resolves in-gradient sedimentation profiles for ~87-88% of annotated C. difficile transcripts and ~50% of annotated proteins, providing a comprehensive RNA-protein complexome resource
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Helicobacter pylori: after the genomes, back to biology.
PMID 12668641 · PMC2193897 · The Journal of experimental medicine · 2003 · 8 claims · 5 setups
STM screening of 960 H. pylori mutants in gerbils identifies genes required for in vivo colonization
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Evidence of recombination in Hepatitis C Virus populations infecting a hemophiliac patient.
PMID 19922637 · PMC2784780 · Virology journal · 2009 · 7 claims · 6 setups
A new intragenotypic recombinant HCV strain (1b/1a), named H23, was detected in 1 of 10 hemophiliac patients studied
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Analysis of a set of missense, frameshift, and in-frame deletion variants of BRCA1.
PMID 18992264 · PMC2682550 · Mutation research · 2009 · 8 claims · 8 setups
A combined functional assay, bioinformatics prediction, and structural modeling approach can classify BRCA1 variants of uncertain significance
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Phenotypic screening, transcriptional profiling, and comparative genomic analysis of an invasive and non-invasive strain of Candida albicans.
PMID 18950481 · PMC2579918 · BMC microbiology · 2008 · 8 claims · 8 setups
Strain SC5314 is invasive and virulent whereas strain ATCC10231 is non-invasive and strongly attenuated in virulence
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Has reproduction · 63
Genetic analysis of Leishmania donovani tropism using a naturally attenuated cutaneous strain.
PMID 24992200 · PMC4081786 · PLoS pathogens · 2014 · 8 claims · 8 setups
The CL-SL L. donovani isolate is severely attenuated for survival in visceral organs (liver, spleen) of BALB/c mice compared with the VL-SL isolate, while inducing transient footpad swelling that VL-SL does not.
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Pathway analysis for intracellular Porphyromonas gingivalis using a strain ATCC 33277 specific database.
PMID 19723305 · PMC2753363 · BMC microbiology · 2009 · 8 claims · 5 setups
Using the ATCC 33277-specific genome annotation improves proteome coverage (more proteins identified and more abundance ratios calculated) compared to the W83 annotation
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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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Four genomic islands that mark post-1995 pandemic Vibrio parahaemolyticus isolates.
PMID 16672049 · PMC1464126 · BMC genomics · 2006 · 8 claims · 7 setups
Seven genomic islands (VPaI-1 to VPaI-7, 10-81 kb) were identified in V. parahaemolyticus RIMD2210633 by aberrant GC content, presence of integrases/transposases, flanking direct repeats, and absence from related Vibrionaceae genomes.
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Short tandem repeat sequences in the Mycoplasma genitalium genome and their use in a multilocus genotyping system.
PMID 18664269 · PMC2515158 · BMC microbiology · 2008 · 8 claims · 7 setups
18 STR loci (1-5 base repeat units, copy number 4-26) were identified in the M. genitalium G37 genome via bioinformatics analysis.
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Genome analysis of multi- and extensively-drug-resistant tuberculosis from KwaZulu-Natal, South Africa.
PMID 19890396 · PMC2767505 · PloS one · 2009 · 8 claims · 4 setups
Rifampicin resistance (rpoB) and pyrazinamide resistance (pncA) mutations occur at different nucleotide positions in the MDR and XDR strains, showing they were acquired independently and that the XDR strain did not evolve directly from this MDR strain.
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Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.
PMID 17912347 · PMC1989137 · PloS one · 2007 · 8 claims · 8 setups
MIP is the evolutionary predecessor/ancestor of the pathogenic Mycobacterium avium intracellulare complex (MAIC), having retained a free-living lifestyle rather than undergoing parasitic reductive genome evolution
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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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Comparative genomic analysis of the gut bacterium Bifidobacterium longum reveals loci susceptible to deletion during pure culture growth.
PMID 18505588 · PMC2430713 · BMC genomics · 2008 · 8 claims · 8 setups
Comparative genomics of B. longum DJO10A (minimally cultured) and NCC2705 (culture collection strain) reveals 17 unique DNA regions in DJO10A and 6 in NCC2705 despite otherwise high genome collinearity and identity
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Forward genetic analysis of the apicomplexan cell division cycle in Toxoplasma gondii.
PMID 18282098 · PMC2242837 · PLoS pathogens · 2008 · 8 claims · 6 setups
A high-throughput ENU mutagenesis screen isolated 165 temperature-sensitive (ts) Toxoplasma growth mutants from ~60,000 clones.
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Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies.
PMID 19915672 · PMC2772813 · PloS one · 2009 · 8 claims · 8 setups
MLSA of 89 genes across 108 global MTBC strains yields a single, highly robust phylogeny with virtually no homoplasy, congruent across parsimony, NJ, ML, and Bayesian methods.
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NeMeSys: a biological resource for narrowing the gap between sequence and function in the human pathogen Neisseria meningitidis.
PMID 19818133 · PMC2784325 · Genome biology · 2009 · 8 claims · 5 setups
Determined and manually annotated the complete genome sequence of N. meningitidis clinical isolate strain 8013
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Has reproduction · 86
Comprehensive Genomic and Phenotypic Characterization of Escherichia coli O78:H9 Strain HPVN24 Isolated from Diarrheic Poultry in Vietnam.
PMID 41156725 · PMC12565876 · Microorganisms · 2025 · 7 claims · 8 setups
HPVN24 is an avian pathogenic E. coli serotype O78:H9, sequence type ST23, with a 5.05 Mb genome and 50.57% GC content.
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Has reproduction · 46
De novo transcriptome assembly and comprehensive assessment provide insight into fruiting body formation of Sparassis latifolia.
PMID 35773379 · PMC9247108 · Scientific reports · 2022 · 6 claims · 7 setups
De novo transcriptome assembly of S. latifolia produced 48,549 unigenes, 71.53% (34,728) of which were annotated against KEGG, GO, and/or KOG databases
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Has reproduction · 100
Analysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen Pectobacterium aroidearum in Amorphophallus konjac Using Comparative Genomics.
PMID 35910650 · PMC9326479 · Frontiers in microbiology · 2022 · 8 claims · 8 setups
The causal agent of konjac soft rot in China is Pectobacterium aroidearum, confirmed via in vitro/in vivo pathogenicity tests, ANI, dDDH, and phylogenomic analysis.