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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Towards the identification of essential genes using targeted genome sequencing and comparative analysis.
PMID 17052348 · PMC1624830 · BMC genomics · 2006 · 8 claims · 8 setups
Phyletic retention (ortholog presence across organisms) is the single most predictive feature of gene essentiality in both E. coli and S. cerevisiae.
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Assisted large fragment insertion by Red/ET-recombination (ALFIRE)--an alternative and enhanced method for large fragment recombineering.
PMID 17517785 · PMC1904275 · Nucleic acids research · 2007 · 6 claims · 7 setups
ALFIRE allows insertion of any fragment into small or large episomes without requiring an antibiotic selection gene in the final construct
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Bacteriophage Mu integration in yeast and mammalian genomes.
PMID 18953026 · PMC2602771 · Nucleic acids research · 2008 · 8 claims · 8 setups
In vitro-assembled Mu transpososomes, delivered by electroporation, efficiently integrate marker genes into yeast, mouse ES, human HeLa, and human ES cell genomes
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The use of multiple displacement amplification to amplify complex DNA libraries.
PMID 18285362 · PMC2275127 · Nucleic acids research · 2008 · 7 claims · 8 setups
MDA alone cannot select against/remove plasmid ligation multimers, unlike bacterial propagation
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A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm.
PMID 18034894 · PMC2241821 · BMC biotechnology · 2007 · 7 claims · 7 setups
A human scFv library was built on the single scFv13R4 framework with CDR3 loops diversified to mimic natural human CDR3 amino-acid distributions.
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Generation of a restriction minus enteropathogenic Escherichia coli E2348/69 strain that is efficiently transformed with large, low copy plasmids.
PMID 18681975 · PMC2518929 · BMC microbiology · 2008 · 8 claims · 7 setups
E2348/69 possesses a type I restriction-modification system encoded by an hsdMSR-like operon identified by homology to known Hsd proteins.
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An "omics" approach to uropathogenic Escherichia coli vaccinology.
PMID 19758805 · PMC2770165 · Trends in microbiology · 2009 · 8 claims · 8 setups
An 'omics'-based screening strategy integrating genomic, proteomic, and metabolomic data can identify PASivE UPEC proteins as vaccine candidates
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Zinc finger nucleases: custom-designed molecular scissors for genome engineering of plant and mammalian cells.
PMID 16251401 · PMC1270952 · Nucleic acids research · 2005 · 8 claims · 8 setups
ZFNs combining the FokI nuclease domain with custom zinc finger proteins can deliver site-specific double-strand breaks to plant and mammalian genomes.
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ksgA mutations confer resistance to kasugamycin in Neisseria gonorrhoeae.
PMID 19097863 · PMC2723803 · International journal of antimicrobial agents · 2009 · 8 claims · 6 setups
Spontaneous KSG-resistant N. gonorrhoeae mutants arise exclusively through mutations in ksgA, not rpsI
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Replication in mammalian cells recapitulates the locus-specific differences in somatic instability of genomic GAA triplet-repeats.
PMID 17142224 · PMC1669776 · Nucleic acids research · 2006 · 8 claims · 8 setups
Pure (GAA·TTC)44+ alleles at the FXN locus are unstable in human somatic cells in vivo, showing both expansions and contractions.
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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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Rapid creation of BAC-based human artificial chromosome vectors by transposition with synthetic alpha-satellite arrays.
PMID 15673719 · PMC548352 · Nucleic acids research · 2005 · 8 claims · 5 setups
Presence of CENP-B box elements is required for efficient de novo centromere formation in HAC vectors
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Retroposition and evolution of the DNA-binding motifs of YY1, YY2 and REX1.
PMID 17478514 · PMC1904287 · Nucleic acids research · 2007 · 8 claims · 5 setups
62 YY1-related sequences were identified across genomes ranging from flying insects to humans, with high zinc finger domain conservation
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Genomics: applications in mechanism elucidation.
PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups
Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.
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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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Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.
PMID 38587191 · PMC11077057 · Nucleic acids research · 2024 · 6 claims · 8 setups
A dual fluorescence (GFP-mCherry) readthrough reporter with a PAS inserted between the two reporters enables measurement of 3' end processing efficiency in living cells.