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 · 89
TrEMOLO: accurate transposable element allele frequency estimation using long-read sequencing data combining assembly and mapping-based approaches.
PMID 37013657 · PMC10069131 · Genome biology · 2023 · 6 claims · 6 setups
TrEMOLO combines an assembly-based INSIDER module and a mapping-based OUTSIDER module to detect TE insertions/deletions from long-read sequencing data and estimate their allele frequency
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Collagen VI glycine mutations: perturbed assembly and a spectrum of clinical severity.
PMID 18825676 · PMC2743946 · Annals of neurology · 2008 · 8 claims · 6 setups
All eight new patients had heterozygous glycine substitution mutations toward the N-terminal end of the collagen VI triple helix
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Has reproduction · 89
Comparative genomics of dairy-associated Staphylococcus aureus from selected sub-Saharan African regions reveals milk as reservoir for human-and animal-derived strains and identifies a putative animal-related clade with presumptive novel siderophore.
PMID 36046020 · PMC9421002 · Frontiers in microbiology · 2022 · 7 claims · 8 setups
Milk serves as a reservoir for both human- and animal-derived S. aureus strains in sub-Saharan Africa
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Has reproduction · 75
A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics.
PMID 36748417 · PMC9836091 · Microbial genomics · 2022 · 8 claims · 6 setups
Long-read metagenomics enables isolation-independent identification and characterization of eae-positive STEC directly from raw milk.
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Has reproduction · 50
MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.
PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 6 claims · 6 setups
MEDUSA is an automated, Conda-installable and Snakemake-managed pipeline performing preprocessing, assembly, alignment, taxonomic classification, and functional annotation on shotgun data.
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Characterizing natural variation using next-generation sequencing technologies.
PMID 19801172 · PMC3994700 · Trends in genetics : TIG · 2009 · 8 claims · 8 setups
Next-generation sequencing enables complete, genome-wide surveys of genetic variation at unprecedented resolution, overcoming limitations of genotyping panels and microarrays.
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Human stool contains a previously unrecognized diversity of novel astroviruses.
PMID 19814825 · PMC2765957 · Virology journal · 2009 · 8 claims · 8 setups
Human stool contains a previously unrecognized diversity of astroviruses beyond the classic 8 serotypes and AstV-MLB1/AstV-VA1
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Has reproduction · 89
Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.
PMID 27092297 · PMC4820441 · Frontiers in cellular and infection microbiology · 2016 · 7 claims · 7 setups
STEC are prevalent in surface waters of four Lower Mainland BC watersheds, recovered from 21.6, 23.2, 19.5, and 9.2% of samples across sites, with seasonal variation (13.3% in fall to 34.3% in winter).
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Has reproduction · 50
Polymorphism identification and improved genome annotation of Brassica rapa through Deep RNA sequencing.
PMID 25122667 · PMC4232532 · G3 (Bethesda, Md.) · 2014 · 8 claims · 8 setups
330,995 SNPs were identified in transcribed regions between B. rapa genotypes R500 and IMB211, at an average frequency of one SNP per 200 bases.