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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V-MitoSNP: visualization of human mitochondrial SNPs.
PMID 16907992 · PMC1564046 · BMC bioinformatics · 2006 · 6 claims · 4 setups
V-MitoSNP integrates RFLP genotyping information with mitochondria-related cancer/disease data in a user-friendly, interactive, color-coded visual web interface
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Design factors that influence PCR amplification success of cross-species primers among 1147 mammalian primer pairs.
PMID 17029642 · PMC1635982 · BMC genomics · 2006 · 8 claims · 7 setups
The number of index-species (IS) mismatches in a primer pair significantly reduces amplification success, with an estimated 6-8% decrease in success rate per additional mismatch.
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Has reproduction · 99
Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets.
PMID 36513983 · PMC9749362 · BMC bioinformatics · 2022 · 8 claims · 7 setups
Long-read classifiers generally performed best among the 11 methods tested
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Detection of mutations in EGFR in circulating lung-cancer cells.
PMID 18596266 · PMC3551471 · The New England journal of medicine · 2008 · 8 claims · 7 setups
The CTC-chip microfluidic device isolates CTCs from NSCLC patients in sufficient quantity and purity to permit EGFR mutational analysis
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A novel role for mitochondria in regulating epigenetic modification in the nucleus.
PMID 18458531 · PMC2639623 · Cancer biology & therapy · 2008 · 8 claims · 6 setups
Mitochondria regulate epigenetic (DNA methylation) modification in the nucleus
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Analysis of copy number variation using quantitative interspecies competitive PCR.
PMID 18697816 · PMC2553599 · Nucleic acids research · 2008 · 7 claims · 6 setups
qicPCR uses the entire genome of a single chimpanzee as a competitor, requiring only one reference sample for all assays and enabling large-scale multiplexing
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Has reproduction · 99
Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing.
PMID 34103501 · PMC8187371 · Nature communications · 2021 · 7 claims · 4 setups
Nanopore methylation detection tools exhibit a tradeoff between false positives and false negatives and high dispersion relative to expected per-site methylation frequencies.
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Population history and natural selection shape patterns of genetic variation in 132 genes.
PMID 15361935 · PMC515367 · PLoS biology · 2004 · 7 claims · 5 setups
Developed a rigorous computational approach that corrects for multiple hypothesis testing and models population demographic history to test for natural selection
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BAC to the future! or oligonucleotides: a perspective for micro array comparative genomic hybridization (array CGH).
PMID 16439806 · PMC1356528 · Nucleic acids research · 2006 · 8 claims · 7 setups
oaCGH, not BAC CGH arrays, is the platform that will prevail in the future
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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.