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
RNA modifications detection by comparative Nanopore direct RNA sequencing.
PMID 34893601 · PMC8664944 · Nature communications · 2021 · 7 claims · 5 setups
Nanocompore is a model-free comparative method that uses a 2-component Gaussian mixture model (GMM) and univariate statistical tests on signal intensity/dwell time to detect RNA modifications in Nanopore direct RNA sequencing data without needing a training set
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Full-text index only
Identifying protein function--a call for community action.
PMID 15024411 · PMC368155 · PLoS biology · 2004 · 7 claims · 2 setups
Hypothetical and conserved hypothetical open reading frames together often represent more than half of the potential protein-coding regions of a sequenced genome, and their functions remain undetermined.
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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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Has reproduction · 44
Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.
PMID 23516341 · PMC3597545 · PLoS computational biology · 2013 · 8 claims · 7 setups
Local sequence context strongly determines position-specific polymerase kinetic rate: roughly 80% of IPD variation is explained by a 10 bp context (7 bases upstream, 2 bases downstream of the incorporation site), saturating at 7 bases upstream.