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 · 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.
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Testing groups of genomic locations for enrichment in disease loci using linkage scan data: a method for hypothesis testing.
PMID 16848972 · PMC3525155 · Human genomics · 2006 · 8 claims · 2 setups
A method testing enrichment of a group of genomic locations for disease loci by comparing the average NPL score of the group to a null distribution from randomly drawn groups of equal size
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Has reproduction · 59
Nucleosome regulatory dynamics in response to TGFβ.
PMID 24771338 · PMC4066760 · Nucleic acids research · 2014 · 8 claims · 7 setups
SuMMIt, a Bayesian strand-based mixture model requiring support from both ends of sequenced fragments, enables precise nucleosome mid-position calling, fuzziness scoring and between-condition change detection.
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Analyses and comparison of accuracy of different genotype imputation methods.
PMID 18958166 · PMC2569208 · PloS one · 2008 · 8 claims · 3 setups
Stronger LD produces higher imputation accuracy rates for all five methods
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Has reproduction · 67
binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.
PMID 36239393 · PMC9677464 · Briefings in bioinformatics · 2022 · 8 claims · 8 setups
binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods (MetaBAT2, MaxBin2, CONCOCT, VAMB, SemiBin, MetaDecoder)
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A qualitative assessment of direct-labeled cDNA products prior to microarray analysis.
PMID 15762992 · PMC1079821 · BMC genomics · 2005 · 5 claims · 5 setups
The Agilent 2100 Bioanalyzer can be used in a novel assay to assess the quality/quantity of direct-labeled Cy-dye cDNA prior to microarray hybridization
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Direct inference of SNP heterozygosity rates and resolution of LOH detection.
PMID 18052545 · PMC2098867 · PLoS computational biology · 2007 · 6 claims · 7 setups
A large proportion of SNPs in dbSNP have high-variance HET rate estimates, limiting their reliability for LOH study design.
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Has reproduction · 45
Identifying and classifying trait linked polymorphisms in non-reference species by walking coloured de bruijn graphs.
PMID 23536903 · PMC3607606 · PloS one · 2013 · 8 claims · 9 setups
Bubbleparse detects sequence variants directly from NGS reads without a reference genome, using the coloured de Bruijn graph implementation of Cortex plus a new depth-first bubble-finding module.
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Has reproduction · 33
Tracing truth: dynamic temporal networks for multi-modal fake news detection.
PMID 40989433 · PMC12453775 · PeerJ. Computer science · 2025 · 8 claims · 5 setups
The proposed dynamic temporal network (DTN) model improves multi-modal fake news detection accuracy by capturing temporal dynamics of propagation nodes and dynamically fusing multi-modal information.