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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Prediction of catalytic residues using Support Vector Machine with selected protein sequence and structural properties.
PMID 16790052 · PMC1534064 · BMC bioinformatics · 2006 · 8 claims · 7 setups
The Sequential Minimal Optimization (SMO) SVM algorithm was the best-performing classifier among 26 WEKA classifiers for predicting catalytic residues
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Evolutionary algorithms for the selection of single nucleotide polymorphisms.
PMID 12875658 · PMC183839 · BMC bioinformatics · 2003 · 8 claims · 3 setups
Evolutionary algorithms are well suited to multiobjective optimization problems with large, intractable search spaces such as SNP selection, unlike exact methods (exhaustive enumeration) or single-objective search techniques (tabu search, simulated annealing).
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iMapper: a web application for the automated analysis and mapping of insertional mutagenesis sequence data against Ensembl genomes.
PMID 18974167 · PMC2639305 · Bioinformatics (Oxford, England) · 2008 · 6 claims · 3 setups
iMapper is a web application for automated analysis and mapping of insertional mutagenesis sequence data against vertebrate and invertebrate Ensembl genomes (human, mouse, rat, zebrafish, Drosophila, S. cerevisiae).
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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.