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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A statistical approach designed for finding mathematically defined repeats in shotgun data and determining the length distribution of clone-inserts.
PMID 15626332 · PMC5172250 · Genomics, proteomics & bioinformatics · 2003 · 8 claims · 6 setups
Repeats of different copy number have distinct probabilities of appearance in shotgun data, which can be modeled statistically to define recognition thresholds (MDRs) at different shotgun coverages.
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Identifying drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.
PMID 19997482 · PMC2776985 · PLoS computational biology · 2009 · 7 claims · 4 setups
An ILP formulation of the Boolean pathway optimization problem fits phosphoproteomic data faster and more efficiently than the previously used genetic algorithm (GA) approach.
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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.