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).

• Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome.

  PMID 15892868 · PMC1175952 · Genome biology · 2005 · 8 claims · 6 setups

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  Two quantitative benchmarks (functional-annotation-based and physical-interaction-based log likelihood ratio scores) can measure relative accuracy of human PPI datasets

  medline annotated interactions consolidated conditional co-citation bayesian

• Integration of text- and data-mining using ontologies successfully selects disease gene candidates.

  PMID 15767279 · PMC1065256 · Nucleic acids research · 2005 · 7 claims · 6 setups

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  Integrating eVOC anatomical ontology-based text-mining of PubMed abstracts with data-mining of gene expression annotation successfully selects and prioritizes candidate disease genes

  biomedical refseq training independent text-mining data-mining candidate

• Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information.

  PMID 15941473 · PMC1164402 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  A combined linguistic+statistical+rule-based method achieves precision 0.61 and recall 0.97 (f=0.74) detecting yeast protein-protein interactions across 12,300 Medline abstracts.

  yeast yeast-related interaction random dictionary-based manual graph

• Application of two machine learning algorithms to genetic association studies in the presence of covariates.

  PMID 19014573 · PMC2620353 · BMC genetics · 2008 · 8 claims · 3 setups

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  The relative performance of RF and MARS for detecting genotype-trait associations depends on both the strategy used to handle covariates and the true underlying model of association (e.g., confounding vs. mediation vs. interaction).

  simulated cohort simulation applied

• Feature context-dependency and complexity-reduction in probability landscapes for integrative genomics.

  PMID 18783599 · PMC2559821 · Theoretical biology & medical modelling · 2008 · 8 claims · 2 setups

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  Probability landscapes permit systematic detection, analysis, and utilization of feature context-dependency in genomic data.

  specified probability microarray

• Extraction of human kinase mutations from literature, databases and genotyping studies.

  PMID 19758464 · PMC2745582 · BMC bioinformatics · 2009 · 7 claims · 6 setups

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  A literature mining pipeline combining MutationFinder, false-positive filtering, and SVM-based classification can extract and disambiguate single-point mutation mentions from abstracts and full text

  pubmed large labeled swissprot literature supervised comparative

• Genome-wide prioritization of disease genes and identification of disease-disease associations from an integrated human functional linkage network.

  PMID 19728866 · PMC2768980 · Genome biology · 2009 · 6 claims · 6 setups

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  Integrating 16 genomic features (32 sub-features) via a naïve Bayes classifier produces a genome-scale FLN of 21,657 human genes and 22,388,609 weighted links that outperforms any individual data source for inferring functional linkages.

  genome gene omim known naïve linkage disease-centric

• Biocomputing enters its adolescence.

  PMID 15960815 · PMC1175967 · Genome biology · 2005 · 8 claims · 8 setups

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  A 'match augmentation' algorithm efficiently matches structural motifs by prioritizing functionally significant residues, enabling function prediction between evolutionarily unrelated proteins

  bank antibody-antigen yeast genome protein-protein empirical integrative

• Emergent dynamics of underlying regulatory network links EMT and androgen receptor-dependent resistance in prostate cancer.

  PMID 36851919 · PMC9957767 · Computational and structural biotechnology journal · 2023 · 8 claims · 7 setups

  Has reproduction · 78

  Simulations of the EMT-AR crosstalk network reveal four possible phenotypes: epithelial-sensitive (ES), epithelial-resistant (ER), mesenchymal-resistant (MR), and mesenchymal-sensitive (MS), with MS occurring rarely

  gene racipe clinical tcga racipe influence principal