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).

• GeneKeyDB: a lightweight, gene-centric, relational database to support data mining environments.

  PMID 15790402 · PMC1274265 · BMC bioinformatics · 2005 · 8 claims · 6 setups

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  GeneKeyDB is a lightweight, gene-centric relational database that supports data mining and integration with computational analysis tools.

  genekeydb database gene automated

• g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments.

  PMID 17478515 · PMC1933153 · Nucleic acids research · 2007 · 8 claims · 5 setups

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  g:Profiler integrates four modules (g:Profiler core, g:Convert, g:Orth, g:Sorter) into a single cross-linked web tool for gene list analysis

  input 1000-bp microarray organisms functional transcription gene

• BIPASS: BioInformatics Pipeline Alternative Splicing Services.

  PMID 17584795 · PMC1933140 · Nucleic acids research · 2007 · 8 claims · 4 setups

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  BIPASS offers two complementary services for alternative splicing (AS) research: BIPAS-SpliceDB, a queryable pre-computed AS data warehouse, and BIPAS-Align&Splice, an online pipeline for user-submitted sequences.

  transcript aligned pre-computed user-submitted sequence alternative database

• R2DT is a framework for predicting and visualising RNA secondary structure using templates.

  PMID 34108470 · PMC8190129 · Nature communications · 2021 · 8 claims · 6 setups

  Has reproduction · 87

  R2DT is a template-based computational framework/pipeline that predicts and visualises RNA 2D structure in standardised, community-accepted layouts

  rnacentral query input aligned covariance trna-specific structure-guided

• SNPmasker: automatic masking of SNPs and repeats across eukaryotic genomes.

  PMID 16845091 · PMC1538889 · Nucleic acids research · 2006 · 8 claims · 4 setups

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  SNPmasker is a web service combining SNP masking and repeat masking, supporting both coordinate-defined and homology-search-defined input regions, a combination not offered by prior tools

  genome reference genomic runtime sequence comparative

• Peptide bioinformatics: peptide classification using peptide machines.

  PMID 19065810 · PMC7122642 · Methods in molecular biology (Clifton, N.J.) · 2008 · 8 claims · 4 setups

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  The bio-basis function, which converts peptides into numerical vectors using nongapped pairwise homology alignment scores against indicator peptides, can statistically quantify peptide similarity for classification.

  illustrative query generic synthetic bio-basis orthogonal hyperplane

• Gene-disease relationship discovery based on model-driven data integration and database view definition.

  PMID 19042916 · PMC2639000 · Bioinformatics (Oxford, England) · 2009 · 8 claims · 4 setups

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  Explicit gene–disease relationships can be formulated as candidate gene definitions (e.g., co-localization, dysregulation, functional similarity) that may include intermediary orthologous or interacting genes

  acgr disease term-based database case

• PA-GOSUB: a searchable database of model organism protein sequences with their predicted Gene Ontology molecular function and subcellular localization.

  PMID 15608166 · PMC540074 · Nucleic acids research · 2005 · 7 claims · 4 setups

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  PA-GOSUB significantly extends the coverage of GO molecular function and subcellular localization annotations for 10 model organism proteomes compared with existing databases (GOA, Swiss-Prot).

  sequences query swiss-prot naive-bayes blast feature