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).

• ChimerDB 2.0--a knowledgebase for fusion genes updated.

  PMID 19906715 · PMC2808913 · Nucleic acids research · 2010 · 8 claims · 4 setups

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  ChimerDB 2.0 is an updated knowledgebase integrating fusion transcripts from GenBank transcriptome analysis with Sanger CGP, OMIM, PubMed, and Mitelman's database data.

  genbank sra pubmed transcript-to-genome ngs literature

• QTL MatchMaker: a multi-species quantitative trait loci (QTL) database and query system for annotation of genes and QTL.

  PMID 16381937 · PMC1347390 · Nucleic acids research · 2006 · 8 claims · 5 setups

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  QTL MatchMaker integrates QTL information with physical, genetic and cytogenetic maps across human, mouse and rat genomes

  pubmed ucsc laser-captured literature genome comparative

• CancerGenes: a gene selection resource for cancer genome projects.

  PMID 17088289 · PMC1781153 · Nucleic acids research · 2007 · 6 claims · 4 setups

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  CancerGenes is a gene list-centric web resource that combines expert-annotated gene lists with data from public databases (Entrez Gene, Ensembl BioMart, Kim et al. promoter data, Sanger COSMIC) to support gene selection for cancer re-sequencing projects.

  genes chip-on-chip literature entrez

• ChimerDB--a knowledgebase for fusion sequences.

  PMID 16381848 · PMC1347382 · Nucleic acids research · 2006 · 8 claims · 6 setups

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  ChimerDB integrates bioinformatics analysis of mRNA/EST sequences, manually collected literature data, and OMIM translocation data into a single fusion sequence knowledgebase

  genome candidate pubmed omim blat splice-site ecgene

• A modular analysis framework for blood genomics studies: application to systemic lupus erythematosus.

  PMID 18631455 · PMC2727981 · Immunity · 2008 · 7 claims · 8 setups

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  Transcriptional modules constructed from coordinately expressed genes across 8 diseases form stable, biologically coherent functional units

  pbmc genes monocytes original microarray literature stimulation

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• G2Cdb: the Genes to Cognition database.

  PMID 18984621 · PMC2686544 · Nucleic acids research · 2009 · 7 claims · 7 setups

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  G2Cdb integrates experimentally validated synapse proteome datasets with mouse/human genomic annotation, phenotype, and human disease data in a gene-centric database.

  brain nervous genome synaptic proteomic large-scale sequence

• The European Bioinformatics Institute's data resources: towards systems biology.

  PMID 15608238 · PMC539980 · Nucleic acids research · 2005 · 8 claims · 5 setups

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  Since 2003 the EBI has launched new databases covering protein-protein interactions (IntAct), pathways (Reactome) and small molecules (ChEBI)

  proteins varies vertebrate newly macromolecular microarray protein-protein

• Systematic analysis of human kinase genes: a large number of genes and alternative splicing events result in functional and structural diversity.

  PMID 16351747 · PMC1866387 · BMC bioinformatics · 2005 · 8 claims · 7 setups

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  Systematic in silico search identified 5 novel human kinase genes (on chromosomes 1, 11, 13, 15, 16) and 1 pseudogene (chromosome X) absent from KinBase

  genome genomic kinase psi-blast comparative genscan