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).

• ARED 3.0: the large and diverse AU-rich transcriptome.

  PMID 16381826 · PMC1347415 · Nucleic acids research · 2006 · 7 claims · 6 setups

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  ARED 3.0 computationally mapped more than 4000 ARE-mRNAs to the human genome, representing 5-8% of human genes.

  records est est-derived combined computational est sequence

• An integrated database-pipeline system for studying single nucleotide polymorphisms and diseases.

  PMID 19091018 · PMC2638159 · BMC bioinformatics · 2008 · 6 claims · 5 setups

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  Existing SNP/disease databases are fragmented; no combined resource widely supports gene-, SNP-, and disease-related information together

  private disease uniprot snps database controlled sequence

• SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry.

  PMID 19036792 · PMC2686442 · Nucleic acids research · 2009 · 8 claims · 7 setups

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  SysPIMP is a web-based platform integrating disease mutation databases with X!Tandem and BLAST to identify disease-related mutated proteins from MS results

  omim pmd swissprot msipi database sequence tandem

• Designating eukaryotic orthology via processed transcription units.

  PMID 18445630 · PMC2425467 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Existing ortholog databases discard/ignore alternative splicing via all-against-all protein comparisons, causing ambiguous ortholog calls and misclassification of AS isoforms as in-paralogs

  ortholog blat exon-intron blast-based

• GenBank.

  PMID 16381837 · PMC1347519 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  GenBank is a comprehensive public database of nucleotide sequences with supporting bibliographic and biological annotation, built and distributed by NCBI.

  sapiens organisms genbank large-scale genome expressed blast

• Structure SNP (StSNP): a web server for mapping and modeling nsSNPs on protein structures with linkage to metabolic pathways.

  PMID 17537826 · PMC1933130 · Nucleic acids research · 2007 · 7 claims · 5 setups

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  StSNP integrates dbSNP, PDB, KEGG, and NCBI Entrez data into a single web server for nsSNP analysis

  glutathione aldehyde sequences dbsnp comparative sequence-structure database

• MODBASE, a database of annotated comparative protein structure models and associated resources.

  PMID 18948282 · PMC2686492 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  MODBASE contains 5,152,695 reliable comparative protein structure models for 1,593,209 unique protein sequences.

  sequences chains template chain comparative pairwise ligand