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).

• Ensembl 2009.

  PMID 19033362 · PMC2686571 · Nucleic acids research · 2009 · 8 claims · 6 setups

  Full-text index only

  Ensembl provides comprehensive, consistently annotated genome information for chordate genomes with automatically generated genesets and comparative genomics data

  horse mammalian chromosome ensembl post-gene-build genome gerp

• RNASEQR--a streamlined and accurate RNA-seq sequence analysis program.

  PMID 22199257 · PMC3315322 · Nucleic acids research · 2012 · 8 claims · 7 setups

  Has reproduction · 86

  RNASEQR is a new RNA-seq mapper/aligner that combines a BWT-based (Bowtie) transcriptomic/genomic alignment with hash-based BLAT local alignment in three sequential steps: transcriptome mapping, novel exon detection, and anchor-and-align novel splice junction identification.

  ccds glioblastoma experimental simulated simulated bulk quality

• Functional analysis of novel SNPs and mutations in human and mouse genomes.

  PMID 19091009 · PMC2638150 · BMC bioinformatics · 2008 · 8 claims · 7 setups

  Full-text index only

  FANS streamlines functional analysis of novel SNPs and mutations into a simplified, few-click, four-step procedure.

  apoe 11-nucleotide sequence genomic manual automated exonic

• An optimized procedure for the design and evaluation of Ecotilling assays.

  PMID 18973671 · PMC2586031 · BMC genomics · 2008 · 8 claims · 7 setups

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  An optimized procedure integrating Vector NTI, Ensembl, Genomatix Suite, GelBuddy, and sequencing/functional-prediction tools streamlines the design, evaluation and interpretation of human Ecotilling assays

  genomic gene pcr cdna ecotilling sequence sanger

• miRBase: tools for microRNA genomics.

  PMID 17991681 · PMC2238936 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  miRBase release 10.0 contains 5071 miRNA hairpin loci from 58 species, expressing 5922 distinct mature miRNA sequences, a growth of over 2000 sequences in 2 years

  species utrs genomic chromosome genome-wide target transcription

• A Deluge of Complex Repeats: The Solanum Genome.

  PMID 26241045 · PMC4524691 · PloS one · 2015 · 8 claims · 7 setups

  Has reproduction · 94

  ~50–60% of the S. tuberosum and S. lycopersicum genomes are composed of repetitive elements

  tuberosum orthologous identified de-novo genome-wide transcriptional

• SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements.

  PMID 18174224 · PMC2238826 · Nucleic acids research · 2008 · 6 claims · 5 setups

  Full-text index only

  Standard genome annotation pipelines misannotate selenoprotein genes because they rely on UGA as a universal stop codon, failing to recognize its dual role as the selenocysteine-recoding codon.

  genomic cdna known sequence homology transcript

• SelTarbase, a database of human mononucleotide-microsatellite mutations and their potential impact to tumorigenesis and immunology.

  PMID 19820113 · PMC2808963 · Nucleic acids research · 2010 · 7 claims · 6 setups

  Full-text index only

  SelTarbase is a curated relational database of published mononucleotide-repeat mutation data from MSI-H human colorectal, gastric, endometrial tumors and colon cancer cell lines.

  msi-h aggregated genome mnr sigmoid genome-wide

• The vertebrate genome annotation (Vega) database.

  PMID 18003653 · PMC2238886 · Nucleic acids research · 2008 · 8 claims · 8 setups

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  Vega is a database for viewing manual genome annotation of human, mouse and zebrafish genomic sequences produced at the Wellcome Trust Sanger Institute.

  genome zebrafish pig nod manual comparative transcript