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).

• SVC: structured visualization of evolutionary sequence conservation.

  PMID 15991338 · PMC1160265 · Nucleic acids research · 2005 · 7 claims · 5 setups

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  SVC aligns protein-coding sequences of orthologous gene pairs and maps them back onto their encoding exons/introns to generate a scaffold of conserved gene structure.

  orthologous exonic tblastx blastn sliding-window

• Human SNPs resulting in premature stop codons and protein truncation.

  PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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  Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

  genome transcripts validated x-snp-encoded database blast exon-intron

• 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

• Expoldb: expression linked polymorphism database with inbuilt tools for analysis of expression and simple repeats.

  PMID 17038195 · PMC1618849 · BMC genomics · 2006 · 8 claims · 6 setups

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  EXPOLDB is a novel database integrating human gene expression variability data (including monozygotic twin comparisons) with (TG/CA)n repeat polymorphism information

  blood genomic genes housekeeping microarray repeat est-based

• Distribution and effects of nonsense polymorphisms in human genes.

  PMID 18852891 · PMC2561068 · PloS one · 2008 · 8 claims · 8 setups

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  Nonsense SNPs occur at a lower density than nonsynonymous SNPs, indicating stronger purifying selection against premature stop codons than amino acid changes.

  genome genes nonsense snps genome-wide snp codon

• Genome informatics: taming the avalanche of genomic data.

  PMID 15642109 · PMC549058 · Genome biology · 2005 · 8 claims · 7 setups

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  Ultraconserved regions (>100 bp, 100% conserved among mammals) exist in the genome and their function remains unknown

  genes arabidopsis genome vertebrate comparative conservation whole-genome