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).

• Application of functional genomics to the chimeric mouse model of HCV infection: optimization of microarray protocols and genomics analysis.

  PMID 16725047 · PMC1482685 · Virology journal · 2006 · 6 claims · 4 setups

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  Mouse liver mRNA cross-hybridizes to corresponding human gene probes on the Agilent Human 22K oligonucleotide microarray

  liver genomic hcv-infected agilent two-color semi-quantitative real-time

• Ab initio identification of putative human transcription factor binding sites by comparative genomics.

  PMID 15865625 · PMC1097714 · BMC bioinformatics · 2005 · 8 claims · 5 setups

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  An integrated algorithm combining human-mouse genomic comparison, motif overrepresentation, and coregulation filters (GO annotation and microarray coexpression) can identify candidate transcription factor binding sites genome-wide

  human-mouse conserved gene consensus comparative statistical gene

• Transcription of the human and rodent SPAM1 / PH-20 genes initiates within an ancient endogenous retrovirus.

  PMID 15804358 · PMC1079825 · BMC genomics · 2005 · 8 claims · 8 setups

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  Human, mouse, and rat SPAM1/Spam1 transcripts initiate within an ERV1 pol (internal coding) region rather than within an LTR

  testis panel genome 5'-race non-quantitative

• 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

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

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

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  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

• H-DBAS: human-transcriptome database for alternative splicing: update 2010.

  PMID 19969536 · PMC2808982 · Nucleic acids research · 2010 · 8 claims · 4 setups

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  RNA-Seq tags from the polysome fraction identify AS exons that are very likely used for protein synthesis

  dld-1 rna-seq western real-time

• Computing Ka and Ks with a consideration of unequal transitional substitutions.

  PMID 16740169 · PMC1552089 · BMC evolutionary biology · 2006 · 7 claims · 7 setups

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  MYN, a modified version of the Yang-Nielsen (YN) algorithm based on the Tamura-Nei Model, allows unequal transitional substitution rates between purines (κR) and pyrimidines (κY) plus codon frequency bias

  simulated pairs human-mouse human-dog computer comparative

• Ultraconserved coding regions outside the homeobox of mammalian Hox genes.

  PMID 18816392 · PMC2566984 · BMC evolutionary biology · 2008 · 7 claims · 7 setups

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  Ultraconserved coding regions (UCRs, ≥120 nt with no synonymous or nonsynonymous substitutions) exist outside the homeobox in mammalian Hox genes

  orthologous hox concatenated intronic sliding comparative molecular