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).

• Genome-wide analyses of retrogenes derived from the human box H/ACA snoRNAs.

  PMID 17175533 · PMC1802619 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  202 novel box H/ACA RNA-related sequences were identified in the human genome

  genome chimpanzee aca flanking megablast comparative sequence

• Integrative analysis of the human cis-antisense gene pairs, miRNAs and their transcription regulation patterns.

  PMID 19906709 · PMC2811022 · Nucleic acids research · 2010 · 8 claims · 5 setups

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  A genome-wide catalog of up to ~9000 overlapping antisense loci (23,782 non-redundant SAT pairs, clustered into 8894) was compiled and stored in the USAGP database

  genome affymetrix antisense mirna computational microarray sage

• G-quadruplexes: the beginning and end of UTRs.

  PMID 18832370 · PMC2577360 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  UTRs show significant strand asymmetry with C-PQS more common than G-PQS, consistent with general depletion of G-quadruplex-forming RNA

  genome 5'-utr simulated protein-coding computational high-resolution utr

• G-quadruplexes in promoters throughout the human genome.

  PMID 17169996 · PMC1802602 · Nucleic acids research · 2007 · 8 claims · 6 setups

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  Promoter regions (1 kb upstream of TSS) are significantly enriched in quadruplex motifs (PQS) relative to the rest of the genome

  genome quiescent gene synthetic computational nuclease gene

• Short tandem repeats in human exons: a target for disease mutations.

  PMID 18789129 · PMC2543027 · BMC genomics · 2008 · 8 claims · 6 setups

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  STRs are present in exons of 92% of known human genes, unlike longer tandem repeats which are rare in exons

  reference genome genes genome-wide indel disease

• Performance assessment of promoter predictions on ENCODE regions in the EGASP experiment.

  PMID 16925837 · PMC1810552 · Genome biology · 2006 · 6 claims · 3 setups

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  Promoter predictors that combine promoter prediction with gene prediction (N-SCAN, Fprom) achieve better performance than pure ab initio promoter predictors, mainly by reducing the promoter search space and false positives

  genome encode computational tss manual

• Identification of the proliferation/differentiation switch in the cellular network of multicellular organisms.

  PMID 17166053 · PMC1664705 · PLoS computational biology · 2006 · 8 claims · 8 setups

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  Integrating interactome and transcriptome data reveals a pair of transcriptionally anticorrelated network modules (P and D) each comprising hundreds of genes, present across individuals and species.

  postmortem genes gene proteins microarray protein-protein hierarchical

• The distribution of SNPs in human gene regulatory regions.

  PMID 16209714 · PMC1260019 · BMC genomics · 2005 · 8 claims · 6 setups

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  SNPs occur with higher density closer to the transcriptional start site within gene promoter regions than in further upstream regions

  gene mammalian promoter experimentally genome-wide computational binding

• Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

  PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups

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  Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments

  zebrafish computational seven consolidated whole-adult-organism supervised quantitative

• How accurately is ncRNA aligned within whole-genome multiple alignments?

  PMID 17963514 · PMC2206062 · BMC bioinformatics · 2007 · 7 claims · 4 setups

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  MULTIZ does a fairly accurate job of aligning ncRNA regions across 17 vertebrate genomes, but better alignments exist in some regions.

  genome vertebrate nonhuman genomic sequence whole-genome covariance

• GeneSeer: a sage for gene names and genomic resources.

  PMID 16176584 · PMC1266031 · BMC genomics · 2005 · 7 claims · 4 setups

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  GeneSeer aggregates gene name synonyms from GenBank, FlyBase, ExPASy, HUGO, ENSEMBL, UCSC and Gene Ontology into a name-translation database that maps any familiar name to a reference (SOFAR) identifier.

  sofar clusters rnai gene blast sequence shrna

• 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

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  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

• Single-molecule sequencing of an individual human genome.

  PMID 19668243 · PMC4117198 · Nature biotechnology · 2009 · 8 claims · 7 setups

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  Single-molecule sequencing without cloning, amplification or ligation can sequence an individual human genome on one instrument by a single operator in four runs

  genome staphylococcus single-molecule snp sanger

• Tri-nucleotide threading for parallel amplification of minute amounts of genomic DNA.

  PMID 16582098 · PMC1421508 · Nucleic acids research · 2006 · 6 claims · 5 setups

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  TnT enables parallel amplification of 75 SNPs from sub-nanogram amounts of genomic DNA

  genomic dbsnp tnt duplex bioinformatic