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).

• In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

  PMID 17201911 · PMC1774567 · BMC genomics · 2007 · 8 claims · 5 setups

  Full-text index only

  A computational EST-based pipeline can identify UTR-SNPs that are statistically over-represented in cancerous versus normal tissue libraries

  est acute 100-nt whole-genome est-based pcr-based secondary

• Ab initio identification of human microRNAs based on structure motifs.

  PMID 18088431 · PMC2238772 · BMC bioinformatics · 2007 · 8 claims · 7 setups

  Full-text index only

  MiRPred predicts miRNA precursors ab initio using only predicted secondary structure motifs, ignoring nucleotide sequence

  genome mirna hairpins chromosome secondary linear five-fold

• Proceedings of the First International Conference on Phylogenomics. March 15-19, 2006. Quebec, Canada.

  PMID 17288567 · PMC1796603 · BMC evolutionary biology · 2007 · 8 claims · 8 setups

  Full-text index only

  Gene tree parsimony applied to EST data with widespread gene duplication can infer an organismal phylogeny in excellent agreement with the expected angiosperm phylogeny.

  angiosperms animal oryza proteobacteria gene site-heterogeneous codon

• Non-EST based prediction of exon skipping and intron retention events using Pfam information.

  PMID 16204458 · PMC1243800 · Nucleic acids research · 2005 · 7 claims · 5 setups

  Full-text index only

  A novel ab initio method predicts exon skipping and intron retention events using only Pfam domain annotation, via a Viterbi-like dynamic programming algorithm applied to the Pfam alignment.

  refseq dbest genome pfam initio est comparative

• Mice have a transcribed L-threonine aldolase/GLY1 gene, but the human GLY1 gene is a non-processed pseudogene.

  PMID 15757516 · PMC555945 · BMC genomics · 2005 · 8 claims · 8 setups

  Full-text index only

  Mouse has a transcribed, 7-exon L-threonine aldolase (GLY1) gene on chromosome 11 encoding a 400-residue protein homologous to bacterial threonine aldolase

  liver genomic tissues embryos rt-pcr genomic secondary

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

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

  Full-text index only

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

  genome chimpanzee aca flanking megablast comparative sequence

• Comparative analysis of genome tiling array data reveals many novel primate-specific functional RNAs in human.

  PMID 17288572 · PMC1796608 · BMC evolutionary biology · 2007 · 8 claims · 6 setups

  Full-text index only

  Widespread transcription occurs across the human genome outside known gene annotations, and the bulk of TARs represent genuine transcripts rather than experimental artifacts

  liver chimpanzee h-invitational tar genome blastn secondary

• DG-CST (Disease Gene Conserved Sequence Tags), a database of human-mouse conserved elements associated to disease genes.

  PMID 15608249 · PMC539965 · Nucleic acids research · 2005 · 5 claims · 8 setups

  Full-text index only

  Comparative human-mouse genome analysis identifies conserved sequence tags (CSTs, >=70% identity over >=100bp) that frequently correspond to non-coding elements with putative regulatory or structural roles

  identified cst csts comparative coding exon

• Tandem repeats modify the structure of human genes hosted in segmental duplications.

  PMID 19954527 · PMC2812944 · Genome biology · 2009 · 8 claims · 6 setups

  Full-text index only

  Around 7% of primate-specific genes located within segmental duplications contain variable internal tandem repeats (ITRs).

  genome genomic est paired genome-wide comparative cnv