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).

• Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

  PMID 15103394 · PMC393292 · PLoS biology · 2004 · 8 claims · 5 setups

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  41,118 full-length human cDNAs from six high-throughput sequencing projects were exhaustively integratively characterized

  genome transcriptome gene genes full-length genome cdna

• The genome and development-dependent transcriptomes of Pyronema confluens: a window into fungal evolution.

  PMID 24068976 · PMC3778014 · PLoS genetics · 2013 · 8 claims · 8 setups

  Has reproduction · 76

  The 50 Mb P. confluens genome with 13,369 predicted protein-coding genes is more characteristic of higher filamentous ascomycetes than of the large, repeat-rich Tuber melanosporum genome, showing that the truffle's expanded genome is not typical of the Pezizales.

  pyronema confluens fungal whole-genome k-mer rna-seq

• Mutations in CHD7, encoding a chromatin-remodeling protein, cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome.

  PMID 18834967 · PMC2561938 · American journal of human genetics · 2008 · 7 claims · 6 setups

  Has reproduction · 70

  Heterozygous CHD7 mutations cause idiopathic hypogonadotropic hypogonadism and Kallmann syndrome without the CHARGE phenotype.

  ihh additional chd7 sanger targeted rt-pcr

• Organismal complexity, cell differentiation and gene expression: human over mouse.

  PMID 17881362 · PMC2095826 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Human shows a greater fraction of tissue-specific genes and a greater ratio of total expression of tissue-specific to housekeeping genes than mouse across 32 homologous tissues

  human-mouse oligonucleotide exon comparative

• Comprehensive annotation of bidirectional promoters identifies co-regulation among breast and ovarian cancer genes.

  PMID 17447839 · PMC1853124 · PLoS computational biology · 2007 · 8 claims · 8 setups

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  A new algorithm using spliced ESTs (cross-validated against Known Genes and GenBank mRNA) comprehensively maps bidirectional promoters in the human genome

  genome transcripts tissues proteins comparative taf250 cpg

• Trans-natural antisense transcripts including noncoding RNAs in 10 species: implications for expression regulation.

  PMID 18653530 · PMC2528163 · Nucleic acids research · 2008 · 8 claims · 7 setups

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  A new computational pipeline identifies trans-SAs using ESTs (not just mRNAs) across 10 animal species, improving coverage over prior methods

  est unannotated trans-sa tus computational coding hybridization