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).

• The association of Alu repeats with the generation of potential AU-rich elements (ARE) at 3' untranslated regions.

  PMID 15610565 · PMC544599 · BMC genomics · 2004 · 6 claims · 4 setups

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  Alu repeats are a source of AREs at 3' UTRs of human mRNA, via poly-A regions of Alu generating complementary poly-T/poly-U regions that acquire regular adenine insertions to form ARE motifs.

  utr computationally are repeat positional

• Satellog: a database for the identification and prioritization of satellite repeats in disease association studies.

  PMID 15949044 · PMC1181805 · BMC bioinformatics · 2005 · 7 claims · 6 setups

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  Satellog is a database cataloging all pure 1-16 unit satellite repeats in the human genome with supplementary polymorphism, gene-location, and expression data for prioritizing repeats in disease-association studies.

  reference unigene ensembl normal tandem polymorphism gene

• Pigs in sequence space: a 0.66X coverage pig genome survey based on shotgun sequencing.

  PMID 15885146 · PMC1142312 · BMC genomics · 2005 · 8 claims · 7 setups

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  Pig sequence is closer to human than mouse is, across exons, UTRs, introns, intergenic regions, ultra-conserved elements, and miRNAs

  sus pig concatenated three-species whole-genome repeat comparative

• Constitutional genetic variation at the human aromatase gene (Cyp19) and breast cancer risk.

  PMID 10027313 · PMC2362434 · British journal of cancer · 1999 · 7 claims · 5 setups

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  Allelic distribution of the Cyp19 intron 4 STRP differs significantly between breast cancer cases and controls

  peripheral ceph individuals cases strp genotyping fluorescent

• Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence.

  PMID 15588320 · PMC544879 · BMC genomics · 2004 · 8 claims · 8 setups

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  The hg16 automatic assembly of the 8p23.1 DEF locus contains misassemblies caused by segmental duplications and interindividual/intraindividual genetic variation

  bac genome metaphase overlapping manual repeat fluorescence

• CEAS: cis-regulatory element annotation system.

  PMID 16845068 · PMC1538818 · Nucleic acids research · 2006 · 7 claims · 5 setups

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  CEAS is the first web server to streamline genome-scale ChIP-chip downstream analyses for biologists without strong bioinformatics support

  genome genomic chip-chip repeat-masked conservation

• 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

• Human and mouse introns are linked to the same processes and functions through each genome's most frequent non-conserved motifs.

  PMID 18450818 · PMC2425492 · Nucleic acids research · 2008 · 8 claims · 5 setups

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  Pyknons (recurrent, genome-specific, ≥16nt motifs with ≥30 intact intergenic/intronic copies and ≥1 exonic copy) span a substantial fraction of previously uncharacterized intronic space (7.4% human, 4.4% mouse)

  pyknon computational comparative term

• Genetic variants of chemokine receptor CCR7 in patients with systemic lupus erythematosus, Sjogren's syndrome and systemic sclerosis.

  PMID 17587445 · PMC1913537 · BMC genetics · 2007 · 6 claims · 4 setups

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  CCR7 gene variants occur at extremely low frequency (allelic frequencies ≤5%) in the German population

  genomic hut78 t-cells direct pcr dual

• The Vertebrate Genome Annotation (Vega) database.

  PMID 15608237 · PMC540089 · Nucleic acids research · 2005 · 8 claims · 8 setups

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  Vega is a community database for browsing manual annotation of finished vertebrate genome sequences, based on an extended Ensembl-style schema.

  chromosomes genomic manual sequence initio