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).

• Expression of RAB4B, a protein governing endocytic recycling, is co-regulated with MHC class II genes.

  PMID 17175541 · PMC1802633 · Nucleic acids research · 2007 · 7 claims · 7 setups

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  A typical MHC-II-like S-Y module is present upstream of the RAB4B transcription start site, identified by genome-wide profile scanning

  genomic raji monocyte-derived rj2.2.5 computational chip-on-chip chromatin

• N-acetyltransferase 8, a positional candidate for blood pressure and renal regulation: resequencing, association and in silico study.

  PMID 18402670 · PMC2330028 · BMC medical genetics · 2008 · 7 claims · 6 setups

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  NAT8 is a novel positional candidate gene for blood pressure and renal function based on its chromosomal location within a BP linkage region and its expression in embryonic/adult kidney and liver

  random reference healthy long-term resequencing quantitative sequence

• oPOSSUM-3: advanced analysis of regulatory motif over-representation across genes or ChIP-Seq datasets.

  PMID 22973536 · PMC3429929 · G3 (Bethesda, Md.) · 2012 · 8 claims · 6 setups

  Has reproduction · 49

  oPOSSUM-3 is a web-accessible system that identifies over-represented TFBS and TFBS families in DNA sequences of co-expressed genes or in sequences from high-throughput methods such as ChIP-Seq.

  hg19 large-scale gene-based jaspar tfbs sequence-based anchored

• TEMP: a computational method for analyzing transposable element polymorphism in populations.

  PMID 24753423 · PMC4066757 · Nucleic acids research · 2014 · 8 claims · 8 setups

  Has reproduction · 61

  TEMP combines pair-end (discordant) read and split (soft-clipped) read information to identify both presence and absence of TE insertions in genomic DNA from heterogeneous/pooled samples.

  drosophila five four melanogaster simulated comparative whole-genome

• Fast and systematic genome-wide discovery of conserved regulatory elements using a non-alignment based approach.

  PMID 15693947 · PMC551538 · Genome biology · 2005 · 7 claims · 8 setups

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  FastCompare, a non-alignment-based, linear-time algorithm, computes a genome-wide conservation score for all k-mers (7-9 nt) between two genomes to identify conserved regulatory elements

  cerevisiae elegans randomized computational randomized microarray

• Downstream high-speed plasma jet generation as a direct consequence of shock reformation.

  PMID 35105885 · PMC8807623 · Nature communications · 2022 · 7 claims · 6 setups

  Has reproduction · 67

  High-speed downstream jets at Earth's bow shock are generated as a direct consequence of shock reformation.

  earth's mms mms2 upstream in-situ cross-correlation reduced

• The evolution and genomic landscape of CGB1 and CGB2 genes.

  PMID 17055150 · PMC2599907 · Molecular and cellular endocrinology · 2007 · 8 claims · 5 setups

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  CGB1 and CGB2 arose via insertion of a DNA fragment (736/724 bp) replacing part of the ancestral hCGβ promoter and 5'-UTR, creating a novel exon 1 and causing a frameshift that produces a completely different 132-aa protein unrelated to hCGβ

  genomic great cgb1 chimpanzee pcr population hka

• Automatic annotation of eukaryotic genes, pseudogenes and promoters.

  PMID 16925832 · PMC1810547 · Genome biology · 2006 · 8 claims · 6 setups

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  Fgenesh++ gene prediction pipeline identifies 91% of coding nucleotides with 90% specificity

  encode regions genes chromosome computational pseudogene promoter

• Polymorphisms in the glucocerebrosidase gene and pseudogene urge caution in clinical analysis of Gaucher disease allele c.1448T>C (L444P).

  PMID 16887033 · PMC1559599 · BMC medical genetics · 2006 · 6 claims · 5 setups

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  A multiplexed suspension bead array (Luminex) assay was developed to genotype 8 Ashkenazi-prevalent disease alleles including GBA c.1448T>C

  genomic de-identified multiplex sanger clinical

• QuadBase: genome-wide database of G4 DNA--occurrence and conservation in human, chimpanzee, mouse and rat promoters and 146 microbes.

  PMID 17962308 · PMC2238983 · Nucleic acids research · 2008 · 8 claims · 3 setups

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  QuadBase is a compendium of G4 DNA (quadruplex) motifs focused on their occurrence and conservation in promoters, composed of EuQuad and ProQuad

  chimpanzee prokaryotic promoters genome-wide cross-species

• ABO exon and intron analysis in individuals with the AweakB phenotype reveals a novel O1v-A2 hybrid allele that causes four missense mutations in the A transferase.

  PMID 14617382 · PMC305365 · BMC genetics · 2003 · 8 claims · 7 setups

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  A novel O1v-A2 hybrid allele, containing four missense mutations, causes the A weak B phenotype in five individuals of African descent

  genomic red computational abo sequencing blood

• Genetic microheterogeneity and phenotypic variation of Helicobacter pylori arginase in clinical isolates.

  PMID 17408487 · PMC1853099 · BMC microbiology · 2007 · 8 claims · 8 setups

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  Arginase activity varies more than 100-fold among H. pylori clinical isolates and laboratory-adapted strains

  minimally-passaged pylori coli arginase urease heterologous

• Identifying related L1 retrotransposons by analyzing 3' transduced sequences.

  PMID 12734010 · PMC156586 · Genome biology · 2003 · 8 claims · 6 setups

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  L1 elements with transduction-derived 3' sequence (L1-TDs) can be computationally identified using RepeatMasker/TSDfinder and grouped into families sharing a common progenitor via BLAST comparison of downstream sequences.

  genome database l1-td ncbi genome-wide blast pairwise