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 many uses of a genome sequence.

  PMID 11423005 · PMC138940 · Genome biology · 2001 · 8 claims · 8 setups

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  Solved protein structures from structural genomics efforts can be used to model many other proteins by homology, aiding function prediction

  recombinant mammalian chromosome chimpanzee x-ray quantitative tiling

• miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes.

  PMID 18029362 · PMC2238982 · Nucleic acids research · 2008 · 8 claims · 6 setups

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  miRNAMap 2.0 is a resource collecting experimentally verified miRNAs and experimentally verified miRNA target genes in human, mouse, rat and other metazoan genomes

  major tissues conserved predicted quantitative bead-based microarray

• Systems biology in human health and disease.

  PMID 17893698 · PMC2013921 · Molecular systems biology · 2007 · 8 claims · 5 setups

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  High-throughput quantitative proteomics of signaling networks (e.g., HER2 overexpression) can be correlated with biological responses like proliferation and migration to better understand pathways deregulated in cancer.

  her2 biological prostate model quantitative combinatorial genome-wide

• A screen for proteins that interact with PAX6: C-terminal mutations disrupt interaction with HOMER3, DNCL1 and TRIM11.

  PMID 16098226 · PMC1208879 · BMC genetics · 2005 · 8 claims · 7 setups

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  PAX6 interacts with three novel proteins: HOMER3, DNCL1 and TRIM11

  pax6 brain yeast sequence yeast semi-quantitative

• A search for structurally similar cellular internal ribosome entry sites.

  PMID 17591613 · PMC1950536 · Nucleic acids research · 2007 · 8 claims · 7 setups

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  Cellular IRES are not defined by an overall conserved structure (unlike viral IRES) but instead depend on short RNA motifs and shared trans-acting factors (ITAFs)

  transcribed hek 293t enzymatic chemical structural

• Fibroblasts from patients with Diamond-Blackfan anaemia show abnormal expression of genes involved in protein synthesis, amino acid metabolism and cancer.

  PMID 19765279 · PMC2760583 · BMC genomics · 2009 · 8 claims · 5 setups

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  Global microarray profiling reveals 421 genes differentially expressed in DBA patient fibroblasts compared to healthy controls

  dermal same fibroblasts analysis microarray quantitative rt-pcr

• The 10 sea urchin receptor for egg jelly proteins (SpREJ) are members of the polycystic kidney disease-1 (PKD1) family.

  PMID 17629917 · PMC1934368 · BMC genomics · 2007 · 8 claims · 5 setups

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  Sea urchins possess 10 SpREJ (PKD1 family) genes, compared to five in humans, all defined by possession of a ~600 residue REJ domain

  strongylocentrotus sprej purpuratus full-length cdna secondary real-time

• Structural modeling and functional characterization of a novel gain-of-function TLR8 variant causing severe inflammatory syndrome.

  PMID 41729082 · PMC12956005 · JCI insight · 2026 · 8 claims · 8 setups

  Has reproduction · 89

  TLR8 A518T is a gain-of-function variant that enhances NF-κB activation and increases secretion of proinflammatory cytokines upon stimulation compared with WT TLR8

  plasma pbmcs expressing tlr8 targeted plasma quantitative

• Identification of the Wheat (Triticum aestivum) IQD Gene Family and an Expression Analysis of Candidate Genes Associated with Seed Dormancy and Germination.

  PMID 35456910 · PMC9025732 · International journal of molecular sciences · 2022 · 8 claims · 8 setups

  Has reproduction · 78

  73 IQD gene family members (TaIQD1-73) were identified in the wheat genome and phylogenetically divided into six major groups.

  triticum taiqd wheat promoter genome-wide phylogenetic synteny

• Widespread A-to-I RNA editing of Alu-containing mRNAs in the human transcriptome.

  PMID 15534692 · PMC526178 · PLoS biology · 2004 · 8 claims · 6 setups

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  Intramolecular pairs of oppositely oriented Alu elements within the same pre-mRNA form dsRNA foldback structures that are major substrates for A-to-I RNA editing

  huge brain pre-mrna greater genomic rt-pcr quantitative

• Systems biology and the host response to viral infection.

  PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

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  Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

  lung cd4 rhesus kshv microarray quantitative genomic

• Evaluation of the OPTC gene in primary open angle glaucoma: functional significance of a silent change.

  PMID 17359525 · PMC1838427 · BMC molecular biology · 2007 · 8 claims · 8 setups

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  OPTC is a candidate gene involved in POAG pathogenesis

  genomic pcr optc retinal pcr-sscp dhplc sequencing

• Mutations in TRPV4 cause Charcot-Marie-Tooth disease type 2C.

  PMID 20037586 · PMC2812627 · Nature genetics · 2010 · 8 claims · 8 setups

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  Heterozygous missense mutations in TRPV4 (c.805C>T/R269C and c.806G>A/R269H) cause CMT2C

  cmt2c affected spinal drg genetic sanger quantitative

• Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

  PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

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  Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

  msi-h computational rb1cc1 normal pcr nonlinear real-time

• International sequencing consortium.

  PMID 15174459 · PMC1315987 · Environmental health perspectives · 2004 · 8 claims · 6 setups

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  The p19 viral silencing-suppressor protein selectively recognizes short (21-22 nt) silencing siRNAs by measuring duplex length, using tryptophan residues (Trp39, Trp42) as molecular calipers that stack against the siRNA end base pairs.

  cirv blood sampled rice x-ray site-directed mass

• Systematic analysis of CNGCs in cotton and the positive role of GhCNGC32 and GhCNGC35 in salt tolerance.

  PMID 35931984 · PMC9356423 · BMC genomics · 2022 · 7 claims · 8 setups

  Has reproduction

  114 CNGC genes were identified across 4 cotton species (G. arboreum 20, G. raimondii 20, G. hirsutum 38, G. barbadense 36), clustering into 5 groups (I, II, III, IVa, IVb).

  plant cotton hirsutum ghcngc genome-wide phylogenetic conserved

• Combined subtractive cDNA cloning and array CGH: an efficient approach for identification of overexpressed genes in DNA amplicons.

  PMID 15018647 · PMC365025 · BMC genomics · 2004 · 8 claims · 8 setups

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  Combined SSH subtractive cloning and array CGH is an efficient strategy to identify overexpressed genes located within DNA amplicons.

  imr-32 subtracted mycn-amplified suppression differential array

• Transcriptome profiling of Giardia intestinalis using strand-specific RNA-seq.

  PMID 23555231 · PMC3610916 · PLoS computational biology · 2013 · 8 claims · 8 setups

  Has reproduction · 74

  Most of the G. intestinalis genome is transcribed in in vitro-grown trophozoites, but at vastly different expression levels.

  intestinalis same rna-seq strand-specific technical reverse

• 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

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  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

• Atypical haemolytic uraemic syndrome associated with a hybrid complement gene.

  PMID 17076561 · PMC1626556 · PLoS medicine · 2006 · 6 claims · 7 setups

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  Affected members of a previously genetically unsolved aHUS family carry a heterozygous CFH/CFHL1 hybrid gene (exons 1-21 from CFH, exons 22/23 from CFHL1)

  peripheral genomic convalescent cdna genomic breakpoint-spanning