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).

• Identifying human pre-mRNA cleavage and polyadenylation factors by genome-wide CRISPR screens using a dual fluorescence readthrough reporter.

  PMID 38587191 · PMC11077057 · Nucleic acids research · 2024 · 6 claims · 8 setups

  Has reproduction · 68

  A dual fluorescence (GFP-mCherry) readthrough reporter with a PAS inserted between the two reporters enables measurement of 3' end processing efficiency in living cells.

  hek293 coli dual genome-wide western

• From linear genome sequence to three-dimensional organization of the cell nucleus.

  PMID 12620101 · PMC153456 · Genome biology · 2003 · 8 claims · 8 setups

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  Chromosome conformation capture (3C) can quantify in vivo physical interaction frequencies between genomic loci by crosslinking, digestion, and intramolecular ligation followed by PCR

  saccharomyces mitotic nucleoplasm hela chromosome translocation stretched

• Ontological visualization of protein-protein interactions.

  PMID 15707487 · PMC550656 · BMC bioinformatics · 2005 · 8 claims · 8 setups

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  Aggregating independently made GO 'protein binding' (IPI) annotations reveals larger, previously undescribed mouse protein-protein interaction networks

  gene interacting interaction annotation yeast co-immunoprecipitation

• Interactome networks: the state of the science.

  PMID 16515723 · PMC1431712 · Genome biology · 2006 · 8 claims · 8 setups

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  Spastin interacts with CHMP1B, an ESCRT-III-associated protein, supporting a role for spastin in intracellular membrane trafficking relevant to hereditary spastic paraplegia

  genes tnfα orf proteins yeast tandem interference

• Human Protein Reference Database--2009 update.

  PMID 18988627 · PMC2686490 · Nucleic acids research · 2009 · 8 claims · 8 setups

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  HPRD is a curated database of experimentally derived human protein-protein interactions, post-translational modifications, and tissue expression data

  mastl proteins phosphorylation yeast mass

• Regulation of P2X2 receptors by the neuronal calcium sensor VILIP1.

  PMID 18922787 · PMC3523710 · Science signaling · 2008 · 8 claims · 8 setups

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  VILIP1 was identified via a proteomic (GST pull-down) approach as a protein interacting with the P2X2 receptor C-terminal tail

  brain hek gst co-immunoprecipitation immunocytochemistry

• The potential of optical proteomic technologies to individualize prognosis and guide rational treatment for cancer patients.

  PMID 19756916 · PMC2778706 · Targeted oncology · 2009 · 8 claims · 5 setups

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  Genomic/gene expression profiling alone is insufficient to identify tumors with molecular pathway changes predictive of treatment outcome; protein-level functional assessment (activation states, PTMs, interactions) is also required

  microarray ffpe models cancer immunohistochemistry fret fret-flim

• Proteomics and genomics: perspectives on drug and target discovery.

  PMID 18302945 · PMC2386992 · Current opinion in chemical biology · 2008 · 8 claims · 8 setups

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  Protein kinases account for approximately 25% of research and development projects in biotechnology and pharma

  proteins blood carbohydrate medicinal x-ray microarrays glycan

• Arabidopsis RBV is a conserved WD40 repeat protein that promotes microRNA biogenesis and ARGONAUTE1 loading.

  PMID 35260568 · PMC8904849 · Nature communications · 2022 · 7 claims · 8 setups

  Has reproduction · 55

  RBV, a WD40 repeat protein, is required for global microRNA biogenesis in Arabidopsis

  amir-sul col 14-day-old arabidopsis small rna-seq gel

• The tumour suppressor L(3)mbt inhibits neuroepithelial proliferation and acts on insulator elements.

  PMID 21857667 · PMC3173870 · Nature cell biology · 2011 · 8 claims · 8 setups

  Has reproduction · 90

  Brain tumors in l(3)mbt mutants originate from overproliferation of neuroepithelial cells of the optic lobes, not from defects in asymmetric cell division.

  drosophila chip-seq chip immunostaining

• Sequencing the regulatory genome.

  PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

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  Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

  interphase nine beta-globin drosophila nuclear digital chip

• Research Spotlight: New multiparameter bioanalytical technologies for applications in personalized medicine, drug discovery and fundamental biology.

  PMID 21083072 · PMC3106349 · Bioanalysis · 2009 · 8 claims · 8 setups

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  High-density arrays of silicon photonic microring resonators enable label-free, multiplexed detection of DNA, miRNA, and protein biomarkers from a single small-volume sample

  silicon undiluted model label-free multiplexed cytokine