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).

• An integrated database of genes responsive to the Myc oncogenic transcription factor: identification of direct genomic targets.

  PMID 14519204 · PMC328458 · Genome biology · 2003 · 8 claims · 6 setups

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  The Myc Target Gene database integrates literature evidence to prioritize candidate Myc-responsive genes and cluster them into functional groups

  p493 rodent types quantitative chromatin northern

• Applying proteomics to the diagnosis and treatment of ALS and related diseases.

  PMID 19670321 · PMC2836583 · Muscle & nerve · 2009 · 8 claims · 8 setups

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  Protein-based biomarkers for ALS/MND require further verification and large-scale validation/qualification studies, including disease mimics, before clinical use

  csf spinal biofluid muscle 2d-dige antibody luminex

• New perspectives on an old disease: proteomics in cancer research.

  PMID 17472735 · PMC1895992 · Genome biology · 2007 · 8 claims · 8 setups

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  The HUPO Plasma Proteome Project has catalogued over 3,020 non-redundant gene products (>7,000 proteins/isoforms) in human plasma, many originating from tissues/organs rather than being plasma-intrinsic.

  plasma breast tumor genetically shotgun proteomics glycopeptide

• Proteomic approaches to cancer biomarkers.

  PMID 19931265 · PMC2873613 · Gastroenterology · 2010 · 8 claims · 8 setups

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  Combining abundant-protein depletion, offline fractionation, and subproteome (e.g., glycoproteome) enrichment with 2D LC-MS/MS increases the dynamic range and depth of blood proteome analysis for biomarker discovery.

  plasma serum capan-2 apcδ580 lectin silac elisa

• Bisulfite sequencing of chromatin immunoprecipitated DNA (BisChIP-seq) directly informs methylation status of histone-modified DNA.

  PMID 22466171 · PMC3371705 · Genome research · 2012 · 8 claims · 8 setups

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  BisChIP-seq — bisulfite sequencing of chromatin immunoprecipitated DNA — enables direct genome-wide, base-resolution interrogation of DNA methylation on histone-modified DNA molecules

  lncap sonicated adaptor-modified native bischip-seq chromatin chip-qpcr

• Functional genomics in zebrafish permits rapid characterization of novel platelet membrane proteins.

  PMID 19109564 · PMC2680375 · Blood · 2009 · 8 claims · 6 setups

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  Zebrafish morpholino knockdown combined with a laser-induced arterial thrombosis assay is a fast, powerful method for initial functional screening of novel platelet genes.

  blood platelets platelet-rich platelet whole-genome quantitative flow

• HITS-CLIP yields genome-wide insights into brain alternative RNA processing.

  PMID 18978773 · PMC2597294 · Nature · 2008 · 8 claims · 8 setups

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  HITS-CLIP, combining CLIP with high-throughput sequencing, provides a genome-wide, unbiased method to map protein-RNA interactions in vivo.

  neocortex brain 293t hits-clip traditional exon

• A combination of genomic approaches reveals the role of FOXO1a in regulating an oxidative stress response pathway.

  PMID 18301748 · PMC2244703 · PloS one · 2008 · 8 claims · 7 setups

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  FOXO1a mRNA and protein expression are elevated in human liver compared to chimpanzee liver

  chimpanzee hepg2 promoters liver quantitative western sirna

• Discovery and identification of potential biomarkers of papillary thyroid carcinoma.

  PMID 19785722 · PMC2761863 · Molecular cancer · 2009 · 8 claims · 7 setups

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  A 3-peak (m/z 9190, 6631, 8697 Da) SVM classification model discriminates PTC from non-cancer controls with high sensitivity and specificity

  serum hplc-purified trypsin-digested crude seldi-tof-ms solid-phase maldi-tof-ms

• Finding the needle in the haystack: why high-throughput screening is good for your health.

  PMID 12100740 · PMC138735 · Breast cancer research : BCR · 2002 · 8 claims · 8 setups

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  HTS is essential for finding lead compounds, especially for novel targets whose active-site structure is unknown

  raf-1 mitotic mutant tumor biochemical cell-based conformational

• Identification of the REST regulon reveals extensive transposable element-mediated binding site duplication.

  PMID 16899447 · PMC1557810 · Nucleic acids research · 2006 · 8 claims · 8 setups

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  The RE1 PSSM identifies functional RE1 binding sites with greater sensitivity and selectivity than the previously used RE1 consensus sequence

  fibroblast hela hek293 set genome-wide electrophoretic rt-pcr

• Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

  PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

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  SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

  blood family unrelated subjects snp family-based linkage

• High-throughput genomic technology in research and clinical management of breast cancer. Plasma-based proteomics in early detection and therapy.

  PMID 17184556 · PMC1797031 · Breast cancer research : BCR · 2006 · 8 claims · 8 setups

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  Plasma is well suited to proteomic biomarker discovery because it is easily obtained, routinely used diagnostically, and has a rich proteome.

  plasma serum maldi-tof seldi-tof tandem

• Validation of reverse phase protein array for practical screening of potential biomarkers in serum and plasma: accurate detection of CA19-9 levels in pancreatic cancer.

  PMID 18615426 · PMC2992687 · Proteomics · 2008 · 8 claims · 6 setups

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  RPPA-measured CA19-9 levels correlate strongly with ELISA-measured levels in the same patient samples

  serum same pancreatic candidate reverse elisa rppa

• Assembling a jigsaw puzzle with 20,000 parts.

  PMID 12801408 · PMC193613 · Genome biology · 2003 · 8 claims · 8 setups

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  Re-routing the intracellular interaction domains of receptor tyrosine kinases can redirect their signaling output, e.g. converting a growth signal into an apoptosis signal.

  yeast caenorhabditis escherichia proteome-wide microarray yeast rnai