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).
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Identification of beta-secretase (BACE1) substrates using quantitative proteomics.
PMID 20041192 · PMC2793532 · PloS one · 2009 · 7 claims · 5 setups
Quantitative proteomics of conditioned medium from BACE1-overexpressing HEK and HeLa cells identified 68 putative β-secretase substrates
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DNA methylation and mRNA expression of SYN III, a candidate gene for schizophrenia.
PMID 19102774 · PMC2630979 · BMC medical genetics · 2008 · 8 claims · 6 setups
Variation in SYN III distal CpG island methylation is not related to schizophrenia in the population sample or in a monozygotic twin pair discordant for schizophrenia
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Proteomic profiling of gamma-secretase substrates and mapping of substrate requirements.
PMID 18942891 · PMC2570425 · PLoS biology · 2008 · 8 claims · 5 setups
An unbiased SILAC-based proteomic screen identified a relatively small cohort of γ-secretase substrates among thousands of proteins in HeLa cells, all of which are type I transmembrane proteins.
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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
FOXO1a mRNA and protein expression are elevated in human liver compared to chimpanzee liver
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Has reproduction · 92
Synergism between IL7R and CXCR4 drives BCR-ABL induced transformation in Philadelphia chromosome-positive acute lymphoblastic leukemia.
PMID 32581241 · PMC7314847 · Nature communications · 2020 · 8 claims · 8 setups
IL7R interacts/colocalizes with CXCR4 on the cell surface, recruiting BCR-ABL1 and JAK kinases into close proximity to form a platform for transformation
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Has reproduction · 83
Public Omics Explorer (POE): Enabling integrative semantic search across GEO omics datasets based on PubMed publications.
PMID 41282419 · PMC12636342 · Computational and structural biotechnology journal · 2025 · 6 claims · 4 setups
POE is a web platform that semantically links GEO datasets and ENA records through their associated PubMed publications for literature-informed dataset retrieval
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Proteomics-based identification of novel factor inhibiting hypoxia-inducible factor (FIH) substrates indicates widespread asparaginyl hydroxylation of ankyrin repeat domain-containing proteins.
PMID 18936059 · PMC2649815 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 5 setups
DMOG pretreatment acts as a pharmacological 'substrate trap' that stabilizes transient FIH-substrate interactions, enabling their identification by SILAC-based proteomics
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A distinct epigenetic signature at targets of a leukemia protein.
PMID 17266773 · PMC1796549 · BMC genomics · 2007 · 7 claims · 7 setups
Combining gene expression microarray analysis with bioinformatic search for AML1-consensus sequences identifies direct AML1 targets that expression analysis alone cannot resolve
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Proteomic analysis of differential proteins in pancreatic carcinomas: Effects of MBD1 knock-down by stable RNA interference.
PMID 18445260 · PMC2386481 · BMC cancer · 2008 · 8 claims · 5 setups
Stable RNAi-mediated MBD1 knock-down was successfully established in the BxPC-3 pancreatic cancer cell line using a recombinant siRNA plasmid
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Multiplex amplification of all coding sequences within 10 cancer genes by Gene-Collector.
PMID 17317684 · PMC1874629 · Nucleic acids research · 2007 · 7 claims · 7 setups
Gene-Collector is a method for multiplex nucleic acid amplification that specifically circularizes only correctly paired (cognate) PCR primer products on a Collector probe, degrading non-cognate artifacts by exonuclease treatment.
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Functional analysis of human hematopoietic stem cell gene expression using zebrafish.
PMID 16089502 · PMC1166352 · PLoS biology · 2005 · 8 claims · 8 setups
277 unique transcripts are differentially expressed between Rho lo and Rho hi HSC-enriched/depleted populations, conserved across both umbilical cord blood and bone marrow
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A pharmacogenetics study of the human glucuronosyltransferase UGT1A4.
PMID 19890225 · PMC6177227 · Pharmacogenetics and genomics · 2009 · 7 claims · 6 setups
Extensive sequencing of UGT1A4 (promoter to exon 1+2000bp) identified numerous novel polymorphisms: 13 intronic, 39 promoter, and 14 exonic variants (10 causing amino acid changes)
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A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.
PMID 17186946 · PMC1860054 · Molecular & cellular proteomics : MCP · 2007 · 8 claims · 8 setups
Three complementary membrane-enrichment proteomic methods (lectin affinity, biotin/NeutrAvidin affinity, free flow electrophoresis) combined with LC-MS/MS identify 136 transmembrane proteins in human platelets, including many novel ones.