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 drug effects via pathway alterations using an integer linear programming optimization formulation on phosphoproteomic data.

  PMID 19997482 · PMC2776985 · PLoS computational biology · 2009 · 7 claims · 4 setups

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  An ILP formulation of the Boolean pathway optimization problem fits phosphoproteomic data faster and more efficiently than the previously used genetic algorithm (GA) approach.

  hepg2 computational same bead-based integer comparative

• Antibody binding loop insertions as diversity elements.

  PMID 17023486 · PMC1635297 · Nucleic acids research · 2006 · 7 claims · 8 setups

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  A lysozyme-binding VHH CDR3 loop can be grafted into two surface-exposed loops of superfolder GFP, conferring lysozyme-binding activity while the protein remains fluorescent.

  gfp-anti-lysozyme coli full-length gfp-hcdr3 elisa flow surface

• Proteomic analyses of monocyte-derived macrophages infected with human immunodeficiency virus type 1 primary isolates from Hispanic women with and without cognitive impairment.

  PMID 19115125 · PMC2947716 · Journal of neurovirology · 2009 · 7 claims · 5 setups

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  HIV-1 isolates from CI patients induce a distinct macrophage proteome signature compared to isolates from NC patients and SF162

  monocyte-derived mdm mdms western p24 seldi-tof sds-page

• Proteomic analyses associate cystatin B with restricted HIV-1 replication in placental macrophages.

  PMID 18951626 · PMC3867668 · Placenta · 2008 · 6 claims · 6 setups

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  Placental macrophages support significantly lower HIV-1 replication than monocyte-derived macrophages

  placental mdm hiv-1 seldi-tof sds-page

• Genetic Dissection of Tissue-Specific Apolipoprotein E Function for Hypercholesterolemia and Diet-Induced Obesity.

  PMID 26695075 · PMC4687855 · PloS one · 2015 · 8 claims · 8 setups

  Has reproduction

  Hepatocyte apoE is required for normal VLDL production and protects against diet-induced dyslipidemia

  liver plasma pooled real-time western elisa

• Late onset thrombosis in a case of severe protein S deficiency due to compound heterozygosity for PROS1 mutations.

  PMID 18433462 · PMC2632602 · Journal of thrombosis and haemostasis : JTH · 2008 · 6 claims · 6 setups

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  A novel 14 bp deletion in intervening sequence L (putative branch point of intron L), which likely impairs PROS1 pre-mRNA splicing, was found in all family members with low free protein S.

  plasma genomic apc free ps-direct

• Three assays show differences in binding of wild-type and mutant p53 to unique gene sequences.

  PMID 19925028 · PMC2917581 · Technology in cancer research & treatment · 2009 · 7 claims · 6 setups

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  Three different DNA binding assays (EMSA, SPA, streptavidin magnetic bead assay) show differences in binding of wild-type and mutant p53 to unique gene sequences

  nuclear wro electrophoretic binding streptavidin

• Screening of Diagnostic Biomarkers and Immune Infiltration Characteristics Linking Rheumatoid Arthritis and Rosacea Based on Bioinformatics Analysis.

  PMID 39104909 · PMC11299729 · Journal of inflammation research · 2024 · 8 claims · 8 setups

  Has reproduction · 48

  277 co-expressed DEGs shared between RA and rosacea are enriched in immune processes and chemokine-mediated signaling pathways

  synovial rosacea co-expressed serum microarray weighted protein-protein

• mtDNA depletion confers specific gene expression profiles in human cells grown in culture and in xenograft.

  PMID 18980691 · PMC2612029 · BMC genomics · 2008 · 8 claims · 8 setups

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  mtDNA depletion confers specific, shared gene expression profiles in A549 cells grown in culture and as xenografts

  a549 growth oxygen mtdna

• Salivary proteomics for oral cancer biomarker discovery.

  PMID 18829504 · PMC2877125 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 5 setups

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  Subtractive salivary proteomics reveals proteins differentially present/expressed between OSCC patients and matched healthy controls.

  pooled saliva shotgun two-dimensional elisa

• Proteomic analysis identifies MMP-9, DJ-1 and A1BG as overexpressed proteins in pancreatic juice from pancreatic ductal adenocarcinoma patients.

  PMID 18706098 · PMC2528014 · BMC cancer · 2008 · 7 claims · 6 setups

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  MMP-9, DJ-1 and A1BG are overexpressed in pancreatic juice and tissue from PDAC patients compared with cancer-free/normal controls

  pooled individual trypsin-digested pancreatic two-dimensional difference maldi-tof-ms

• Antibody protein array analysis of the tear film cytokines.

  PMID 18677223 · PMC3786218 · Optometry and vision science : official publication of the American Academy of Optometry · 2008 · 7 claims · 4 setups

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  Tear fluid contains factors with affinity for plastic, capture antibodies, and IgG that create matrix effects profoundly impacting dot ELISA/array reliability

  tear normalized antibody 12-plex two-step

• Anesthetics impact the resolution of inflammation.

  PMID 18382663 · PMC2268966 · PloS one · 2008 · 8 claims · 8 setups

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  Lidocaine delays and blocks key events in the resolution of acute inflammation

  peritoneal cell-free zymosan-induced lipid apoptosis

• Proteomic analysis of mechanisms of hypoxia-induced apoptosis in trophoblastic cells.

  PMID 17299580 · PMC1796955 · International journal of medical sciences · 2006 · 8 claims · 7 setups

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  Hypoxia induces apoptosis in JAR trophoblastic cells, shown by time-dependent increase in internucleosomal DNA fragmentation

  jar powerblot mtt death

• Endogenous retroviral elements LTR8B and MER65 rewire PSG9 regulation to control trophoblast syncytialization and pre-eclampsia risk.

  PMID 41796334 · PMC12969887 · Genome biology · 2026 · 8 claims · 8 setups

  Has reproduction · 68

  Retrovirus-derived LTR8B acts as a trophoblast-specific cis-regulatory element within the PSG array, with LTR8B at PSG9 influencing other PSG family members as a master regulator

  sghpl-4 trophoblast placenta bewo chip-exonuclease crispr-cas9 chromatin