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).

• Proteomic characterization of plasma-derived clotting factor VIII-von Willebrand factor concentrates.

  PMID 19768705 · PMC3030255 · Electrophoresis · 2009 · 8 claims · 8 setups

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  Commercial plasma-derived FVIII/VWF concentrates contain significant amounts of non-FVIII/VWF plasma proteins as impurities

  plasma-derived octanate sec fviii sds-page size-exclusion lc-esi-ms

• Application of proteomics methods for pathogen discovery.

  PMID 19751767 · PMC7119679 · Journal of virological methods · 2010 · 8 claims · 6 setups

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  Proteomic techniques can detect and characterize unknown infectious agents in cell culture without prior knowledge of the pathogen

  hlf sequences synthetic conventional 2d-dige gelc-ms

• Methods for the proteomic identification of protease substrates.

  PMID 19729334 · PMC2787889 · Current opinion in chemical biology · 2009 · 8 claims · 8 setups

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  Gel-based methods (2D-DiGE, diagonal electrophoresis, PROTOMAP) identify protease substrates by comparing proteolyzed versus control samples via electrophoretic migration differences followed by MS identification

  lysate jurkat apoptotic yeast 2d-dige protomap cofradic

• Novel insights into adipogenesis from omics data.

  PMID 19689276 · PMC2765082 · Current medicinal chemistry · 2009 · 8 claims · 8 setups

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  Pparg and Cebpa are the two master transcriptional regulators governing adipogenesis

  3t3-l1 embryonic multipotent nih-3t3 microarray gel non-gel-based

• Building exposure biology centers to put the E into "G x E" interaction studies.

  PMID 19672377 · PMC2721881 · Environmental health perspectives · 2009 · 8 claims · 4 setups

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  Nongenetic factors account for high attributable risk (often 80-90%) across many chronic diseases, underscoring the importance of environmental exposure.

  mars water archived dried capillary surface adductomics

• Toward proteome-scale identification and quantification of isoaspartyl residues in biological samples.

  PMID 19663459 · PMC2756321 · Journal of proteome research · 2009 · 8 claims · 4 setups

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  In ECD MS/MS, isoaspartyl (but not aspartyl) residues produce specific fragments c_n•+58.0054 (C2H2O2) and z_(l-n)-56.9976 (C2HO2), which serve as markers for Asp isomerization

  a431 brain ecd cad label-free

• Global effects of kinase inhibitors on signaling networks revealed by quantitative phosphoproteomics.

  PMID 19651622 · PMC2816010 · Molecular & cellular proteomics : MCP · 2009 · 7 claims · 4 setups

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  Less than 10% of quantified phosphopeptides showed a response pattern indicative of being direct targets of the MAPK inhibitors U0126 or SB202190.

  hela k562 quantitative

• Differential 14-3-3 affinity capture reveals new downstream targets of phosphatidylinositol 3-kinase signaling.

  PMID 19648646 · PMC2773716 · Molecular & cellular proteomics : MCP · 2009 · 7 claims · 6 setups

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  Four known insulin-regulated proteins (PFK-2, PRAS40, AS160, MYO1C) show high d0/d4 ratios, i.e. increased 14-3-3 binding upon insulin stimulation, validating the screen

  hek293 hela far-western quantitative tio2

• Acute high-dose irradiation disrupts cell adhesion and Silk-Ovarioid formation in human primary ovarian cells.

  PMID 41485059 · PMC12930946 · Journal of ovarian research · 2026 · 8 claims · 6 setups

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  Acute 10 Gy X-ray irradiation does not significantly affect viability (ATP levels, mitochondrial dehydrogenase activity) of cPOCs and mPOCs over 7 days.

  kgn cpocs celltiter-glo mtt immunofluorescence

• Integrative multi-omics analysis of dietary fibre-induced modulations in the composition and function of chicken caecal microbiota.

  PMID 41741451 · PMC13046836 · NPJ biofilms and microbiomes · 2026 · 6 claims · 6 setups

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  High inulin supplementation (4%) significantly altered caecal microbial composition and promoted broader microbial metabolic adaptations, indicating a strong fermentative response to soluble fibre

  caecal shotgun metatranscriptomics eukaryotic

• SVNeoPP: A Workflow for Structural-Variant-Derived Neoantigen Prediction and Prioritization Using Multi-Omics Data.

  PMID 41892252 · PMC13024079 · Biology · 2026 · 8 claims · 7 setups

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  SVNeoPP is an end-to-end Snakemake workflow that takes WGS and RNA-seq as input to call/annotate SVs, reconstruct altered transcripts and coding sequences in an isoform-aware, traceable manner, and generate candidate peptides.

  tumor hcc sv-derived candidate whole-genome rna-seq peptide

• Estrogen Production in Pancreatic Cancer Shapes a Tumor-Suppressive Stromal Microenvironment.

  PMID 41258799 · PMC12862343 · Cancer research · 2026 · 8 claims · 6 setups

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  Serum levels of stromal biomarkers associated with favorable outcomes were significantly higher in female patients with PDAC than in male patients

  pdac pdx magnetic bioinformatic single-nucleus

• Bioinformatics methods for learning radiation-induced lung inflammation from heterogeneous retrospective and prospective data.

  PMID 19704920 · PMC2688763 · Journal of biomedicine & biotechnology · 2009 · 8 claims · 3 setups

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  Kernel-based methods (e.g., SVM) can capture nonlinear dose-volume interactions relevant to predicting radiation pneumonitis

  nsclc inoperable blood retrospective prospective 3-way

• The development of an integrated platform to identify breast cancer glycoproteome changes in human serum.

  PMID 19782370 · PMC4142217 · Journal of chromatography. A · 2010 · 8 claims · 6 setups

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  M-LAC (multi-lectin affinity chromatography combining Con A, WGA and Jacalin) provides comprehensive capture of glycoproteins from biological fluids based on differing glycan specificities

  pooled m-lac excised individual high-performance sds-page lectin

• Characterization of protein isoform diversity in human umbilical vein endothelial cells via long-read proteogenomics.

  PMID 36457147 · PMC9721438 · RNA biology · 2022 · 8 claims · 7 setups

  Has reproduction · 93

  Long-read RNA-seq detected 53,863 transcript isoforms from 10,426 genes in HUVECs, of which 22,195 were novel

  huvecs huvec long-read bottom-up offline

• From genomes to systems.

  PMID 15535877 · PMC545775 · Genome biology · 2004 · 8 claims · 8 setups

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  Biological networks (protein-gene interactions in the genome, protein-protein interactions in the proteome, biochemical reactions in the metabolome) are scale-free rather than random

  serum trypanosoma alzheimer's complexes gel maldi-ms ft-icr

• The use of proteomics in biomarker discovery in neurodegenerative diseases.

  PMID 15920295 · PMC3850612 · Disease markers · 2005 · 8 claims · 8 setups

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  A combination of low CSF-β-amyloid(1-42) with high CSF-tau and high CSF-phospho-tau is associated with an AD diagnosis

  csf serum two-dimensional seldi liquid-phase

• Proteomics studies reveal important information on small molecule therapeutics: a case study on plasma proteins.

  PMID 18973825 · PMC7185545 · Drug discovery today · 2008 · 8 claims · 8 setups

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  Abundant plasma proteins (albumin, IgG, transferrin) act as 'molecular sponges' that bind and transport low molecular weight proteins/peptides and drugs, extending their half-life by preventing rapid renal clearance.

  blood schizophrenia sjl serum proteomic differential comparative

• Endurance exercise as a countermeasure for aging.

  PMID 18716044 · PMC2570389 · Diabetes · 2008 · 8 claims · 8 setups

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  Reduced insulin sensitivity with age is likely related to adiposity and physical inactivity rather than being an inevitable consequence of aging.

  vastus mitochondria mitochondrial extracted euglycemic-hyperinsulinemic mitochondrial citrate

• 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