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).

• Analyzing biomarker discovery: Estimating the reproducibility of biomarker sets.

  PMID 35901020 · PMC9333302 · PloS one · 2022 · 8 claims · 6 setups

  Has reproduction · 83

  Non-reproducibility is a common problem in biomarker discovery: independently derived biomarker sets for the same phenotype frequently share very few features across studies

  gse7390 geo ega tcga-brca t-test-based reproducibility genome-wide

• The impact of new research technologies on our understanding of environmental causes of disease: the concept of clinical vulnerability.

  PMID 19948053 · PMC2793242 · Environmental health : a global access science source · 2009 · 8 claims · 8 setups

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  GWAS-identified genetic variants confer only modest relative risks (1.15-1.5), comparable in magnitude to weak/contested environmental exposures

  polish cohort nonsmokers low genome-wide biomarker epidemiological

• Mass spectrometry-based biomarker discovery: toward a global proteome index of individuality.

  PMID 20636062 · PMC3140421 · Annual review of analytical chemistry (Palo Alto, Calif.) · 2009 · 8 claims · 4 setups

  Full-text index only

  Very few large-scale longitudinal MS-based proteomics studies have been performed to establish analytical variability relative to true biological variability.

  normal plasma longitudinal bottom-up top-down

• Biomarker discovery in neurodegenerative diseases: a proteomic approach.

  PMID 18938247 · PMC2939006 · Neurobiology of disease · 2009 · 6 claims · 8 setups

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  Proteomic profiling of CSF and plasma can identify candidate protein biomarkers that distinguish AD patients from controls with high sensitivity and specificity

  csf plasma brain 2-dge lc-ms seldi-tof-ms

• Different Intestinal Microbiota with Growth Stages of Three-Breed Hybrid Pig.

  PMID 35978648 · PMC9377885 · BioMed research international · 2022 · 7 claims · 5 setups

  Has reproduction · 75

  The composition and relative abundance of intestinal microbiota in three-breed hybrid pigs differ significantly across growth stages (60, 120, 180 days)

  fecal same 16s otu alpha

• 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

  Full-text index only

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

  pooled saliva shotgun two-dimensional elisa

• Tissue compartment analysis for biomarker discovery by gene expression profiling.

  PMID 19901995 · PMC2771357 · PloS one · 2009 · 8 claims · 5 setups

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  TCA method quantifies the fractional volume of constitutive structures in a heterogeneous tissue sample by comparing marker mRNA levels in the whole sample to those in pure isolated structures

  kidney pure serial rt-pcr sage histo-morphometry

• Causal models in epidemiology: past inheritance and genetic future.

  PMID 16859537 · PMC1557493 · Environmental health : a global access science source · 2006 · 8 claims · 3 setups

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  Interaction is a fundamental characteristic of any causal process involving probabilistic steps, not a second-order phenomenon identified after accounting for main effects

  smokers population cohort observational biomarker pulmonary

• Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

  PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups

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  Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.

  serum frozen ig-depleted clinical seldi-tof maldi lc-ms

• Comparing protein abundance and mRNA expression levels on a genomic scale.

  PMID 12952525 · PMC193646 · Genome biology · 2003 · 8 claims · 8 setups

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  Correlations between mRNA expression and protein abundance are generally poor or limited across most studies reviewed, including in yeast and human cancers

  yeast laser-dissected serum myeloid two-dimensional seldi-tof isotope-coded

• Zebrafish whole-adult-organism chemogenomics for large-scale predictive and discovery chemical biology.

  PMID 18618001 · PMC2442223 · PLoS genetics · 2008 · 8 claims · 6 setups

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  Zebrafish whole-adult-organism chemogenomics generates robust prediction models that discriminate P(H)AHs from ECs across independent experiments

  zebrafish computational seven consolidated whole-adult-organism supervised quantitative

• A mouse to human search for plasma proteome changes associated with pancreatic tumor development.

  PMID 18547137 · PMC2504036 · PLoS medicine · 2008 · 7 claims · 8 setups

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  GEM models combined with in-depth proteomic analysis provide a useful strategy to identify candidate cancer markers applicable to human disease with potential for early detection

  plasma immunodepleted pancreatic shotgun two-dimensional immunodepletion

• Identification of TYR, TYRP1, DCT and LARP7 as related biomarkers and immune infiltration characteristics of vitiligo via comprehensive strategies.

  PMID 34107850 · PMC8806433 · Bioengineered · 2021 · 7 claims · 8 setups

  Has reproduction · 55

  131 robust DEGs (89 upregulated, 42 downregulated) were identified by RRA integration of three vitiligo datasets and are closely associated with melanogenesis and vitiligo development

  lesional merged robust verification gene robust weighted

• STAT1 and IL-7 as potential diagnostic biomarkers for distinguishing high-grade from low-grade serous ovarian cancer: a multi-cohort analysis.

  PMID 42058211 · PMC13120972 · Frontiers in immunology · 2026 · 8 claims · 7 setups

  Has reproduction · 50

  STAT1 and IL-7 are differentially expressed immune-related genes that can distinguish HGSOC from LGSOC with strong diagnostic performance in the training cohort (AUC 0.908 and 0.842).

  hgsoc dirgs hub stat1 bulk functional protein-protein

• Integrative bioinformatics and artificial intelligence analyses of transcriptomics data identified genes associated with major depressive disorders including NRG1.

  PMID 37583471 · PMC10423927 · Neurobiology of stress · 2023 · 7 claims · 5 setups

  Has reproduction · 66

  Differentially expressed genes in MDD patients are enriched in immune response, inflammatory response, neurodegeneration, and cerebellar atrophy pathways.

  blood transcriptomic postmortem saliva gsea machine differential

• Glycomics and disease markers.

  PMID 19775929 · PMC2788081 · Current opinion in chemical biology · 2009 · 8 claims · 7 setups

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  Over 70% of all human proteins are glycosylated

  serum glycoprotein-derived sera maldi-fticr glycan nanoflow