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).

Publications 1.3k Datasets 392.5k Experiments 271

Assay: concentration ✕ Clear

Detection of venous thromboembolism by proteomic serum biomarkers.

PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups

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A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays

serum anova-selected citrated depleted direct artificial d-dimer
A novel variable number of tandem repeat of the natriuretic peptide precursor B gene's 5'-flanking region is associated with essential hypertension among Japanese females.

PMID 17554401 · PMC1885554 · International journal of medical sciences · 2007 · 8 claims · 6 setups

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A novel VNTR polymorphism (TTTC repeat) was discovered at -1241 nucleotides in the 5'-flanking region of NPPB, with 8 alleles ranging from 9 to 19 repeats.

genomic plasma serum n=317 pcr-sscp nucleotide genotyping
Pulmonary biomarkers based on alterations in protein expression after exposure to arsenic.

PMID 17450228 · PMC1852690 · Environmental health perspectives · 2007 · 5 claims · 6 setups

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Chronic low-dose As exposure (10/50 ppb) consistently alters expression of specific proteins (RAGE, GST-omega-1, contraspin, ApoA-I, ApoA-IV, peroxiredoxin-6, enolase-1) in mouse lung-lining fluid.

c57bl balf induced first 2-d multidimensional western
Proteomic profiling of the amniotic fluid to detect inflammation, infection, and neonatal sepsis.

PMID 17227133 · PMC1769412 · PLoS medicine · 2007 · 8 claims · 8 setups

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Higher MR scores (severe, 3-4) are associated with significantly shorter amniocentesis-to-delivery intervals than minimal (1-2) or no (0) inflammation

amniotic placental blood seldi-tof elisa clinical
Increasing the number of SNP loci does not necessarily improve prediction power at least in the comparison of MTHFR SNP and haplotypes.

PMID 19075497 · PMC4771609 · Journal of epidemiology · 2008 · 7 claims · 6 setups

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Increasing the number of typed SNP loci does not necessarily improve prediction power, at least for the MTHFR gene

healthy genomic genotype trial randomized snp haplotype
Proteomic analysis of RCL2 paraffin-embedded tissues.

PMID 19012729 · PMC4506168 · Journal of cellular and molecular medicine · 2008 · 8 claims · 8 setups

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RCL2-fixed paraffin-embedded (RCL2P) tissue consistently gives the highest protein yield compared to FFPE and frozen tissue across extraction protocols

normal rcl2p ffpe frozen yield 1-dimensional 2-dimensional
A proteomic analysis of IVF follicular fluid in women

PMID 18980758 · PMC3916005 · Fertility and sterility · 2009 · 8 claims · 4 setups

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2D-PAGE proteomic evaluation of follicular fluid can identify potential biomarkers distinguishing good versus poor IVF responders in matched patient pairs

follicular excised clinical polyacrylamide liquid direct
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
Familial pulmonary alveolar proteinosis caused by mutations in CSF2RA.

PMID 18955570 · PMC2585845 · The Journal of experimental medicine · 2008 · 7 claims · 8 setups

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Familial primary PAP is caused by compound heterozygous mutations in CSF2RA: a paternal G174R point mutation and a maternal 1.6-Mb deletion at Xp22.33 encompassing CSF2RA.

peripheral pbmc blood lung flow western gm-csf
Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry.

PMID 18939861 · PMC2669493 · Journal of proteome research · 2008 · 8 claims · 5 setups

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IEF provides superior reproducibility and resolution of peptide fractionation compared to SCX, for both large (100 µg) and small (10 µg) protein inputs

rko rectal bovine shotgun comparative ief
Tracheobronchial air-liquid interface cell culture: a model for innate mucosal defense of the upper airways?

PMID 18931053 · PMC2636953 · American journal of physiology. Lung cellular and molecular physiology · 2009 · 8 claims · 5 setups

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A mass spectrometry approach based on prior density-gradient separation of mucins from other proteins enables comprehensive identification of mucins in mucous secretions, overcoming underrepresentation in prior proteomic studies

tracheobronchial normal apical lc-ms isopycnic sds-page
Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

PMID 18923431 · PMC2692715 · Genes and immunity · 2009 · 7 claims · 6 setups

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A two-stage strategy (Random Forest filtering followed by decision tree modeling) can integrate categorical genetic and continuous proteomic data to identify biomarkers of AE risk

ebv-transformed serum combined rf-filtered snp serum random
HIT: a versatile proteomics platform for multianalyte phenotyping of cytokines, intracellular proteins and surface molecules.

PMID 18849997 · PMC3334282 · Nature medicine · 2008 · 8 claims · 8 setups

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HIT uses oligonucleotide-tagged (Fab- or mSA-conjugated) antibodies, T7 polymerase amplification, and DNA microarray hybridization to indirectly measure multiple analytes in a fluid-phase multiplex format

hsp70-coated hsp70 secreted jurkat fluid-phase multiplex hit
Integrating genomic based information into clinical warfarin (Coumadin) management: an illustrative case report.

PMID 18763667 · PMC3696193 · Connecticut medicine · 2008 · 8 claims · 6 setups

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Combined CYP2C9 and VKORC1 genotype can explain up to 45% of warfarin dose variability

genomic edta plasma cardiac genotyping extraction inr
Cancer screening: a mathematical model relating secreted blood biomarker levels to tumor sizes.

PMID 18715113 · PMC2517618 · PLoS medicine · 2008 · 8 claims · 4 setups

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A linear one-compartment mathematical model can relate secreted blood tumor biomarker levels to tumor burden/size at steady state

ovarian serum model culture clinical mathematical
A novel GCAP1(N104K) mutation in EF-hand 3 (EF3) linked to autosomal dominant cone dystrophy.

PMID 18706439 · PMC2584361 · Vision research · 2008 · 8 claims · 7 setups

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A novel N104K mutation in GCAP1's third EF-hand (EF3) motif was identified in two affected members of a family with autosomal dominant cone dystrophy, the first naturally occurring mutation in the EF3 Ca2+-binding loop.

genomic patients high recombinant pcr full-field paired-flash
An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer.

PMID 18676830 · PMC2680495 · Cancer research · 2008 · 8 claims · 5 setups

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PIK3CA mutations are more common in hormone receptor-positive and HER2-positive tumors than in basal-like breast cancers

breast hormone early-stage mass sanger reverse-phase
Bioengineering a humanized acne microenvironment model: proteomics analysis of host responses to Propionibacterium acnes infection in vivo.

PMID 18651708 · PMC2699546 · Proteomics · 2008 · 8 claims · 6 setups

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A dermis-based cell-trapped system (DBCTS) with human sebocytes inserted into a subcutaneous tissue chamber creates a humanized acne microenvironment in mice

chamber infiltrated de-epidermized sebocyte cfu sandwich immunofluorescence
A prospective, cross-sectional survey study of the natural history of Niemann-Pick disease type B.

PMID 18625664 · PMC2692309 · Pediatrics · 2008 · 8 claims · 8 setups

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NPD type B involves multisystem disease including hepatosplenomegaly, interstitial lung disease, dyslipidemia, thrombocytopenia, and growth delay

leukocyte peripheral serum plasma gene enzyme chitotriosidase
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

Experiments

Detection of venous thromboembolism by proteomic serum biomarkers.

A novel variable number of tandem repeat of the natriuretic peptide precursor B gene's 5'-flanking region is associated with essential hypertension among Japanese females.

Pulmonary biomarkers based on alterations in protein expression after exposure to arsenic.

Proteomic profiling of the amniotic fluid to detect inflammation, infection, and neonatal sepsis.

Increasing the number of SNP loci does not necessarily improve prediction power at least in the comparison of MTHFR SNP and haplotypes.

Proteomic analysis of RCL2 paraffin-embedded tissues.

A proteomic analysis of IVF follicular fluid in women

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

Familial pulmonary alveolar proteinosis caused by mutations in CSF2RA.

Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry.

Tracheobronchial air-liquid interface cell culture: a model for innate mucosal defense of the upper airways?

Integrated analysis of genetic and proteomic data identifies biomarkers associated with adverse events following smallpox vaccination.

HIT: a versatile proteomics platform for multianalyte phenotyping of cytokines, intracellular proteins and surface molecules.

Integrating genomic based information into clinical warfarin (Coumadin) management: an illustrative case report.

Cancer screening: a mathematical model relating secreted blood biomarker levels to tumor sizes.

A novel GCAP1(N104K) mutation in EF-hand 3 (EF3) linked to autosomal dominant cone dystrophy.

An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer.

Bioengineering a humanized acne microenvironment model: proteomics analysis of host responses to Propionibacterium acnes infection in vivo.

A prospective, cross-sectional survey study of the natural history of Niemann-Pick disease type B.

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.