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 26

System / cell line: frequency ✕ Assay: mass ✕ Clear

VEGF, FGF1, FGF2 and EGF gene polymorphisms and psoriatic arthritis.

PMID 17204151 · PMC1781940 · BMC musculoskeletal disorders · 2007 · 7 claims · 5 setups

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The T allele of VEGF +936 (rs3025039) is significantly less frequent in PsA cases than in controls, suggesting a protective effect against PsA.

blood same subject psa snp allele hardy-weinberg
Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

PMID 19907653 · PMC2771352 · PloS one · 2009 · 8 claims · 7 setups

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IL10 haplotype 1 (rs1800871, rs1800872, rs3024490, rs1554286) is associated with a pro-inflammatory ex vivo cytokine response (lower IL-10, higher TNF-alpha) relative to the population mean

population blood genomic hapmap snp survival allele
Proteogenomic analysis prioritises functional single nucleotide variants in cancer samples.

PMID 29221171 · PMC5707065 · Oncotarget · 2017 · 8 claims · 6 setups

Has reproduction · 73

A customised SAAV peptide database built from RNA-seq/WGS variant calls can be used to search proteomics data and detect single amino acid variant (SAAV)-containing peptides at the protein level

jurkat rna-seq genome proteomics
A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise.

PMID 18615428 · PMC2855839 · Proteomics · 2008 · 6 claims · 4 setups

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Noise in SELDI-TOF/MALDI-TOF mass spectrometry data is heteroscedastic across the m/z range, with larger variance at lower m/z values, contrary to the homogeneous noise assumption of existing wavelet denoising methods.

serum raw denoised simulated seldi-tof wavelet-based peak
Profiling critical cancer gene mutations in clinical tumor samples.

PMID 19924296 · PMC2774511 · PloS one · 2009 · 7 claims · 4 setups

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OncoMap, a panel of ~400 mass-spectrometric genotyping assays targeting 33 cancer genes, enables robust mutation profiling of clinical fresh-frozen and FFPE tumor DNA.

clinical fresh same pediatric mass sanger barcoded
Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.

PMID 19733729 · PMC2748225 · Analytica chimica acta · 2009 · 8 claims · 4 setups

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ACA-based wavelet coefficient feature selection can achieve up to 100% classification accuracy on training, validating, and independent testing sets using only 5 selected features.

blood baseline-corrected 953-dimensional training seldi-tof wavelet ant
Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

PMID 16026601 · PMC1637030 · BMC bioinformatics · 2005 · 8 claims · 2 setups

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DF-SNPs, a novel adaptation of the Decision Forest method, can classify esophageal cancer cases vs. controls based on SNP genotype data with high concordance, sensitivity, and specificity.

genomic snp high-throughput decision
In vivo pharmaco-proteomic analysis of hydroxyurea induced changes in the sickle red blood cell membrane proteome.

PMID 19914412 · PMC2818491 · Journal of proteomics · 2010 · 8 claims · 4 setups

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2D-DIGE combined with tandem mass spectrometry identified 32 distinct sickle RBC membrane proteins that significantly changed in abundance after in vivo HU therapy

sickle excised patients 2d-dige tandem immunoblot
Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.

PMID 19912651 · PMC2784748 · BMC cell biology · 2009 · 7 claims · 7 setups

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hnRNP L is a novel Sam68-interacting protein partner identified by proteomics and confirmed by co-immunoprecipitation

lncap hek293 nih3t3 co-immunoprecipitation sucrose indirect
Expanding the clinical spectrum of COL2A1 related disorders by a mass like phenotype.

PMID 35296718 · PMC8927422 · Scientific reports · 2022 · 8 claims · 8 setups

Has reproduction · 84

Four FBN1-negative patients from three families with a MASS-like phenotype carry likely pathogenic or uncertain-significance missense variants in the propeptide-coding regions of COL2A1

blood-derived four patients col2a1 targeted clinical transthoracic
A Chronic Fatigue Syndrome - related proteome in human cerebrospinal fluid.

PMID 16321154 · PMC1326206 · BMC neurology · 2005 · 7 claims · 6 setups

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CFS, PGI and fibromyalgia are highly overlapping symptom complexes likely reflecting a shared underlying pathophysiological mechanism rather than distinct diseases

pooled individual cerebrospinal subjects capillary trypsin elisa
Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

PMID 16895448 · PMC1523240 · PLoS genetics · 2006 · 8 claims · 8 setups

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MALDI-TOF MS-based primer extension assays (hME, iPLEX) enable cost-effective, high-throughput multiplexed SNP genotyping

genomic domestic pooled colorectal snp pooling microsatellite
Target SNP selection in complex disease association studies.

PMID 15248903 · PMC487897 · BMC bioinformatics · 2004 · 7 claims · 3 setups

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A computational pipeline can retrieve gene sequence, collect SNP variation data, and annotate SNPs falling in functional motifs (promoter, exon-intron structure, AU-rich elements, TF binding sites, splice sites) with expression in target tissue

genes pooled primer computational maldi-tof blast
An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

PMID 16872505 · PMC1550395 · BMC medical genetics · 2006 · 7 claims · 7 setups

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Marginally significant (uncorrected) transmission distortion was found for four SNPs after stratification by HLA-DRB1*1501 status, disease course, or gender.

pooled australian independent trio pool snapshot snplex
A variant of the SLC10A2 gene encoding the apical sodium-dependent bile acid transporter is a risk factor for gallstone disease.

PMID 19823678 · PMC2757911 · PloS one · 2009 · 6 claims · 4 setups

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SLC10A2 is a novel susceptibility gene for cholelithiasis in humans

genomic pooled sanger maldi-tof genotype-phenotype
Proteomic analysis of Alzheimer's disease cerebrospinal fluid from neuropathologically diagnosed subjects.

PMID 19689240 · PMC2832860 · Current Alzheimer research · 2009 · 8 claims · 6 setups

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2D DIGE analysis of postmortem V-CSF pools identified 21-22 protein spots that significantly differ among neuropathologically-diagnosed AD, non-demented controls (NDC), and non-AD dementia (non-ADD) groups

postmortem trypsin-digested individual subjects difference mass micro
Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.

PMID 40458122 · PMC12127311 · Frontiers in cell and developmental biology · 2025 · 8 claims · 8 setups

Has reproduction · 71

DKC1 mRNA and protein expression are significantly upregulated in UCEC tumors compared with non-tumorous endometrial tissue

ucec ishikawa rna-seq proteomics immunohistochemistry
A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.

PMID 17521420 · PMC1929158 · Genome biology · 2007 · 7 claims · 6 setups

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mtcPTM is a hierarchically organized database of human and mouse phosphosites that preserves experimental context, enabling comparison of phosphorylation patterns across conditions

nonredundant database high-throughput homology
Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

PMID 18989384 · PMC2579937 · Molecular vision · 2008 · 8 claims · 4 setups

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Worn silicone hydrogel contact lenses deposit a wide array of proteins from the tear film and other sources.

deposit excised pooled worn sds-page in-gel lc-ms-ms
Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia.

PMID 37217248 · PMC10231005 · Journal for immunotherapy of cancer · 2023 · 8 claims · 8 setups

Has reproduction · 76

High expression of IFN-I signaling/response genes (IFNAR1, IFNAR2, STAT1, MX1, OAS1) predicts favorable relapse-free survival in B-ALL patients

cog b-all eμ-myc crispra gene-expression-based flow mass

Experiments

VEGF, FGF1, FGF2 and EGF gene polymorphisms and psoriatic arthritis.

Selection for genetic variation inducing pro-inflammatory responses under adverse environmental conditions in a Ghanaian population.

Proteogenomic analysis prioritises functional single nucleotide variants in cancer samples.

A novel wavelet-based thresholding method for the pre-processing of mass spectrometry data that accounts for heterogeneous noise.

Profiling critical cancer gene mutations in clinical tumor samples.

Swarm intelligence based wavelet coefficient feature selection for mass spectral classification: an application to proteomics data.

Decision forest analysis of 61 single nucleotide polymorphisms in a case-control study of esophageal cancer; a novel method.

In vivo pharmaco-proteomic analysis of hydroxyurea induced changes in the sickle red blood cell membrane proteome.

Proteomic identification of heterogeneous nuclear ribonucleoprotein L as a novel component of SLM/Sam68 Nuclear Bodies.

Expanding the clinical spectrum of COL2A1 related disorders by a mass like phenotype.

A Chronic Fatigue Syndrome - related proteome in human cerebrospinal fluid.

Matrix-assisted laser desorption/ionisation, time-of-flight mass spectrometry in genomics research.

Target SNP selection in complex disease association studies.

An investigation of polymorphisms in the 17q11.2-12 CC chemokine gene cluster for association with multiple sclerosis in Australians.

A variant of the SLC10A2 gene encoding the apical sodium-dependent bile acid transporter is a risk factor for gallstone disease.

Proteomic analysis of Alzheimer's disease cerebrospinal fluid from neuropathologically diagnosed subjects.

Comprehensive analyses of telomerase component DKC1 and its association with clinical, molecular and immune landscapes in uterine corpus endometrial carcinoma.

A systematic comparative and structural analysis of protein phosphorylation sites based on the mtcPTM database.

Proteomic analysis of protein deposits on worn daily wear silicone hydrogel contact lenses.

Intrinsic suppression of type I interferon production underlies the therapeutic efficacy of IL-15-producing natural killer cells in B-cell acute lymphoblastic leukemia.