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 281

Assay: sensitivity ✕ Clear

Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring.

PMID 19121650 · PMC2706936 · Journal of proteomics · 2009 · 7 claims · 5 setups

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A new MRM worksheet was implemented in The Global Proteome Machine database (GPMDB) that provides all information needed to design MRM transitions based solely on archived observations from previous experiments by other researchers.

platelet proteins reaction midas mrm
Advances in breast cancer: pathways to personalized medicine.

PMID 19088015 · PMC4535810 · Clinical cancer research : an official journal of the American Association for Cancer Research · 2008 · 8 claims · 8 setups

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Germline BRCA1/BRCA2 mutations are strong predictors of breast and ovarian cancer, conferring a 40-80% lifetime risk of breast cancer

population-based women breast high-risk germline genome-wide microarray
Adaptive optics scanning laser ophthalmoscopy images in a family with the mitochondrial DNA T8993C mutation.

PMID 18997096 · PMC4836613 · Investigative ophthalmology & visual science · 2009 · 7 claims · 8 setups

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High T8993C mutant load (>77%) is associated with severe neurologic and/or retinal abnormalities, while low mutant load (42-54%) causes no detectable abnormalities.

retina blood visual adaptive real-time genetic
Cataloging coding sequence variations in human genome databases.

PMID 18974781 · PMC2570488 · PloS one · 2008 · 8 claims · 7 setups

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A significant proportion of CVs overlap between HGMD and dbSNP (4.36% of HGMD CVs registered in dbSNP; 8.11% of dbSNP CVs registered in HGMD), warranting caution when interpreting phenotypic relevance of concurrent CVs.

coding hapmap concurrent nssnps database hapmap amino
Better smelling through genetics: mammalian odor perception.

PMID 18938244 · PMC2590501 · Current opinion in neurobiology · 2008 · 8 claims · 8 setups

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Odorant receptor (OR) gene repertoire size and pseudogene fraction vary dramatically across mammalian species

mammals subjects v1r trpc2 comparative genetic targeted
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
The protein-phosphatome of the human malaria parasite Plasmodium falciparum.

PMID 18793411 · PMC2559854 · BMC genomics · 2008 · 8 claims · 8 setups

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P. falciparum possesses 27 putative protein phosphatase sequences across the four major PP families (PPP, PPM, PTP, NIF), plus 7 additional sequences predicted to dephosphorylate non-protein substrates, totaling 34.

sapiens ppp-domain metallophosphatase pf14_0142 hmm sequence neighbour-net
Tags for labeling protein N-termini with subtiligase for proteomics.

PMID 18762420 · PMC2590642 · Bioorganic & medicinal chemistry letters · 2008 · 6 claims · 4 setups

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Arginine-rich peptide esters (3, 4, 5) are markedly more soluble than the original TEVest2 ester (1) and give significantly higher N-terminal tagging of proteins by subtiligase at higher concentrations.

jurkat neutravidin-coated synthetic proteomic sds-page sandwich aqueous
Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

PMID 18710585 · PMC2533671 · BMC microbiology · 2008 · 7 claims · 6 setups

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A four-SNP set (glnA36, glnA429, glcK180, adhP111) identified via the Not-N algorithm plus empirical testing divides GBS into 10 groups concordant with eBURST-defined population structure.

gbs clinical bioinformatic eburst kinetic
A biomarker panel for peripheral arterial disease.

PMID 18687758 · PMC3133945 · Vascular medicine (London, England) · 2008 · 7 claims · 6 setups

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β2-microglobulin (β2M) and cystatin C had the highest correlation with ABI among all plasma markers tested, higher than age, smoking, or diabetes status

plasma fasting subjects biomarker nephelometric clinical ankle-brachial
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
Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke.

PMID 18616825 · PMC2492849 · BMC medical informatics and decision making · 2008 · 7 claims · 5 setups

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An LAD classification model built from a support-set of 3 peptide peaks can distinguish stroke patients from controls with 75% accuracy on an independent validation set

plasma discretized seldi-tof serum logical
Identification of novel markers for liver fibrosis in HIV/hepatitis C virus coinfected individuals using genomics-based approach.

PMID 18614866 · PMC2654216 · AIDS (London, England) · 2008 · 8 claims · 6 setups

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An 8-marker model combining six serum markers, age, and ART experience predicts liver fibrosis stage with an AUROC of 0.904.

pbmcs liver serum blood microarray liver serum
Detection of mutations in EGFR in circulating lung-cancer cells.

PMID 18596266 · PMC3551471 · The New England journal of medicine · 2008 · 8 claims · 7 setups

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The CTC-chip microfluidic device isolates CTCs from NSCLC patients in sufficient quantity and purity to permit EGFR mutational analysis

blood archived nsclc plasma microfluidic allele-specific standard
Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.

PMID 18588693 · PMC2446391 · BMC bioinformatics · 2008 · 8 claims · 5 setups

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A decision tree built on 10 selected sequence-derived features classifies SAPs as Disease or Polymorphism with 82.6% accuracy and 0.607 MCC in cross-validation.

sap sequence-derived humvar same decision independent greedy
Extension of type 2 diabetes genome-wide association scan results in the diabetes prevention program.

PMID 18544707 · PMC2518503 · Diabetes · 2008 · 8 claims · 4 setups

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None of the selected GWAS-identified SNPs individually were associated with increased diabetes incidence in the DPP cohort

dpp snp cox oral
Probing the cancer genome.

PMID 18492227 · PMC2441462 · Genome biology · 2008 · 8 claims · 8 setups

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Combined Sanger and 454 pyrosequencing of MCF-7 BAC clones identified 157 PCR-confirmed translocation breakpoint junctions, including 10 in-frame junctions confirmed at the transcript level

mcf-7 tumor lung oral sanger solexa gistic
Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

PMID 18366609 · PMC2386062 · BMC genomics · 2008 · 8 claims · 7 setups

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The mapping algorithm identified 5,647 candidate bidirectional promoter regions in the mouse genome, similar in number to those previously found in human.

genome seven genes computational cage comparative
Minisequencing mitochondrial DNA pathogenic mutations.

PMID 18402672 · PMC2377236 · BMC medical genetics · 2008 · 7 claims · 7 setups

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A minisequencing multiplex assay can interrogate 25 pathogenic mtDNA mutations across the whole mtDNA genome in a single reaction using 13 amplicons.

blood-derived same genomic pcr minisequencing automatic multiplex
Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.

PMID 18366646 · PMC2323364 · BMC medical genetics · 2008 · 7 claims · 8 setups

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Common ARNT variants are not associated with type 2 diabetes in European American or African American case-control cohorts

european african individuals nondiabetic snp variant direct

Experiments

Implementation of a data repository-driven approach for targeted proteomics experiments by multiple reaction monitoring.

Advances in breast cancer: pathways to personalized medicine.

Adaptive optics scanning laser ophthalmoscopy images in a family with the mitochondrial DNA T8993C mutation.

Cataloging coding sequence variations in human genome databases.

Better smelling through genetics: mammalian odor perception.

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

The protein-phosphatome of the human malaria parasite Plasmodium falciparum.

Tags for labeling protein N-termini with subtiligase for proteomics.

Assignment of Streptococcus agalactiae isolates to clonal complexes using a small set of single nucleotide polymorphisms.

A biomarker panel for peripheral arterial disease.

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

Logical Analysis of Data (LAD) model for the early diagnosis of acute ischemic stroke.

Identification of novel markers for liver fibrosis in HIV/hepatitis C virus coinfected individuals using genomics-based approach.

Detection of mutations in EGFR in circulating lung-cancer cells.

Identification of deleterious non-synonymous single nucleotide polymorphisms using sequence-derived information.

Extension of type 2 diabetes genome-wide association scan results in the diabetes prevention program.

Probing the cancer genome.

Prediction-based approaches to characterize bidirectional promoters in the mammalian genome.

Minisequencing mitochondrial DNA pathogenic mutations.

Aryl hydrocarbon receptor nuclear translocator (ARNT) gene as a positional and functional candidate for type 2 diabetes and prediabetic intermediate traits: Mutation detection, case-control studies, and gene expression analysis.