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 488

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Accurate whole human genome sequencing using reversible terminator chemistry.

PMID 18987734 · PMC2581791 · Nature · 2008 · 8 claims · 7 setups

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A novel sequencing platform using fluorescent reversible terminator nucleotides on clonally amplified single-molecule DNA clusters generates several billion bases of accurate sequence per experiment at low cost.

bac flow-sorted same yoruba reversible snp targeted
A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

PMID 18940863 · PMC2602776 · Nucleic acids research · 2008 · 7 claims · 4 setups

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A novel Invader assay-based procedure can accurately determine SNP genotypes in trisomic genomic DNA samples in a simple, cost-effective manner

genomic same synthetic invader pyrosequencing hplc
Decision tree-driven tandem mass spectrometry for shotgun proteomics.

PMID 18931669 · PMC2597439 · Nature methods · 2008 · 8 claims · 5 setups

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A decision tree (DT) algorithm that selects CAD or ETD per precursor based on z and m/z yields more peptide identifications than either CAD or ETD alone

saccharomyces proteome embryonic nlc-ms phosphoproteomics sequential
Complex germline and somatic mutation processes at a haploid human minisatellite shown by single-molecule analysis.

PMID 18929582 · PMC2599865 · Mutation research · 2008 · 8 claims · 5 setups

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Overall MSY1 mutation frequencies in sperm (2.68%) and blood (1.88%) are not significantly different

sperm donor hgr1b3 single-molecule fluorescent radioactive
Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

PMID 18927607 · PMC2559870 · PloS one · 2008 · 8 claims · 5 setups

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No pathogenic mutations were found in LRRK2, PRKN, or ATXN3 in a Nigerian cohort of apparently sporadic PD patients.

nigerian same novel sanger targeted repeat
Pharmaco-proteomic study of hydroxyurea-induced modifications in the sickle red blood cell membrane proteome.

PMID 18849548 · PMC4260454 · Experimental biology and medicine (Maywood, N.J.) · 2008 · 6 claims · 6 setups

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50 μM HU treatment of SS RBC membranes causes statistically significant changes in a discrete set of membrane proteins, distinct from HbF induction.

sickle rbc excised 2d-dige tandem immunoblot
Adaptive history of single copy genes highly expressed in the term human placenta.

PMID 18848617 · PMC2759754 · Genomics · 2009 · 8 claims · 6 setups

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222 single copy eutherian genes are highly expressed (>=3x median) in the term human placenta

term single same lists microarray comparative site
Evolutionary origins of human apoptosis and genome-stability gene networks.

PMID 18832373 · PMC2577361 · Nucleic acids research · 2008 · 8 claims · 8 setups

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The entanglement of DNA repair, chromosome stability and apoptosis gene networks appears with the caspase gene family and the antiapoptotic gene BCL2.

apoptosis fully same orthologous protein-protein comparative orthology
WebScipio: an online tool for the determination of gene structures using protein sequences.

PMID 18801164 · PMC2644328 · BMC genomics · 2008 · 7 claims · 4 setups

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WebScipio, a web interface to Scipio, determines gene structure from a query protein sequence against an assembled eukaryotic genome with quality approaching manual annotation.

homo pongo callithrix mus spliced
High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

PMID 18786630 · PMC2659594 · Genomics · 2008 · 8 claims · 7 setups

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WGA product performs well on the Affymetrix 250K SNP array compared to genomic DNA, especially with the BRLMM calling algorithm.

genomic whole-genome same call snp technical genotype
Determination of Ras-GTP and Ras-GDP in patients with acute myelogenous leukemia (AML), myeloproliferative syndrome (MPS), juvenile myelomonocytic leukemia (JMML), acute lymphocytic leukemia (ALL), and malignant lymphoma: assessment of mutational and indirect activation.

PMID 18784923 · PMC2755762 · Annals of hematology · 2009 · 6 claims · 4 setups

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A non-radioactive, enzyme-coupled luminometric assay can quantify Ras activation as %GTP/(GTP+GDP) with high sensitivity (detects 1 fmol GTP)

bone n=23 3t3 ras genomic
The association of membrane frizzled-related protein (MFRP) gene with acute angle-closure glaucoma--a pilot study.

PMID 18781223 · PMC2532703 · Molecular vision · 2008 · 8 claims · 4 setups

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None of the three MFRP sequence variants tested (rs3814762, rs36015759, rs2510143) showed a statistically significant association with acute angle-closure glaucoma

genomic same eyes pcr genotype linkage
Cannabinoid type-1 receptor gene polymorphisms are associated with central obesity in a Southern Brazilian population.

PMID 18776593 · PMC3827795 · Disease markers · 2008 · 8 claims · 5 setups

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The CNR1 4895G allele is associated with waist-to-hip ratio (WHR)

peripheral same pcr-rflp anthropometric biochemical
Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

PMID 18769673 · PMC2518838 · PloS one · 2008 · 8 claims · 6 setups

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The protein sequence-structure map behaves as a noisy digital communication channel whose capacity C exceeds the transmission rate R for native structures, satisfying Shannon's noisy channel theorem

chains pdbselect25 same single-domain statistical channel negative
Analysis of copy number variation using quantitative interspecies competitive PCR.

PMID 18697816 · PMC2553599 · Nucleic acids research · 2008 · 7 claims · 6 setups

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qicPCR uses the entire genome of a single chimpanzee as a competitor, requiring only one reference sample for all assays and enabling large-scale multiplexing

genomic single 22q11ds qicpcr-derived qicpcr mlpa fluorescence
Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

PMID 18681973 · PMC2553082 · Virology journal · 2008 · 8 claims · 6 setups

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14 MEME blocks were identified in the HA protein of H3N2 strains (1968-1999), with blocks 1, 2, 3, and 7 correlating with several biological functions

h3n2 meme sequence entropy
Seasonality of influenza A(H3N2) virus: a Hong Kong perspective (1997-2006).

PMID 18648550 · PMC2481298 · PloS one · 2008 · 7 claims · 4 setups

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Influenza A(H3N2) seasonality is largely explained by global viral migration, with similar viruses appearing in different countries at different times

influenza same hong gene maximum-likelihood protein-coding
Molecular analysis of CHX10 and MFRP in Chinese subjects with primary angle closure glaucoma and short axial length eyes.

PMID 18648522 · PMC2480479 · Molecular vision · 2008 · 8 claims · 4 setups

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A rare CHX10 missense variant (c.728G>A, Gly243Asp) was identified in one PACG patient and absent in 215 controls, and is a possible disease-causing variant

genomic same chx10 pacg pcr case-control cross-species
Evaluation of BRCA1 and BRCA2 mutations and risk-prediction models in a typical Asian country (Malaysia) with a relatively low incidence of breast cancer.

PMID 18627636 · PMC2575532 · Breast cancer research : BCR · 2008 · 8 claims · 5 setups

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27 deleterious BRCA1/BRCA2 mutations were detected in 28 breast cancer patients (14 in BRCA1, 13 in BRCA2) among 187 tested

blood-derived family brca1 direct multiplex boadicea
PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.

PMID 18620604 · PMC2483288 · BMC bioinformatics · 2008 · 8 claims · 4 setups

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PRESTO is an order of magnitude faster than other existing permutation testing software for genetic association studies.

case-control same wtccc genome-wide benchmark stratified

Experiments

Accurate whole human genome sequencing using reversible terminator chemistry.

A novel procedure for genotyping of single nucleotide polymorphisms in trisomy with genomic DNA and the invader assay.

Decision tree-driven tandem mass spectrometry for shotgun proteomics.

Complex germline and somatic mutation processes at a haploid human minisatellite shown by single-molecule analysis.

Analysis of Nigerians with apparently sporadic Parkinson disease for mutations in LRRK2, PRKN and ATXN3.

Pharmaco-proteomic study of hydroxyurea-induced modifications in the sickle red blood cell membrane proteome.

Adaptive history of single copy genes highly expressed in the term human placenta.

Evolutionary origins of human apoptosis and genome-stability gene networks.

WebScipio: an online tool for the determination of gene structures using protein sequences.

High fidelity of whole-genome amplified DNA on high-density single nucleotide polymorphism arrays.

Determination of Ras-GTP and Ras-GDP in patients with acute myelogenous leukemia (AML), myeloproliferative syndrome (MPS), juvenile myelomonocytic leukemia (JMML), acute lymphocytic leukemia (ALL), and malignant lymphoma: assessment of mutational and indirect activation.

The association of membrane frizzled-related protein (MFRP) gene with acute angle-closure glaucoma--a pilot study.

Cannabinoid type-1 receptor gene polymorphisms are associated with central obesity in a Southern Brazilian population.

Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

Analysis of copy number variation using quantitative interspecies competitive PCR.

Correlating novel variable and conserved motifs in the Hemagglutinin protein with significant biological functions.

Seasonality of influenza A(H3N2) virus: a Hong Kong perspective (1997-2006).

Molecular analysis of CHX10 and MFRP in Chinese subjects with primary angle closure glaucoma and short axial length eyes.

Evaluation of BRCA1 and BRCA2 mutations and risk-prediction models in a typical Asian country (Malaysia) with a relatively low incidence of breast cancer.

PRESTO: rapid calculation of order statistic distributions and multiple-testing adjusted P-values via permutation for one and two-stage genetic association studies.