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 417

System / cell line: same ✕ Clear

Genetic linkage study of high-grade myopia in a Hutterite population from South Dakota.

PMID 17327828 · PMC2633468 · Molecular vision · 2007 · 6 claims · 5 setups

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AD non-syndromic high-grade myopia in the Hutterite family MYO-101 shows significant linkage to a locus on chromosome 10q21.1

hutterite same pcdh15 genome-wide fine-point candidate
Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

PMID 17305421 · PMC1797821 · PLoS computational biology · 2007 · 8 claims · 8 setups

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The synonymous substitution rate (dS) of HIV env is strongly correlated with disease progression parameters (progression time, CD4+ decline rate, viral load increase rate), unlike the nonsynonymous rate (dN).

longitudinal backbone env intra-patient relaxed-clock correlation site-to-site
Relative impact of nucleotide and copy number variation on gene expression phenotypes.

PMID 17289997 · PMC2665772 · Science (New York, N.Y.) · 2007 · 8 claims · 5 setups

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SNPs and CNVs capture largely non-overlapping signals of genetic variation affecting gene expression

lymphoblastoid same computational subset gene snp array
A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer.

PMID 17222328 · PMC1784097 · BMC cancer · 2007 · 7 claims · 8 setups

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A workflow combining Alohomora, Mega2, MENDEL, SNPLINK and SimWalk2 enables linkage analysis with high-density SNP arrays in large pedigrees (>35-40 bits) that exceed the capacity of single existing programs

peripheral pedigree nuclear family snp two-point multipoint
Significance of the parkin and PINK1 gene in Jordanian families with incidences of young-onset and juvenile parkinsonism.

PMID 19087301 · PMC2635385 · BMC neurology · 2008 · 8 claims · 8 setups

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A parkin exon 4 deletion segregates with disease in a three-generation family (Family F), homozygous in both affected individuals

consanguineous same affected family sanger multiplex microsatellite
A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

PMID 19087293 · PMC2636810 · BMC bioinformatics · 2008 · 6 claims · 6 setups

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A theoretical exon-exon junction protein database accounting for all in-phase (frame-preserving) exon combinations can be built from the Ensembl Core Database using Perl/Bioperl/MySQL/Ensembl API.

ensembl liver candidate same database tandem decoy
Predictive genomics of cardioembolic stroke.

PMID 19064790 · PMC2752697 · Stroke · 2009 · 8 claims · 4 setups

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A Bayesian network multivariate model achieves 86% predictive accuracy (AUC) for cardioembolic stroke on fitted values

blood-derived gasros same custom bayesian roc
Family history of breast cancer and all-cause mortality after breast cancer diagnosis in the Breast Cancer Family Registry.

PMID 19034644 · PMC2728159 · Breast cancer research and treatment · 2009 · 7 claims · 5 setups

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Family history of breast cancer is not associated with all-cause mortality after breast cancer diagnosis in women without a known germline BRCA1/BRCA2 mutation.

women same breast structured cox germline
Synergistic effects of the MTHFR C677T polymorphism and hypertension on spatial navigation.

PMID 19013496 · PMC2685204 · Biological psychology · 2009 · 7 claims · 4 setups

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Hypertensive carriers of the MTHFR 677T allele show significantly worse spatial navigation (longer distance to platform) than hypertensive C677C homozygotes

healthy same buccal virtual blood mthfr
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

Experiments

Genetic linkage study of high-grade myopia in a Hutterite population from South Dakota.

Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics.

Relative impact of nucleotide and copy number variation on gene expression phenotypes.

A procedure for the detection of linkage with high density SNP arrays in a large pedigree with colorectal cancer.

Significance of the parkin and PINK1 gene in Jordanian families with incidences of young-onset and juvenile parkinsonism.

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data.

Predictive genomics of cardioembolic stroke.

Family history of breast cancer and all-cause mortality after breast cancer diagnosis in the Breast Cancer Family Registry.

Synergistic effects of the MTHFR C677T polymorphism and hypertension on spatial navigation.

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.