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 576

System / cell line: genotype ✕ Clear

Relationship between cyclooxygenase 8473T>C polymorphism and the risk of lung cancer: a case-control study.

PMID 16542464 · PMC1468421 · BMC cancer · 2006 · 8 claims · 4 setups

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The COX-2 8473T>C genotype distribution did not differ significantly between overall lung cancer cases and controls.

peripheral selected lung pcr-based sequencing questionnaire-based
Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish.

PMID 16515697 · PMC1448207 · BMC medical genetics · 2006 · 8 claims · 7 setups

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CMS compares IBS allele/genotype sharing between distantly related (beyond grandparental) affected and unaffected individuals from founder populations to detect disease loci while reducing confounding from population stratification and genetic heterogeneity.

amish unrelated same overall microsatellite combinatorial permutation
Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

PMID 16512914 · PMC1413517 · BMC medical genetics · 2006 · 8 claims · 5 setups

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Patient carries a novel 2.3 Mb deletion in 22q11.2 with proximal breakpoint between RH48663/RH48348 and distal breakpoint between D22S1138/SHGC-145314

genomic maternal 22qtdr chromosome semi-quantitative pcr fish
Multilocus analysis of SNP and metabolic data within a given pathway.

PMID 16412218 · PMC1382210 · BMC genomics · 2006 · 8 claims · 7 setups

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The combinatorial partitioning method (CPM) with optimal thresholds can identify SNPs associated with quantitative metabolite levels rather than only categorical traits.

healthy plasma genomic chi-square combinatorial leave-one-out
Direct maximum parsimony phylogeny reconstruction from genotype data.

PMID 18053244 · PMC2222657 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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The paper presents the first practical method for computing maximum parsimony phylogenies directly from genotype data, using integer linear programming.

simulated mitochondrial lipoprotein coalescent maximum sliding-window
Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'.

PMID 17980034 · PMC2180187 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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CubeX, a Python program/web tool, computes the exact algebraic (Cardan/Nickalls) solution(s) of Hill's cubic equation to estimate pairwise haplotype frequencies, D', r2 and chi-square for each solution

simulated real apoe igf2 cubic pairwise haplotype
Efficacy assessment of SNP sets for genome-wide disease association studies.

PMID 17726055 · PMC2034459 · Nucleic acids research · 2007 · 6 claims · 4 setups

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τ, derived from Shannon entropy and swept radius ɛ, approximates the relative sample size efficiency of a marker set for mapping a causal variant at a given map position compared to a maximally polymorphic SNP

hapmap affymetrix illumina genome-wide swept comparative
Association study of T102C 5-HT(2A) polymorphism in schizophrenic patients: diagnosis, psychopathology, and suicidal behavior.

PMID 17506229 · PMC3181846 · Dialogues in clinical neuroscience · 2007 · 7 claims · 4 setups

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The T102C 5-HT2A genotype/allele frequencies were not associated with suicide attempt history or suicide attempt characteristics (lethality, violence) in schizophrenic patients.

lymphocyte schizophrenic pcr-rflp structured brief
Imputation of missing genotypes: an empirical evaluation of IMPUTE.

PMID 19077279 · PMC2636842 · BMC genetics · 2008 · 8 claims · 7 setups

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IMPUTE achieves 97% median genotype imputation accuracy in Caucasian (NNC) subjects when <10% of SNPs are untyped

caucasian african random thai genome-wide chromosome principal
Role of variation in the serotonin transporter protein gene (SLC6A4) in trait disturbances in the ventral anterior cingulate in bipolar disorder.

PMID 19037205 · PMC2826628 · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2009 · 7 claims · 4 setups

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The 5-HTTLPR s allele contributes to a trait-related, genetically-derived neurobiological subgroup within BD characterized by prominent vACC dysfunction.

participants blood-derived event-related genotyping clinical
Gene-environment interaction and obesity.

PMID 19019037 · PMC3683966 · Nutrition reviews · 2008 · 8 claims · 8 setups

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Obesity susceptibility is largely genetically determined but requires environmental exposure (excess energy intake, low fiber, physical inactivity) to manifest phenotypically.

framingham european individuals healthy genome-wide candidate gene-diet
Nutritional genomics, polyphenols, diets, and their impact on dietetics.

PMID 18954579 · PMC2692306 · Journal of the American Dietetic Association · 2008 · 8 claims · 8 setups

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Nutrient-gene interactions, exemplified by the MTHFR C677T polymorphism, modulate individual metabolic responses (e.g., homocysteine metabolism) and can be offset by adjusting nutrient intake such as folate

mammary embryonic subjects rats gene histone carcinogen-induced
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
MDM2 gene SNP309 T/G and p53 gene SNP72 G/C do not influence diffuse large B-cell non-Hodgkin lymphoma onset or survival in central European Caucasians.

PMID 18433491 · PMC2375899 · BMC cancer · 2008 · 6 claims · 4 setups

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MDM2 SNP309 T/G genotype is not associated with DLBCL or NHL onset, diagnosis, or age of onset in central European Caucasians, including in pre-menopausal women

genomic nhl pcr case-control survival
CALHM1 P86L polymorphism does not alter amyloid-beta or tau in cerebrospinal fluid.

PMID 20005921 · PMC2860374 · Neuroscience letters · 2010 · 5 claims · 4 setups

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CALHM1 P86L genotype does not significantly alter CSF levels of Aβ42, total tau, or phospho-tau in AD or other cognitive disorder patients

swedish csf snp
Iterative pruning PCA improves resolution of highly structured populations.

PMID 19930644 · PMC2790469 · BMC bioinformatics · 2009 · 7 claims · 7 setups

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ipPCA is a novel algorithm that assigns individuals to subpopulations and infers the total number of subpopulations (K) present in genotypic data

simulated hapmap cattle shriver's simulated snp comparative
Involvement of the modifier gene of a human Mendelian disorder in a negative selection process.

PMID 19888326 · PMC2765618 · PloS one · 2009 · 7 claims · 4 setups

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The frequency of SAA1 alpha/alpha homozygotes is much higher among Armenian FMF patients (24%) than Karabakhian FMF patients (4%)

genomic population simulated pcr pearson monte
The D2 dopamine receptor gene and nicotine dependence among bladder cancer patients and controls.

PMID 19842028 · PMC3719969 · Behavior genetics · 2010 · 8 claims · 5 setups

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Among ever-smoking controls, A1 and B1 genotypes were associated with greater smoking intensity and younger age at smoking initiation than A2A2/B2B2

peripheral bladder current genotype pcr-rflp structured fagerström
SNP haplotype tagging from DNA pools of two individuals.

PMID 12709267 · PMC156884 · BMC bioinformatics · 2003 · 8 claims · 3 setups

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An algorithm can reconstruct haplotypes from pools of two individuals' DNA under very general conditions, without requiring Hardy-Weinberg equilibrium.

add2 pooling computational exhaustive
Analysis of polymorphic TGFB1 codons 10, 25, and 263 in a German patient group with non-syndromic cleft lip, alveolus, and palate compared with healthy adults.

PMID 15212689 · PMC441379 · BMC medical genetics · 2004 · 8 claims · 3 setups

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Arg25Pro heterozygous genotype is significantly less frequent in CLP patients (3.3%) than in healthy controls (16.7%)

peripheral genomic platelet-poor real-time sanger enzyme-linked

Experiments

Relationship between cyclooxygenase 8473T>C polymorphism and the risk of lung cancer: a case-control study.

Combinatorial Mismatch Scan (CMS) for loci associated with dementia in the Amish.

Breakpoint Associated with a novel 2.3 Mb deletion in the VCFS region of 22q11 and the role of Alu (SINE) in recurring microdeletions.

Multilocus analysis of SNP and metabolic data within a given pathway.

Direct maximum parsimony phylogeny reconstruction from genotype data.

Cubic exact solutions for the estimation of pairwise haplotype frequencies: implications for linkage disequilibrium analyses and a web tool 'CubeX'.

Efficacy assessment of SNP sets for genome-wide disease association studies.

Association study of T102C 5-HT(2A) polymorphism in schizophrenic patients: diagnosis, psychopathology, and suicidal behavior.

Imputation of missing genotypes: an empirical evaluation of IMPUTE.

Role of variation in the serotonin transporter protein gene (SLC6A4) in trait disturbances in the ventral anterior cingulate in bipolar disorder.

Gene-environment interaction and obesity.

Nutritional genomics, polyphenols, diets, and their impact on dietetics.

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

MDM2 gene SNP309 T/G and p53 gene SNP72 G/C do not influence diffuse large B-cell non-Hodgkin lymphoma onset or survival in central European Caucasians.

CALHM1 P86L polymorphism does not alter amyloid-beta or tau in cerebrospinal fluid.

Iterative pruning PCA improves resolution of highly structured populations.

Involvement of the modifier gene of a human Mendelian disorder in a negative selection process.

The D2 dopamine receptor gene and nicotine dependence among bladder cancer patients and controls.

SNP haplotype tagging from DNA pools of two individuals.

Analysis of polymorphic TGFB1 codons 10, 25, and 263 in a German patient group with non-syndromic cleft lip, alveolus, and palate compared with healthy adults.