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 569

System / cell line: frequency ✕ Clear

ATM variants and cancer risk in breast cancer patients from Southern Finland.

PMID 16914028 · PMC1592307 · BMC cancer · 2006 · 8 claims · 6 setups

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Neither 5557G>A nor ivs38-8T>C, nor any haplotype containing them, was significantly associated with breast cancer risk in any patient group

familial brca1 same genotype genotyping denaturing direct
Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies.

PMID 16899448 · PMC1557808 · Nucleic acids research · 2006 · 7 claims · 4 setups

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3D VizStruct (DFT-based radial mapping + KLD as z-axis) can identify SNPs/polymorphic markers that are predictive of underlying biological class distinctions across diverse datasets

lpl y-chromosome coral simulated snp aflp numerical
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
CEAS: cis-regulatory element annotation system.

PMID 16845068 · PMC1538818 · Nucleic acids research · 2006 · 7 claims · 5 setups

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CEAS is the first web server to streamline genome-scale ChIP-chip downstream analyses for biologists without strong bioinformatics support

genome genomic chip-chip repeat-masked conservation
Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

PMID 16824219 · PMC1534050 · BMC neurology · 2006 · 7 claims · 5 setups

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The C282Y variant allele of HFE is significantly overrepresented in PD patients compared to controls, suggesting it confers higher risk for PD

genomic same pooled pcr-rflp pcr-based cross-tabulation
Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations.

PMID 16789823 · PMC1513265 · PLoS genetics · 2006 · 8 claims · 8 setups

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K63-polyubiquitin chain formation protects human cells against translesion synthesis-induced mutations by promoting error-free recovery of blocked replication forks.

a549 western proliferation clonogenic
Association between alcoholism and the genetic polymorphisms of the GABAA receptor genes on chromosome 5q33-34 in Korean population.

PMID 16778401 · PMC2729963 · Journal of Korean medical science · 2006 · 6 claims · 5 setups

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Genetic polymorphisms of the GABA A α1 and α6 receptor genes are significantly associated with alcohol dependence, surviving Bonferroni correction.

genomic hospitalized pcr-rflp structured
Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

PMID 16759380 · PMC1525190 · BMC genomics · 2006 · 8 claims · 6 setups

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Overall pairwise genomic divergences among cattle, dog and human are relatively constant (0.32–0.37 change/site)

orthologous random cattle aligned three-way pairwise bac
Protein ranking by semi-supervised network propagation.

PMID 16723003 · PMC1810311 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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RankProp, a diffusion-based network propagation algorithm on a PSI-BLAST-derived protein similarity network, significantly outperforms local search methods (BLAST/PSI-BLAST) at detecting remote homologs.

scop similarity same psi-blast rankprop probabilistic
A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

PMID 16626494 · PMC1459863 · Malaria journal · 2006 · 8 claims · 5 setups

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Pyrosequencing, after adjustment to a standard curve, provides accurate and precise estimates of allele frequencies in mixed MSP-1_19 infections

falciparum cloned pyrosequencing pcr
Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

PMID 16542438 · PMC1526716 · BMC medical genetics · 2006 · 8 claims · 6 setups

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Mutations in the OAZ3 gene are not a common cause of male infertility

genomic coding inferred oaz3 direct sscp haplotype
Policy implications of genetic information on regulation under the Clean Air Act: the case of particulate matter and asthmatics.

PMID 16507451 · PMC1392222 · Environmental health perspectives · 2006 · 8 claims · 4 setups

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The Clean Air Act mandates protection of sensitive subpopulations, including asthmatics, from air pollution health effects, creating an opening for genetic susceptibility data in regulation.

u.s epa asthma asthmatic statutory regulatory literature
Bias of selection on human copy-number variants.

PMID 16482228 · PMC1366494 · PLoS genetics · 2006 · 8 claims · 8 setups

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Human CNVs are significantly overrepresented near telomeres and centromeres and enriched in simple tandem repeats relative to the genome as a whole

genome human-mouse cnv-encompassed inbred comparative randomization molecular
Peroxisomal proliferator activated receptor-gamma deficiency in a Canadian kindred with familial partial lipodystrophy type 3 (FPLD3).

PMID 16412238 · PMC1368963 · BMC medical genetics · 2006 · 8 claims · 6 setups

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A novel PPARG nonsense mutation, Y355X, was identified in a mother and daughter with FPLD3-consistent phenotypes and was absent from unaffected relatives and 260 healthy controls

subjects nih3t3 subject healthy sequencing luciferase western
Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

PMID 16405730 · PMC1343542 · BMC medical genetics · 2006 · 8 claims · 4 setups

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Germline mutations of SDHB and SDHC play a minor role in sporadic head and neck paraganglioma

peripheral genomic ebv-transformed conformation pira-pcr rt-pcr
Personalized genomic medicine with a patchwork, partially owned genome.

PMID 18449389 · PMC2347364 · The Yale journal of biology and medicine · 2007 · 8 claims · 6 setups

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Structural variants (CNVs) cover as much as 20 percent of the human genome length and are present in phenotypically normal individuals without apparent negative consequences.

phenotypically single genome chimpanzee molecular diploid encode
Nutrigenomics: the genome--food interface.

PMID 18087577 · PMC2137135 · Environmental health perspectives · 2007 · 8 claims · 8 setups

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Nutrigenomics integrates genomic science with nutrition to study how dietary components affect gene expression, the proteome, and the metabolome.

general humans lymphocytes healthy snp controlled micronucleus
Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

PMID 18084025 · PMC2241897 · Nucleic acids research · 2008 · 5 claims · 7 setups

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QUMA (quantitative real-time PCR) and AUMA (fingerprinting PCR) methods can quantify and individually identify unmethylated Alu elements on a genomic scale using the methylation-sensitive SmaI site as a surrogate marker

paired colorectal genome normal quma auma bioinformatic
Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.

PMID 18047689 · PMC2106846 · Genome biology · 2007 · 8 claims · 6 setups

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Vector insertion site preferences differ substantially between viral vectors and transposons, affecting both oncogenic risk in gene therapy and utility for functional genomics

hela liver gene peripheral retroviral transposon hydrodynamic
Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.

PMID 17945002 · PMC2242669 · Breast cancer research : BCR · 2007 · 8 claims · 7 setups

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-26G>A polymorphism in the BRCA2 5' UTR is functional: the A allele drives roughly twice the reporter gene expression of the G allele in MCF-7 and HeLa cells

mcf-7 hela brca2 peripheral luciferase transcription genotyping

Experiments

ATM variants and cancer risk in breast cancer patients from Southern Finland.

Information-theoretic identification of predictive SNPs and supervised visualization of genome-wide association studies.

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

CEAS: cis-regulatory element annotation system.

Association of HFE common mutations with Parkinson's disease, Alzheimer's disease and mild cognitive impairment in a Portuguese cohort.

Lysine 63-polyubiquitination guards against translesion synthesis-induced mutations.

Association between alcoholism and the genetic polymorphisms of the GABAA receptor genes on chromosome 5q33-34 in Korean population.

Genomic divergences among cattle, dog and human estimated from large-scale alignments of genomic sequences.

Protein ranking by semi-supervised network propagation.

A high-throughput method for quantifying alleles and haplotypes of the malaria vaccine candidate Plasmodium falciparum merozoite surface protein-1 19 kDa.

Identification of polymorphisms and balancing selection in the male infertility candidate gene, ornithine decarboxylase antizyme 3.

Policy implications of genetic information on regulation under the Clean Air Act: the case of particulate matter and asthmatics.

Bias of selection on human copy-number variants.

Peroxisomal proliferator activated receptor-gamma deficiency in a Canadian kindred with familial partial lipodystrophy type 3 (FPLD3).

Mutation analysis of SDHB and SDHC: novel germline mutations in sporadic head and neck paraganglioma and familial paraganglioma and/or pheochromocytoma.

Personalized genomic medicine with a patchwork, partially owned genome.

Nutrigenomics: the genome--food interface.

Genome-wide tracking of unmethylated DNA Alu repeats in normal and cancer cells.

Predicting preferential DNA vector insertion sites: implications for functional genomics and gene therapy.

Implication of BRCA2 -26G>A 5' untranslated region polymorphism in susceptibility to sporadic breast cancer and its modulation by p53 codon 72 Arg>Pro polymorphism.