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 561

System / cell line: genetic ✕ Clear

Computation of haplotypes on SNPs subsets: advantage of the "global method".

PMID 17067372 · PMC1636337 · BMC genetics · 2006 · 6 claims · 4 setups

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The global method for subhaplotyping always yields a lower error rate than the direct method across datasets and SNP subset sizes

gh1 apoe coalescent-model-simulated griv computational genetic
Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

PMID 17012280 · PMC1636463 · Nucleic acids research · 2006 · 7 claims · 5 setups

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DSBs induced at the TRS/vector junction (EcoRV site) generate numerous mutagenic events in flanking sequences, whereas DSBs within the repeat tract (EcoRI site) produce no such mutants

coli plasmids plasmid white plasmid sequencing non-b
GAA repeat expansion mutation mouse models of Friedreich ataxia exhibit oxidative stress leading to progressive neuronal and cardiac pathology.

PMID 16919418 · PMC2842930 · Genomics · 2006 · 8 claims · 8 setups

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Human FXN YAC transgenes containing GAA repeat expansions (YG22, YG8) rescue the embryonic lethality of homozygous Fxn knockout mice

yg22 tissues lysates sciatic breeding semiquantitative western
Novel integrative genomics strategies to identify genes for complex traits.

PMID 16886998 · PMC2367618 · Animal genetics · 2006 · 8 claims · 7 setups

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Forward genetics is restricted to genes harboring mutations, systematically missing network genes that causally influence disease without themselves being mutated.

bxd mice bxh alox5 qtl knockout linkage
Modeling chromosomes in mouse to explore the function of genes, genomic disorders, and chromosomal organization.

PMID 16839184 · PMC1500809 · PLoS genetics · 2006 · 8 claims · 8 setups

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Cre/loxP recombination in ES cells can generate megabase-scale deletions, duplications, and inversions depending on loxP orientation, cis/trans configuration, and cell cycle stage

hybrid recombinant mice homologous cre clone
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
Reduced secretion of fibulin 5 in age-related macular degeneration and cutis laxa.

PMID 16652333 · PMC1828612 · Human mutation · 2006 · 7 claims · 6 setups

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FBLN5 missense mutations are associated with ARMD in a European (UK/Dutch) cohort, confirming prior US findings

armd dutch fibulin pef6-ssflag mutation computational site-directed
Gene losses during human origins.

PMID 16464126 · PMC1361800 · PLoS biology · 2006 · 7 claims · 7 setups

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A comparative genomic screen identified 67 new human-specific nonprocessed pseudogenes, bringing the total (with 13 from prior literature) to 80 human-specific pseudogenes.

pseudogene chimpanzee human-specific population comparative phylogenetic fisher's
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
Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling.

PMID 18157127 · PMC2397541 · Nature genetics · 2008 · 8 claims · 8 setups

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Homozygous truncating mutations in PCNT cause Seckel syndrome

consanguineous genomic lymphoblastoid lcls snp-microarray sanger immunofluorescence
Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

PMID 18036263 · PMC2246181 · Breast cancer research : BCR · 2007 · 8 claims · 8 setups

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Revised multifactorial likelihood analysis incorporating ER, CK5/6, and CK14 tumor immunohistochemistry improves classification of BRCA1 unclassified variants

archival kconfab myriad lymphoblastoid immunohistochemistry multifactorial co-occurrence
Impact of genomics on animal agriculture and opportunities for animal health.

PMID 18022262 · PMC7114270 · Trends in biotechnology · 2008 · 8 claims · 7 setups

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Genomics tools (single-gene tests, SNP chips, genomic selection) will speed genetic improvement of livestock production traits

cattle chicken pig snp whole-genome transgenic
Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.

PMID 17912347 · PMC1989137 · PloS one · 2007 · 8 claims · 8 setups

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MIP is the evolutionary predecessor/ancestor of the pathogenic Mycobacterium avium intracellulare complex (MAIC), having retained a free-living lifestyle rather than undergoing parasitic reductive genome evolution

mip diagnostic is900-specific pgg
Paired-end mapping reveals extensive structural variation in the human genome.

PMID 17901297 · PMC2674581 · Science (New York, N.Y.) · 2007 · 8 claims · 8 setups

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Paired-end mapping (PEM) combining 3-kb fragment paired-end capture, massive 454 sequencing, and computational mapping detects SVs ~3 kb or larger with an average breakpoint resolution of 644 bp

genomic na15510 stretched reference paired-end pcr array
Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

PMID 17713557 · PMC2435172 · Genes and immunity · 2007 · 7 claims · 8 setups

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SNPs in LECT2 and TGFBI show independent associations with the DTH+ phenotype, indicating two separate genes in this region control DTH+

blood family unrelated subjects snp family-based linkage
Sequence polymorphisms cause many false cis eQTLs.

PMID 17637838 · PMC1906859 · PloS one · 2007 · 8 claims · 7 setups

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Many reported local/cis eQTLs are false positives caused by probe-region sequence polymorphisms affecting hybridization rather than true cis-regulatory expression differences.

lymphoblastoid hematopoietic caenorhabditis genome anova-based sanger eqtl
Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

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Current syndromic disease classification lacks specificity despite historically serving clinicians well

prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene
A newly identified insertion mutation in the thyroid hormone receptor-beta gene in a Korean family with generalized thyroid hormone resistance.

PMID 17596672 · PMC2693656 · Journal of Korean medical science · 2007 · 7 claims · 8 setups

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Two members of a Korean family (mother and son) with generalized RTH harbor a novel insertion mutation, 1358_1359insC, in exon 10 of the THRB gene, causing a frameshift (Leu454PhefsX11)

peripheral serum thyroid pcr radioimmunoassay thyroid
A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

PMID 17571925 · PMC1904362 · PLoS genetics · 2007 · 8 claims · 5 setups

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A genomic pathway approach using axon-guidance pathway SNPs strongly predicts PD susceptibility, survival free of PD, and age at onset of PD

cases patients postmortem whole-genome cox linear
A novel variable number of tandem repeat of the natriuretic peptide precursor B gene's 5'-flanking region is associated with essential hypertension among Japanese females.

PMID 17554401 · PMC1885554 · International journal of medical sciences · 2007 · 8 claims · 6 setups

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A novel VNTR polymorphism (TTTC repeat) was discovered at -1241 nucleotides in the 5'-flanking region of NPPB, with 8 alleles ranging from 9 to 19 repeats.

genomic plasma serum n=317 pcr-sscp nucleotide genotyping

Experiments

Computation of haplotypes on SNPs subsets: advantage of the "global method".

Double-strand breaks in the myotonic dystrophy type 1 and the fragile X syndrome triplet repeat sequences induce different types of mutations in DNA flanking sequences in Escherichia coli.

GAA repeat expansion mutation mouse models of Friedreich ataxia exhibit oxidative stress leading to progressive neuronal and cardiac pathology.

Novel integrative genomics strategies to identify genes for complex traits.

Modeling chromosomes in mouse to explore the function of genes, genomic disorders, and chromosomal organization.

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

Reduced secretion of fibulin 5 in age-related macular degeneration and cutis laxa.

Gene losses during human origins.

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

Mutations in pericentrin cause Seckel syndrome with defective ATR-dependent DNA damage signaling.

Identification of BRCA1 missense substitutions that confer partial functional activity: potential moderate risk variants?

Impact of genomics on animal agriculture and opportunities for animal health.

Molecular analysis of a leprosy immunotherapeutic bacillus provides insights into Mycobacterium evolution.

Paired-end mapping reveals extensive structural variation in the human genome.

Genes at human chromosome 5q31.1 regulate delayed-type hypersensitivity responses associated with Leishmania chagasi infection.

Sequence polymorphisms cause many false cis eQTLs.

Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

A newly identified insertion mutation in the thyroid hormone receptor-beta gene in a Korean family with generalized thyroid hormone resistance.

A genomic pathway approach to a complex disease: axon guidance and Parkinson disease.

A novel variable number of tandem repeat of the natriuretic peptide precursor B gene's 5'-flanking region is associated with essential hypertension among Japanese females.