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 18

System / cell line: allele ✕ Assay: probability ✕ Clear

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
A novel polymorphism in the 1A promoter region of the vitamin D receptor is associated with altered susceptibilty and prognosis in malignant melanoma.

PMID 15238985 · PMC2364794 · British journal of cancer · 2004 · 7 claims · 6 setups

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A novel A-1012G (adenine-guanine) polymorphism exists in the VDR exon 1a promoter region, identified by SSCP screening and sequencing

blood variant patients same sscp sanger pcr-rflp
No evidence of a Neanderthal contribution to modern human diversity.

PMID 18304371 · PMC2374707 · Genome biology · 2008 · 8 claims · 7 setups

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There is no evidence of any Neanderthal contribution to modern human genetic diversity

neanderthal culture modern genomic mitochondrial nuclear gene-specific
Calculating expected DNA remnants from ancient founding events in human population genetics.

PMID 18928554 · PMC2588638 · BMC genetics · 2008 · 8 claims · 3 setups

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Genetic parameters (native/migrant population size, mutation rate, generations since admixture) strongly determine the final frequency of migrant alleles detectable today.

simulated forward-based size
Quantitative analysis of single nucleotide polymorphisms within copy number variation.

PMID 19093001 · PMC2600609 · PloS one · 2008 · 8 claims · 2 setups

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Copy number variation is a major factor in HWE violation for SNPs with small minor allele frequency, large sample size, and 0-1% genotyping error rate

biallelic simulated bayesian chi-square
Widespread ultraconservation divergence in primates.

PMID 18492662 · PMC2464743 · Molecular biology and evolution · 2008 · 8 claims · 4 setups

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The number of UCEs has decreased throughout primate evolution, from ~1,000 in ancestral primates to 635 in modern humans.

hg18 genome genes computed comparative snp gene
Female monozygotic twins discordant for hemophilia A due to nonrandom X-chromosome inactivation.

PMID 18645989 · PMC5715470 · American journal of hematology · 2008 · 7 claims · 8 setups

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Monozygotic twin A (severe hemophilia A, FVIII:C <1%) shows complete nonrandom X-inactivation skewed toward the paternal (normal factor VIII) X-chromosome

peripheral cheek genomic twin factor karyotype microsatellite
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
Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene.

PMID 16429166 · PMC1342637 · PLoS genetics · 2005 · 8 claims · 5 setups

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PANTHER subPSEC scores correctly predicted the functional impact of >94% (16/17) of tested naturally occurring ABCA1 variants

abca1 stably subpsec cholesterol rt-pcr
Shotgun haplotyping: a novel method for surveying allelic sequence variation.

PMID 16221968 · PMC1253838 · Nucleic acids research · 2005 · 8 claims · 7 setups

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A novel shotgun haplotyping method generates haplotypic sequences from long PCR products by shotgun sequencing both alleles concurrently and using read-pair information to separate alleles during assembly

genomic long pcr ampicillin-resistant long cloning short
Modeling genetic inheritance of copy number variations.

PMID 18832372 · PMC2588508 · Nucleic acids research · 2008 · 8 claims · 4 setups

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A joint HMM framework for parents-offspring trios significantly improves CNV call rates and boundary inference accuracy compared to existing methods.

simulated parent-offspring hapmap hmm-based snp genotype
HLA-A gene polymorphism defined by high-resolution sequence-based typing in 161 Northern Chinese Han people.

PMID 15629059 · PMC5172246 · Genomics, proteomics & bioinformatics · 2003 · 7 claims · 5 setups

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HLA-A gene shows high polymorphism in the Northern Chinese Han population, with 74 gene types and 36 alleles detected in 161 individuals

genomic ihwg peripheral allele sequence-based pcr sbt
A missense mutation in LIM2 causes autosomal recessive congenital cataract.

PMID 18596884 · PMC2442473 · Molecular vision · 2008 · 7 claims · 5 setups

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A homozygous missense mutation (Gly154Glu, c.587G>A) in LIM2 causes autosomal recessive congenital cataract in a human family

genomic mp19 patients pcr sscp cosegregation
Prediction and assessment of splicing alterations: implications for clinical testing.

PMID 18951448 · PMC2832470 · Human mutation · 2008 · 8 claims · 5 setups

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Bioinformatic prediction alone is insufficient; in vitro analysis is needed to confirm or establish splicing aberrations for clinical variant classification

brca1 lymphocytes mammalian large bioinformatic cycloheximide mini-gene
Absence of the TAP2 human recombination hotspot in chimpanzees.

PMID 15208713 · PMC423135 · PLoS biology · 2004 · 6 claims · 7 setups

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The human TAP2 recombination hotspot is absent from the homologous region in western chimpanzees.

western haplotype males simulated resequencing ld-based sperm
Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.

PMID 17486137 · PMC2673710 · Molecular systems biology · 2007 · 8 claims · 7 setups

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Global MudPIT-based proteomic profiling across six mouse lung developmental time points (E13.5–P56) identifies thousands of proteins and captures developmental/cell-biological expression patterns.

lung analysis embryonic homologues shotgun microarray k-nearest
Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

PMID 19922672 · PMC2789746 · Malaria journal · 2009 · 8 claims · 8 setups

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Two distinctive COI haplotype groups were consistently detected, corresponding to the Caribbean and Pacific regions.

anopheles mtdna microsatellite population
Ensembl 2013.

PMID 23203987 · PMC3531136 · Nucleic acids research · 2013 · 8 claims · 8 setups

Has reproduction · 85

Ensembl (http://www.ensembl.org) provides genome information for sequenced chordate genomes, currently supporting 70 species with a focus on human, mouse, zebrafish and rat.

genome species supported variants evidence-based rna-seq chip-seq

Experiments

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

A novel polymorphism in the 1A promoter region of the vitamin D receptor is associated with altered susceptibilty and prognosis in malignant melanoma.

No evidence of a Neanderthal contribution to modern human diversity.

Calculating expected DNA remnants from ancient founding events in human population genetics.

Quantitative analysis of single nucleotide polymorphisms within copy number variation.

Widespread ultraconservation divergence in primates.

Female monozygotic twins discordant for hemophilia A due to nonrandom X-chromosome inactivation.

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

Accurate prediction of the functional significance of single nucleotide polymorphisms and mutations in the ABCA1 gene.

Shotgun haplotyping: a novel method for surveying allelic sequence variation.

Modeling genetic inheritance of copy number variations.

HLA-A gene polymorphism defined by high-resolution sequence-based typing in 161 Northern Chinese Han people.

A missense mutation in LIM2 causes autosomal recessive congenital cataract.

Prediction and assessment of splicing alterations: implications for clinical testing.

Absence of the TAP2 human recombination hotspot in chimpanzees.

Integrated proteomic and transcriptomic profiling of mouse lung development and Nmyc target genes.

Population structure analyses and demographic history of the malaria vector Anopheles albimanus from the Caribbean and the Pacific regions of Colombia.

Ensembl 2013.