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 22

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

Sequence determinants of human microsatellite variability.

PMID 20015383 · PMC2806349 · BMC genomics · 2009 · 6 claims · 4 setups

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Mean and maximum number of repeats across individuals are positively correlated with heterozygosity

hgdp-ceph genome calibrated microsatellite blastn sequence
Allelotyping of pooled DNA with 250 K SNP microarrays.

PMID 17367522 · PMC1839100 · BMC genomics · 2007 · 8 claims · 5 setups

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The polynomial based probe specific correction (PPC) algorithm is the most accurate method for estimating allele frequency from pooled DNA.

pool nspi individual snp individual call
The genetics of regulatory variation in the human genome.

PMID 16004727 · PMC3525257 · Human genomics · 2005 · 8 claims · 7 setups

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Naturally-occurring gene expression variation among individuals is common across species (yeast, Drosophila, mouse, fish, maize, primates, humans) and has a significant genetic component.

ceph immortalised lymphoblastoid individuals reporter allelic microarray
CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

PMID 16504045 · PMC1402331 · BMC bioinformatics · 2006 · 8 claims · 5 setups

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CARAT is a novel algorithm that uses SNP probe intensity and genotype-based allelic dosage response in a regression framework to estimate allele-specific copy number genome-wide.

normal genomic sk-br-3 cancer snp quantitative allele-specific
Identification of common genetic variation that modulates alternative splicing.

PMID 17571926 · PMC1904363 · PLoS genetics · 2007 · 7 claims · 8 setups

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Common SNPs located close to intron-exon boundaries are associated with and causally modulate alternative splicing patterns in human genes

ceph lcls skipped additional rt-pcr snp resequencing
Deletion of dinucleotide repeat (Delta 14 allele) in the methylthioadenosine phosphorylase (MTAP) promoter and the allelotype of MTAP promoter in the Japanese population.

PMID 11985785 · PMC5927014 · Japanese journal of cancer research : Gann · 2002 · 8 claims · 4 setups

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DHL-9 lymphoma cells lack detectable MTAP enzyme activity despite possessing an intact (non-deleted) MTAP gene

dhl-9 genomic lymphoblastoid hela pcr allele-specific luciferase
Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

PMID 20037582 · PMC2951730 · Nature biotechnology · 2010 · 8 claims · 7 setups

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A standardized, non-redundant library of 1,889 breakpoint-resolved SVs was assembled from eight published surveys

personal genomic pcr-validated unrelated short-read pcr sanger
Constitutional genetic variation at the human aromatase gene (Cyp19) and breast cancer risk.

PMID 10027313 · PMC2362434 · British journal of cancer · 1999 · 7 claims · 5 setups

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Allelic distribution of the Cyp19 intron 4 STRP differs significantly between breast cancer cases and controls

peripheral ceph individuals cases strp genotyping fluorescent
Analysis of sequence conservation at nucleotide resolution.

PMID 18166073 · PMC2230682 · PLoS computational biology · 2007 · 8 claims · 4 setups

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SCONE (Sequence CONservation Evaluation) is a novel method that estimates evolutionary rate and a neutrality p-value for individual nucleotide positions in a multiple sequence alignment.

encode population comparative snp functional
SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

PMID 18847484 · PMC2576268 · BMC bioinformatics · 2008 · 7 claims · 8 setups

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SPSmart is a novel tool for accessing and combining large-scale SNP genotype databases with population information

hapmap perlegen stanford michigan snp cross-database chromosome
Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.

PMID 16254605 · PMC1270012 · PLoS genetics · 2005 · 8 claims · 6 setups

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Comparative net alignment of human and chimpanzee genome assemblies identifies 1,576 putative inverted regions covering more than 154 Mb of DNA

build chimpanzee unrelated ceph comparative three-color pcr
Human SNPs resulting in premature stop codons and protein truncation.

PMID 16595072 · PMC3500177 · Human genomics · 2006 · 8 claims · 6 setups

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Genome-wide screening of dbSNP identified 28 validated X-SNPs from 28 genes with known minor allele frequencies.

genome transcripts validated x-snp-encoded database blast exon-intron
Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

PMID 17610740 · PMC1925094 · BMC genomics · 2007 · 8 claims · 5 setups

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SNP-MaP can be effectively applied to the Affymetrix 500K GeneChip, providing a cost-effective, reliable and valid initial genomewide screen

independent ceph same unrelated snp individual simulated
GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline.

PMID 33193602 · PMC7541957 · Frontiers in genetics · 2020 · 8 claims · 5 setups

Has reproduction · 80

GenomeChronicler is, to the authors' knowledge, the first pipeline that can be run offline or in the cloud to generate non-disease-limited personal genomics reports from whole genome or whole exome sequencing data.

individuals genotypes personal genomes genome ancestry variant
The homeobox gene CDX2 in colorectal carcinoma: a genetic analysis.

PMID 11161380 · PMC2363702 · British journal of cancer · 2001 · 7 claims · 7 setups

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No CDX2 mutations predisposing to sporadic colorectal cancer were identified

genomic pcr cdna informative sscp pcr automated
Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

PMID 16684361 · PMC1488846 · BMC genomics · 2006 · 8 claims · 5 setups

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The coding region of MRP1 shows evidence of negative selection or recent population expansion based on nucleotide diversity statistics

healthy mrp1 population novo population functional
PRKCA and multiple sclerosis: association in two independent populations.

PMID 16596167 · PMC1420678 · PLoS genetics · 2006 · 8 claims · 8 setups

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PRKCA (protein kinase C alpha) on 17q24 is associated with MS in Finnish families

finnish canadian unrelated blood snp dense multipoint
Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation.

PMID 17562002 · PMC1914356 · BMC genomics · 2007 · 8 claims · 5 setups

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Commercial SNP panels provide levels of coverage in a non-reference Caucasian (Estonian) population similar to those seen in the HapMap CEPH (CEU) population sample

estonian hapmap ceu snp tagsnp marker
Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

PMID 18193213 · PMC2206249 · Immunogenetics · 2008 · 8 claims · 6 setups

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Comparison of eight HLA-homozygous MHC haplotype sequences identified >44,000 variations (substitutions and indels), submitted to dbSNP

hla-homozygous same mhc indel clone-by-clone gene hla
A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.

PMID 20012890 · PMC2797846 · Behavior genetics · 2010 · 6 claims · 4 setups

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SNP Microarrays and Pooling (SNP-MaP) is a valid economical method for genome-wide screening of quantitative trait extremes using pooled DNA on microarrays

teds diagnosed ceph snp individual transmission

Experiments

Sequence determinants of human microsatellite variability.

Allelotyping of pooled DNA with 250 K SNP microarrays.

The genetics of regulatory variation in the human genome.

CARAT: a novel method for allelic detection of DNA copy number changes using high density oligonucleotide arrays.

Identification of common genetic variation that modulates alternative splicing.

Deletion of dinucleotide repeat (Delta 14 allele) in the methylthioadenosine phosphorylase (MTAP) promoter and the allelotype of MTAP promoter in the Japanese population.

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

Constitutional genetic variation at the human aromatase gene (Cyp19) and breast cancer risk.

Analysis of sequence conservation at nucleotide resolution.

SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

Discovery of human inversion polymorphisms by comparative analysis of human and chimpanzee DNA sequence assemblies.

Human SNPs resulting in premature stop codons and protein truncation.

Applicability of DNA pools on 500 K SNP microarrays for cost-effective initial screens in genomewide association studies.

GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline.

The homeobox gene CDX2 in colorectal carcinoma: a genetic analysis.

Nucleotide sequence analyses of the MRP1 gene in four populations suggest negative selection on its coding region.

PRKCA and multiple sclerosis: association in two independent populations.

Evaluating the performance of commercial whole-genome marker sets for capturing common genetic variation.

Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project.

A genome-wide association study of social and non-social autistic-like traits in the general population using pooled DNA, 500 K SNP microarrays and both community and diagnosed autism replication samples.