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 24

System / cell line: genotyping ✕ Assay: free ✕ Clear

KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.

PMID 36195962 · PMC9531401 · Genome biology · 2022 · 7 claims · 7 setups

Has reproduction · 42

KAGE combines population-based kmer count modeling with single-variant prior adjustment into an alignment-free genotyper that matches the accuracy of the best existing alignment-free genotypers while being an order of magnitude faster.

small snps individual hg002 alignment-free kmer-based genotyping
Free energy of DNA duplex formation on short oligonucleotide microarrays.

PMID 17169993 · PMC1807971 · Nucleic acids research · 2007 · 8 claims · 6 setups

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The PDNN model, originally built for DNA/RNA hybridization, can be applied to model DNA/DNA duplex formation on SNP and genome tiling arrays

mapping50k_xba240 dgcr hg-u133a pdnn free correlation
Genome-wide association studies of MRI-defined brain infarcts: meta-analysis from the CHARGE Consortium.

PMID 20044523 · PMC2923092 · Stroke · 2010 · 8 claims · 6 setups

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SNP rs2208454 in intron 3 of MACROD2 (near FLRT3, chr20p12) is associated with lower risk of covert MRI-infarcts (OR=0.76, p=4.64x10-7)

stroke-free elderly african-american cardiovascular genome-wide direct expression
Association of the GSTP1 and NQO1 polymorphisms and head and neck squamous cell carcinoma risk.

PMID 17179690 · PMC2721932 · Journal of Korean medical science · 2006 · 6 claims · 1 setups

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Allele/genotype frequencies of GSTP1 Ile105Val and NQO1 Trp139Arg did not differ significantly between HNSCC cases and controls overall

peripheral pcr-based
Emerging strategies and applications of pharmacogenomics.

PMID 15606999 · PMC3500198 · Human genomics · 2004 · 7 claims · 7 setups

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Effective pharmacogenomics requires infrastructure including informed consent processes, accurate phenotypic data collection, high-throughput genotyping technology, and integrated information technology systems.

subjects ethnically patients genome-wide gene case-control
Joint association of polymorphism of the FGFR4 gene and mutation TP53 gene with bladder cancer prognosis.

PMID 17088904 · PMC2360734 · British journal of cancer · 2006 · 8 claims · 5 setups

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No clear correlation was found between the FGFR4 Gly388Arg genotype and risk of developing bladder cancer.

blood bladder rflp manual genechip
Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

PMID 18778477 · PMC2553089 · BMC medicine · 2008 · 7 claims · 7 setups

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A custom BOAC SNP panel of 3404 SNPs in 983 genes was developed using the Affymetrix GeneChip Targeted Genotyping Platform, focused on non-synonymous coding SNPs and regulatory-region SNPs in candidate genes.

coriell myeloma duplicate snp targeted genotyping machine
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
Identification of novel prognostic markers in cervical intraepithelial neoplasia using LDMAS (LOH Data Management and Analysis Software).

PMID 15673474 · PMC548130 · BMC bioinformatics · 2005 · 8 claims · 3 setups

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LDMAS software integrates LOH molecular data with clinico-pathological data for prognostic marker discovery

archival records combined loh medical statistical
Genomic variability within an organism exposes its cell lineage tree.

PMID 16261192 · PMC1274291 · PLoS computational biology · 2005 · 8 claims · 5 setups

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Somatic mutations accumulated during normal development implicitly encode an organism's entire cell lineage tree with very high precision.

robinia arabidopsis randomly genotyping multiplex computer
A restricted spectrum of NRAS mutations causes Noonan syndrome.

PMID 19966803 · PMC3118669 · Nature genetics · 2010 · 8 claims · 6 setups

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Germline NRAS mutations (T50I, G60E) cause a subset of Noonan syndrome cases via enhanced MAPK activation

cohort cos-7 recombinant nras mutation western ras
Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

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Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

msi-h computational rb1cc1 normal pcr nonlinear real-time
Identification of SLC26A4 gene mutations in Iranian families with hereditary hearing impairment.

PMID 18813951 · PMC4428656 · European journal of pediatrics · 2009 · 7 claims · 6 setups

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SLC26A4 mutations are the most prevalent cause of syndromic hereditary hearing loss (Pendred syndrome) in Iran

affected short pcr perchlorate
An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer.

PMID 18676830 · PMC2680495 · Cancer research · 2008 · 8 claims · 5 setups

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PIK3CA mutations are more common in hormone receptor-positive and HER2-positive tumors than in basal-like breast cancers

breast hormone early-stage mass sanger reverse-phase
Base editing in human cells with monomeric DddA-TALE fusion deaminases.

PMID 35821233 · PMC9276701 · Nature communications · 2022 · 8 claims · 8 setups

Has reproduction · 95

mDdCBEs built from non-toxic full-length DddA_tox variants enable mitochondrial DNA base editing with efficiencies of up to 50% upon transient expression in human cells

hek293t nih3t3 targeted clonal aav2
In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

PMID 17201911 · PMC1774567 · BMC genomics · 2007 · 8 claims · 5 setups

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A computational EST-based pipeline can identify UTR-SNPs that are statistically over-represented in cancerous versus normal tissue libraries

est acute 100-nt whole-genome est-based pcr-based secondary
Mutations of the BRCA1 and BRCA2 genes in patients with bilateral breast cancer.

PMID 11556836 · PMC2375067 · British journal of cancer · 2001 · 7 claims · 3 setups

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BRCA1 and BRCA2 mutations are not significantly more prevalent in patients with bilateral breast cancer than in matched unilateral controls

genomic clinical pcr-sscp restriction kaplan-meier
Mutation analysis of the ATR gene in breast and ovarian cancer families.

PMID 15987455 · PMC1175065 · Breast cancer research : BCR · 2005 · 8 claims · 5 setups

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ATR mediates the DNA damage response by phosphorylating tumor suppressors such as p53, BRCA1 and CHK1, making it a plausible candidate breast/ovarian cancer susceptibility gene

index atr variant mutation direct variant
Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

PMID 15640441 · PMC546178 · Nucleic acids research · 2005 · 8 claims · 7 setups

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NCL aggregation of DNA-modified gold nanoparticles shows extraordinary selectivity against terminal mismatches at the free ends of surface-bound duplexes

probe-modified probe-gnp synthetic four uv-vis ssdna pcr
Nonclassic congenital lipoid adrenal hyperplasia: a new disorder of the steroidogenic acute regulatory protein with very late presentation and normal male genitalia.

PMID 16968793 · PMC1865081 · The Journal of clinical endocrinology and metabolism · 2006 · 8 claims · 7 setups

Full-text index only

Homozygous StAR missense mutations Val187Met and Arg188Cys cause a novel, milder form of lipoid CAH ('non-classic lipoid CAH') presenting at 2-4 years of age rather than in infancy

blood cos-1 bacteria mitochondria sequencing cell-based recombinant

Experiments

KAGE: fast alignment-free graph-based genotyping of SNPs and short indels.

Free energy of DNA duplex formation on short oligonucleotide microarrays.

Genome-wide association studies of MRI-defined brain infarcts: meta-analysis from the CHARGE Consortium.

Association of the GSTP1 and NQO1 polymorphisms and head and neck squamous cell carcinoma risk.

Emerging strategies and applications of pharmacogenomics.

Joint association of polymorphism of the FGFR4 gene and mutation TP53 gene with bladder cancer prognosis.

Genomic variation in myeloma: design, content, and initial application of the Bank On A Cure SNP Panel to detect associations with progression-free survival.

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.

Identification of novel prognostic markers in cervical intraepithelial neoplasia using LDMAS (LOH Data Management and Analysis Software).

Genomic variability within an organism exposes its cell lineage tree.

A restricted spectrum of NRAS mutations causes Noonan syndrome.

Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

Identification of SLC26A4 gene mutations in Iranian families with hereditary hearing impairment.

An integrative genomic and proteomic analysis of PIK3CA, PTEN, and AKT mutations in breast cancer.

Base editing in human cells with monomeric DddA-TALE fusion deaminases.

In silico whole-genome screening for cancer-related single-nucleotide polymorphisms located in human mRNA untranslated regions.

Mutations of the BRCA1 and BRCA2 genes in patients with bilateral breast cancer.

Mutation analysis of the ATR gene in breast and ovarian cancer families.

Non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.

Nonclassic congenital lipoid adrenal hyperplasia: a new disorder of the steroidogenic acute regulatory protein with very late presentation and normal male genitalia.