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 32

System / cell line: probe ✕ Assay: type ✕ Clear

PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

PMID 17105657 · PMC1657037 · BMC bioinformatics · 2006 · 6 claims · 5 setups

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PathogenMIPer designs unique, target-specific MIP probes, assembling all probe components (target-specific sequences, barcodes, universal primers, restriction sites) into ready-to-order probes for any genome.

hpv clinical biotinylated pcr mip molecular microarray
Detection of rare mutant K-ras DNA in a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe.

PMID 16432256 · PMC1345699 · Nucleic acids research · 2006 · 8 claims · 5 setups

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A 17mer PNA spanning K-ras codons 12/13 can serve as both PCR clamp and sensor probe in a single-tube reaction, differentiating all 12 possible point mutations from wild-type by melting temperature shift

wild-type mixture mutant serial melting real-time limit-of-detection
Detecting aberrant DNA methylation in Illumina DNA methylation arrays: a toolbox and recommendations for its use.

PMID 37218167 · PMC10208159 · Epigenetics · 2023 · 8 claims · 7 setups

Has reproduction · 73

Probe-specific upper and lower thresholds for flagging aberrant DNA methylation can be derived from a reference database of >2,000 normal and tumour-adjacent normal samples spanning 25 tissue types.

blood tcga gse40279 most illumina supervised unsupervised
Functional analysis of human mutations in homeodomain transcription factor PITX3.

PMID 17888164 · PMC2093940 · BMC molecular biology · 2007 · 7 claims · 5 setups

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Both S13N and G219fs mutants show partial loss-of-function in DNA-binding and/or transactivation activity, with G219fs more severely affected than S13N

lens western immunocytochemistry electrophoretic
A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

PMID 19911041 · PMC2766639 · PLoS genetics · 2009 · 8 claims · 7 setups

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Padlock probes combined with high-throughput sequencing enable accurate, quantitative, low-bias digital RNA allelotyping of allele-specific expression

genomic pgp1 skin fibroblasts padlock quantitative gene
A colorimetric method for point mutation detection using high-fidelity DNA ligase.

PMID 16257979 · PMC1275593 · Nucleic acids research · 2005 · 8 claims · 8 setups

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High-fidelity Tth DNA ligase combined with allele-specific ligation-based gold nanoparticle assembly enables colorimetric single-base discrimination without precise temperature control

p3-modified nanoparticle synthetic ligated uv-vis colorimetric melting
X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

PMID 17932061 · PMC2238884 · Nucleic acids research · 2008 · 7 claims · 4 setups

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X:Map is a genome annotation database that maps every Affymetrix exon array probeset to Ensembl genome features (genes, ESTs, GenScan predictions) and supports both high-throughput and gene-centric analysis.

ensembl breast mcf7 25-mer probe-to-transcript microarray
Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing.

PMID 19682357 · PMC2782262 · BMC microbiology · 2009 · 8 claims · 5 setups

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The RCA assay correctly identified all ERG11 mutations in eight 'reference' azole-resistant C. albicans isolates with known mutations.

clinical pcr template padlock sequencing antifungal
Multiple K-ras mutations in hyperplasia and carcinoma in cases of human pancreatic carcinoma.

PMID 10543256 · PMC5926143 · Japanese journal of cancer research : Gann · 1999 · 7 claims · 6 setups

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K-ras codon 12 mutations are present in the majority of solid-type (85%) and ductectatic-type (73%) pancreatic carcinomas.

pancreatic mucous microdissected extracted k-ras histopathological microdissection
SNP identification in unamplified human genomic DNA with gold nanoparticle probes.

PMID 15659576 · PMC548375 · Nucleic acids research · 2005 · 8 claims · 5 setups

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A microarray-based method allows multiplex SNP genotyping in total human genomic DNA without target amplification or complexity reduction

unamplified genomic fragmented factor multiplex sequencing poly
A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

PMID 19923232 · PMC2817484 · Nucleic acids research · 2010 · 8 claims · 7 setups

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A Perl-based pipeline that BLASTs/BLATs Illumina probe sequences against genomes and transcript databases (RefSeq, UCSC Known Genes, UniGene/GenBank, Ensembl) can classify probes by quality grade (Perfect/Good/Bad/No match) and is applicable across 8 BeadArray platforms and other array types

maqc hepatocytes japanese illeum microarray dasl sequence
Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

PMID 7606775 · PMC3730239 · Cell · 1995 · 6 claims · 8 setups

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Expression of a specific var gene (A4var) correlates with A4 antigenic type and with binding to ICAM-1

falciparum cdna c18 genomic rt-pcr southern genomic
Detection of YMDD motif mutants by oligonucleotide chips in lamivudine-untreated patients with chronic hepatitis B virus infection.

PMID 15308845 · PMC2816888 · Journal of Korean medical science · 2004 · 6 claims · 5 setups

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An oligonucleotide chip was developed using probes for wild-type YMDD, M552V, and three M552I probe variants to detect HBV polymerase YMDD motif mutations

serum hbv nested pcr oligonucleotide pcr restriction
A novel approach for determining cancer genomic breakpoints in the presence of normal DNA.

PMID 17440616 · PMC1847701 · PloS one · 2007 · 8 claims · 6 setups

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PAMP enriches deletion-breakpoint-spanning DNA because shorter mutant amplicons are preferentially amplified over much longer wild-type sequences when using approximated flanking primer pairs.

detroit serial hs578t pamp individual nested
Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

PMID 19861964 · PMC2778539 · British journal of cancer · 2009 · 7 claims · 8 setups

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BRAF mutations can be detected in serum cfDNA of advanced melanoma patients using an ARMS allele-specific PCR assay

serum-derived tumour serum ht29 arms sanger topo
SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

PMID 17338820 · PMC1839109 · BMC bioinformatics · 2007 · 6 claims · 4 setups

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EVDB is a comprehensive, non-redundant relational database of known human splice variants built from NCBI Entrez Gene and Evidence Viewer data

genome affymetrix probe database microarray interactive
Additional EFNB1 mutations in craniofrontonasal syndrome.

PMID 18627045 · PMC2774847 · American journal of medical genetics. Part A · 2008 · 8 claims · 4 setups

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Loss-of-function mutations in EFNB1 (Xq13.1) are the cause of CFNS in the majority of patients

lymphoblastoid cfns patients additional pcr multiplex molecular
Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.

PMID 33937763 · PMC8061458 · NAR genomics and bioinformatics · 2021 · 8 claims · 6 setups

Has reproduction · 88

Approximately two-thirds of compiled HM450K samples are from blood, one-quarter from brain, and roughly one-third from cancer patients.

hm450k seven annotated illumina beadarray model-based
L2L: a simple tool for discovering the hidden significance in microarray expression data.

PMID 16168088 · PMC1242216 · Genome biology · 2005 · 8 claims · 4 setups

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L2L systematically compares a user's differentially expressed gene list against a database of published differentially expressed gene lists to find statistically significant overlaps and generate hypotheses about shared mechanisms

mammalian user-supplied diabetic uniprot compiled l2l re-analysis
Phenotypic features and genetic characterization of male breast cancer families: identification of two recurrent BRCA2 mutations in north-east of Italy.

PMID 16764716 · PMC1586026 · BMC cancer · 2006 · 8 claims · 6 setups

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The 9106C>T (Q2960X) and IVS16-2A>G BRCA2 mutations are recurrent in MBC families from North-East Italy and may reflect a founder effect.

blood germline tumor family mutation mlpa microsatellite

Experiments

PathogenMIPer: a tool for the design of molecular inversion probes to detect multiple pathogens.

Detection of rare mutant K-ras DNA in a single-tube reaction using peptide nucleic acid as both PCR clamp and sensor probe.

Detecting aberrant DNA methylation in Illumina DNA methylation arrays: a toolbox and recommendations for its use.

Functional analysis of human mutations in homeodomain transcription factor PITX3.

A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells.

A colorimetric method for point mutation detection using high-fidelity DNA ligase.

X:Map: annotation and visualization of genome structure for Affymetrix exon array analysis.

Rapid detection of ERG11 gene mutations in clinical Candida albicans isolates with reduced susceptibility to fluconazole by rolling circle amplification and DNA sequencing.

Multiple K-ras mutations in hyperplasia and carcinoma in cases of human pancreatic carcinoma.

SNP identification in unamplified human genomic DNA with gold nanoparticle probes.

A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data.

Switches in expression of Plasmodium falciparum var genes correlate with changes in antigenic and cytoadherent phenotypes of infected erythrocytes.

Detection of YMDD motif mutants by oligonucleotide chips in lamivudine-untreated patients with chronic hepatitis B virus infection.

A novel approach for determining cancer genomic breakpoints in the presence of normal DNA.

Detection of BRAF mutations in the tumour and serum of patients enrolled in the AZD6244 (ARRY-142886) advanced melanoma phase II study.

SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant analysis.

Additional EFNB1 mutations in craniofrontonasal syndrome.

Human methylome variation across Infinium 450K data on the Gene Expression Omnibus.

L2L: a simple tool for discovering the hidden significance in microarray expression data.

Phenotypic features and genetic characterization of male breast cancer families: identification of two recurrent BRCA2 mutations in north-east of Italy.