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 182

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

Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

PMID 18654622 · PMC2447880 · PLoS computational biology · 2008 · 8 claims · 5 setups

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Bongo identifies mutations causing local and global structural effects with a remarkably low false positive rate

p53 1bpi mutations disease-associated graph correlation structural
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
Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE).

PMID 17697348 · PMC2042502 · BMC genetics · 2007 · 8 claims · 5 setups

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CTCE eliminates the need for laboratory optimization of separation conditions for each exonic target sequence.

pcr-amplified target exonic cycling ctce
Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

PMID 19826477 · PMC2757721 · PloS one · 2009 · 8 claims · 8 setups

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Homozygous mutations of oncogenes are frequent (20%) across 833 cancer cell lines of 12 tumor types in the Sanger database

tumors cancer tumor lung direct database quantitative
Lack of mutation at codon 531 of SRC in advanced colorectal cancers from Italian patients.

PMID 11161376 · PMC2363715 · British journal of cancer · 2001 · 6 claims · 4 setups

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No SRC codon 531 mutation was detected in any of 155 Italian colorectal cancer cases (171 tissue specimens, primary tumours and liver metastases)

colorectal liver scalar subset pcr-rflp direct
Rapid detection of SMARCB1 sequence variation using high resolution melting.

PMID 20003390 · PMC2801682 · BMC cancer · 2009 · 8 claims · 6 setups

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HRM screening of SMARCB1 amplicons has a zero false negative rate compared to direct sequencing

genomic same tumor rhabdoid high direct hrm
Genetic requirement for pneumococcal ear infection.

PMID 18670623 · PMC2593789 · PloS one · 2007 · 7 claims · 8 setups

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STM screening of 5,280 S. pneumoniae ST556 mutants in a chinchilla middle ear infection model identified 169 genes required for ear infection

pneumoniae bioluminescent balb signature-tagged bioluminescent transmission
Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

PMID 19874620 · PMC2774872 · BMC genomics · 2009 · 8 claims · 8 setups

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Phylogenetic profiling of protein clusters across pathogen and non-pathogen genomes can identify candidate generic virulence factors

proteins cdc candidate yersinia all-against-all computational cross-species
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
Molecular genetic analysis of an endotoxin nonresponder mutant cell line: a point mutation in a conserved region of MD-2 abolishes endotoxin-induced signaling.

PMID 11435474 · PMC2193443 · The Journal of experimental medicine · 2001 · 8 claims · 7 setups

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MD-2 is a required component of the LPS signaling complex; a point mutation in MD-2 abolishes LPS-induced signaling

cho hek western nf-kb il-6
Somatic VHL gene alterations in MEN2-associated medullary thyroid carcinoma.

PMID 16707008 · PMC1483898 · BMC cancer · 2006 · 6 claims · 4 setups

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Somatic VHL gene alterations (LOH and mutation) may contribute to pathogenesis of MEN2A-associated MTC, similar to their role in MEN2 pheochromocytoma

microdissected same genomic frozen microsatellite loss vhl
Mosaicism in von Hippel-Lindau disease: an event important to recognize.

PMID 18205710 · PMC4401302 · Journal of cellular and molecular medicine · 2007 · 7 claims · 5 setups

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The proband's father is a somatic mosaic for a VHL missense mutation (R161Q), explaining his mild, late-onset phenotype compared to his daughter's severe early-onset disease.

peripheral father's pcr proband dhplc sanger semiquantitative
Band 3 Courcouronnes (Ser667Phe): a trafficking mutant differentially rescued by wild-type band 3 and glycophorin A.

PMID 18174378 · PMC2605348 · Blood · 2008 · 7 claims · 8 setups

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Homozygous SLC4A1 Ser667Phe mutation causes both hereditary spherocytosis and incomplete distal renal tubular acidosis in the proband

erythrocyte genomic erythrocytes xenopus sds-page sscp dids
The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).

PMID 24598808 · PMC3944810 · PloS one · 2014 · 8 claims · 7 setups

Has reproduction · 58

The Li2 mutation significantly reduces subgenome (homeolog) expression bias in the elongating fiber transcriptome.

developing rna-seq expressed subgenome-biased paired-end rna-seq rt-qpcr
High resolution melting for mutation scanning of TP53 exons 5-8.

PMID 17764544 · PMC2025602 · BMC cancer · 2007 · 7 claims · 5 setups

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HRM is an effective technique for rapid scanning of TP53 mutations that can markedly reduce required sequencing

tp53-mutant ovarian breast high hrm dideoxy
Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

PMID 24885615 · PMC4070566 · BMC genomics · 2014 · 8 claims · 8 setups

Has reproduction · 50

A total of 40 candidate Hfq-dependent sRNAs were identified genome-wide in E. amylovora by combining RNA-seq with a Rho-independent terminator search.

erwinia intergenic candidate wounded small northern race
High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies.

PMID 18495026 · PMC2408599 · BMC cancer · 2008 · 8 claims · 4 setups

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HRM correctly identified all 73 EGFR-mutation-positive FFPE samples previously found by sequencing, giving 100% sensitivity and 90% specificity

ffpe single high direct hrm
Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations.

PMID 17130153 · PMC1702505 · Nucleic acids research · 2007 · 8 claims · 4 setups

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A single Y80A alanine substitution switches Tma endo V from purine-preferring to essentially C-specific mismatch cleavage, including the previously refractory C/C mismatch.

synthetic k-ras endo pcr restriction
Identification of five novel mutations in the long isoform of the USH2A gene in Chinese families with Usher syndrome type II.

PMID 19023448 · PMC2584772 · Molecular vision · 2008 · 8 claims · 7 setups

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Mutations in USH2A are responsible for most cases of USH2

genomic family probands ush2a direct restriction single
Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.

PMID 10449521 · PMC2195597 · The Journal of experimental medicine · 1999 · 7 claims · 8 setups

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A novel C→A point mutation at nucleotide 850 of GCSFR cDNA causes a Pro→His substitution at position 206 (P206H) in the proline-rich hinge of the CRH domain of the G-CSF receptor extracellular domain in an SCN patient hyporesponsive to G-CSF.

bone fibroblast 32d.cl8.6 32d rt-pcr genomic flow

Experiments

Prediction by graph theoretic measures of structural effects in proteins arising from non-synonymous single nucleotide polymorphisms.

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

Technology to accelerate pangenomic scanning for unknown point mutations in exonic sequences: cycling temperature capillary electrophoresis (CTCE).

Oncogene mutations, copy number gains and mutant allele specific imbalance (MASI) frequently occur together in tumor cells.

Lack of mutation at codon 531 of SRC in advanced colorectal cancers from Italian patients.

Rapid detection of SMARCB1 sequence variation using high resolution melting.

Genetic requirement for pneumococcal ear infection.

Steps toward broad-spectrum therapeutics: discovering virulence-associated genes present in diverse human pathogens.

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

Molecular genetic analysis of an endotoxin nonresponder mutant cell line: a point mutation in a conserved region of MD-2 abolishes endotoxin-induced signaling.

Somatic VHL gene alterations in MEN2-associated medullary thyroid carcinoma.

Mosaicism in von Hippel-Lindau disease: an event important to recognize.

Band 3 Courcouronnes (Ser667Phe): a trafficking mutant differentially rescued by wild-type band 3 and glycophorin A.

The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.).

High resolution melting for mutation scanning of TP53 exons 5-8.

Genome-wide identification of Hfq-regulated small RNAs in the fire blight pathogen Erwinia amylovora discovered small RNAs with virulence regulatory function.

High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies.

Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations.

Identification of five novel mutations in the long isoform of the USH2A gene in Chinese families with Usher syndrome type II.

Novel point mutation in the extracellular domain of the granulocyte colony-stimulating factor (G-CSF) receptor in a case of severe congenital neutropenia hyporesponsive to G-CSF treatment.