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 61

System / cell line: drug ✕ Assay: mutation ✕ Clear

The HIV positive selection mutation database.

PMID 17108357 · PMC1669717 · Nucleic acids research · 2007 · 8 claims · 5 setups

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The database provides codon-level Ka/Ks selection pressure maps for HIV protease and the first 381 codons of RT, built from a novel ~50,000-sample clinical dataset.

hiv-1 stanford codon-specific selection conditional
Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report.

PMID 18513421 · PMC2426714 · Retrovirology · 2008 · 7 claims · 6 setups

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HIV-1 quasispecies in PBMCs are more genetically heterogeneous than in plasma

plasma proviral cloned pbmc hiv-1 nested clonal
Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

PMID 17967058 · PMC2042017 · PLoS pathogens · 2007 · 8 claims · 8 setups

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APOBEC3C is necessary and sufficient to induce G-to-A mutation in some HIV-1 strains despite Vif expression

magi pbmc 293t supt1 sensitive rt-pcr western
QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

PMID 36699347 · PMC9722223 · Bioinformatics advances · 2022 · 6 claims · 8 setups

Has reproduction · 78

QuasiFlow is a Nextflow pipeline that runs entirely locally via command-line tools and a local HIVdb database copy to analyze NGS-based HIV-1 drug resistance testing data.

hiv-1 same paired-end reads ngs-based concordance read
Massively parallel pyrosequencing in HIV research.

PMID 18614863 · PMC4221253 · AIDS (London, England) · 2008 · 8 claims · 8 setups

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Massively parallel pyrosequencing platforms (454/Roche, Solexa/Illumina) enable very high-throughput DNA sequencing, up to ~1 billion bases per run

mammoth hiv hiv-infected honey pyrosequencing pcr 16s
Incidence of mutation and deletion in topoisomerase II alpha mRNA of etoposide and mAMSA-resistant cell lines.

PMID 11676865 · PMC5926608 · Japanese journal of cancer research : Gann · 2001 · 7 claims · 6 setups

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Acquired mutations of the topoisomerase IIα gene are an important and frequent mechanism of resistance to topoisomerase II inhibitors, independent of the degree of resistance.

parental lines t47d-vp1 mcf7-vp8 rnase cdna cytotoxicity
SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

PMID 19934256 · PMC2808967 · Nucleic acids research · 2010 · 8 claims · 6 setups

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SuperCYP is a comprehensive relational database aggregating CYP enzyme, drug metabolism, SNP/mutation, and structural information from literature and web resources.

scientific pubmed cyp-drug cyp text mutation manual
Clinical and genotypic findings in HIV-infected patients with the K65R mutation failing first-line antiretroviral therapy in Nigeria.

PMID 19644383 · PMC2815152 · Journal of acquired immune deficiency syndromes (1999) · 2009 · 8 claims · 3 setups

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K65R mutation is present in a substantial proportion (10.9%) of Nigerian patients failing first-line ART, including many with no prior tenofovir exposure

plasma k65r-positive hiv-1 comparative clinical
Detection of mutations in EGFR in circulating lung-cancer cells.

PMID 18596266 · PMC3551471 · The New England journal of medicine · 2008 · 8 claims · 7 setups

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The CTC-chip microfluidic device isolates CTCs from NSCLC patients in sufficient quantity and purity to permit EGFR mutational analysis

blood archived nsclc plasma microfluidic allele-specific standard
Clinico-pathogenetic findings and management of chondrodystrophic myotonia (Schwartz-Jampel syndrome): a case report.

PMID 12839625 · PMC166146 · BMC neurology · 2003 · 8 claims · 7 setups

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The patient is a compound heterozygote with a different splicing mutation in each Perlecan allele, causing a significant reduction in production of the normal (wild-type) protein.

8-year-old muscle lower skeletal molecular immunostaining electromyogram
EGFR mutation status in tumour-derived DNA from pleural effusion fluid is a practical basis for predicting the response to gefitinib.

PMID 17060940 · PMC2360588 · British journal of cancer · 2006 · 7 claims · 4 setups

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EGFR mutations can be detected by direct sequencing of DNA extracted from cell-free pleural effusion fluid supernatant in NSCLC patients

cell-free pleural nsclc direct extraction clinical
Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma.

PMID 18632602 · PMC2586155 · Cancer research · 2008 · 8 claims · 7 setups

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A novel somatic MEK1 K57N mutation was identified in 2 of 207 primary lung adenocarcinomas

nsclc 293t il-3-independent mutational site-directed cytokine-independence
Novel heteroduplex method using small cytology specimens with a remarkably high success rate for analysing EGFR gene mutations with a significant correlation to gefitinib efficacy in non-small-cell lung cancer.

PMID 17047654 · PMC2360725 · British journal of cancer · 2006 · 7 claims · 5 setups

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LH-MSA enables EGFR mutation analysis using small numbers of cancer cells from cytology specimens with a remarkably high success rate

cytology excised nsclc gefitinib-treated lh-mobility pcr clinical
Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.

PMID 17318599 · PMC1915625 · Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2007 · 7 claims · 7 setups

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The T309V mutation shifts the CYP2D6 heme spin equilibrium toward the six-coordinate low-spin (6cLS) state, decreasing the five-coordinate high-spin (5cHS) fraction relative to wild type.

recombinant cyp2d6 computational resonance uv-vis sds-page
Genomics: applications in mechanism elucidation.

PMID 19166886 · PMC2698023 · Advanced drug delivery reviews · 2009 · 8 claims · 8 setups

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Genomic tools require no a priori knowledge of a compound's mode of action and can reveal biological pathways (metabolism, distribution, off-target effects) in addition to the precise mechanism of action.

extract panel saccharomyces inbred affinity cytotoxicity genome-wide
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
Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

PMID 18507500 · PMC2429944 · PLoS medicine · 2008 · 7 claims · 7 setups

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At least 36 of the 189 newly mutated CAN genes are targets of promoter CpG island hypermethylation, often in both colon and breast cancer cell lines

breast same selected hct116 expression methylation-specific rt-pcr
Utilization of genomic signatures to identify phenotype-specific drugs.

PMID 19714244 · PMC2729377 · PloS one · 2009 · 8 claims · 8 setups

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A RAS pathway gene expression signature applied to NCI-60 cells identifies compounds selectively active against RAS-activated cells, including the MEK inhibitor Hypothemycin

nci-60 breast mda-mb-231 signature-drug gene signature
Personalized medicine: the future is not what it used to be.

PMID 19958922 · PMC2844719 · Surgery · 2009 · 8 claims · 8 setups

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Many rare tumors harbor a genomic Achilles heel that can be exploited for targeted therapy

sw13 h295r drosophila acc drug synthetic gene
Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.

PMID 38529307 · PMC10962337 · PeerJ · 2024 · 8 claims · 8 setups

Has reproduction · 58

PPARA, PPARD and PPARG are more abnormally expressed in STAD samples and cell lines compared to most of 32 cancer types in TCGA

cancer tcga-stad stomach ges1 rna-seq pearson gsva

Experiments

The HIV positive selection mutation database.

Highly diversified multiply drug-resistant HIV-1 quasispecies in PBMCs: a case report.

Target cell APOBEC3C can induce limited G-to-A mutation in HIV-1.

QuasiFlow: a Nextflow pipeline for analysis of NGS-based HIV-1 drug resistance data.

Massively parallel pyrosequencing in HIV research.

Incidence of mutation and deletion in topoisomerase II alpha mRNA of etoposide and mAMSA-resistant cell lines.

SuperCYP: a comprehensive database on Cytochrome P450 enzymes including a tool for analysis of CYP-drug interactions.

Clinical and genotypic findings in HIV-infected patients with the K65R mutation failing first-line antiretroviral therapy in Nigeria.

Detection of mutations in EGFR in circulating lung-cancer cells.

Clinico-pathogenetic findings and management of chondrodystrophic myotonia (Schwartz-Jampel syndrome): a case report.

EGFR mutation status in tumour-derived DNA from pleural effusion fluid is a practical basis for predicting the response to gefitinib.

Novel MEK1 mutation identified by mutational analysis of epidermal growth factor receptor signaling pathway genes in lung adenocarcinoma.

Novel heteroduplex method using small cytology specimens with a remarkably high success rate for analysing EGFR gene mutations with a significant correlation to gefitinib efficacy in non-small-cell lung cancer.

Altered spin state equilibrium in the T309V mutant of cytochrome P450 2D6: a spectroscopic and computational study.

Genomics: applications in mechanism elucidation.

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

Convergence of mutation and epigenetic alterations identifies common genes in cancer that predict for poor prognosis.

Utilization of genomic signatures to identify phenotype-specific drugs.

Personalized medicine: the future is not what it used to be.

Comprehensive analysis of peroxisome proliferator-activated receptors to predict the drug resistance, immune microenvironment, and prognosis in stomach adenocarcinomas.