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 117

System / cell line: negative ✕ Assay: positive ✕ Clear

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
p53 expression and its relationship to DNA alterations in bone and soft tissue sarcomas.

PMID 8260365 · PMC1968651 · British journal of cancer · 1993 · 8 claims · 6 setups

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25.7% (29/113) of bone and soft tissue sarcomas show positive p53 immunostaining

frozen subset saos-2 immunohistochemistry southern pcr-single
Cell clusters overlying focally disrupted mammary myoepithelial cell layers and adjacent cells within the same duct display different immunohistochemical and genetic features: implications for tumor progression and invasion.

PMID 14580259 · PMC314413 · Breast cancer research : BCR · 2003 · 7 claims · 4 setups

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ER-negative cell clusters are far more likely than ER-positive clusters to overlie disrupted myoepithelial cell layers, both at the case level and the individual-disruption level

paraffin selected microdissected double immunohistochemistry loss
The specificity of the FOXL2 c.402C>G somatic mutation: a survey of solid tumors.

PMID 19956657 · PMC2777318 · PloS one · 2009 · 6 claims · 4 setups

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The FOXL2 c.402C>G mutation is not commonly found in a wide variety of other cancers and is likely pathognomonic for A-GCTs and closely related tumors.

tumor ovarian kgn high sanger taqman
Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease.

PMID 18974839 · PMC2572839 · PloS one · 2008 · 7 claims · 6 setups

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Pseudomonas 16S rDNA is significantly more prevalent in ileal biopsies of CD patients than non-IBD patients

ileal p16s otu pseudomonas nested cloning
MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.

PMID 35330728 · PMC8940201 · Frontiers in genetics · 2022 · 6 claims · 6 setups

Has reproduction · 50

MEDUSA is an automated, Conda-installable and Snakemake-managed pipeline performing preprocessing, assembly, alignment, taxonomic classification, and functional annotation on shotgun data.

bovine simulated cami trimming decontamination assembly
CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes.

PMID 15796777 · PMC1274267 · BMC bioinformatics · 2005 · 8 claims · 2 setups

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CGMIM is a Perl program that text-mines OMIM entries to identify cancer-gene associations and genetically-related cancer type pairs.

omim automated manual
A functional map of NFkappaB signaling identifies novel modulators and multiple system controls.

PMID 17553156 · PMC2394752 · Genome biology · 2007 · 8 claims · 6 setups

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154 positive and 88 negative modulators of NFκB signaling were identified from genomic screens

hek-293t tissues gain-of-function loss-of-function glucocorticoid
Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma.

PMID 37161060 · PMC10170109 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 73

In HPV-associated HNSCC, the mitophagy process affects tumour development, immune cell infiltration and prognosis.

tcga-hnscc gse65858 hpv-positive tcga bulk microarray qrt-pcr
Microarray analysis: genome-scale hypothesis scanning.

PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups

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Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.

drosophila yeast diffuse breast microarray integrated gene
SNPdetector: a software tool for sensitive and accurate SNP detection.

PMID 16261194 · PMC1274293 · PLoS computational biology · 2005 · 7 claims · 7 setups

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SNPdetector, which models human visual inspection of sequencing traces, achieves low false positive and false negative rates in automated SNP and mutation detection

inbred unrelated zebra same pcr manual comparative
TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

PMID 17199898 · PMC1774580 · BMC bioinformatics · 2007 · 7 claims · 8 setups

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TPRpred detects divergent/remote-homolog TPR repeat units that existing resources (Pfam, SMART, REP) fail to detect

scop-derived malt nr-70 scop profile-based dali remote
Peptide bioinformatics: peptide classification using peptide machines.

PMID 19065810 · PMC7122642 · Methods in molecular biology (Clifton, N.J.) · 2008 · 8 claims · 4 setups

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The bio-basis function, which converts peptides into numerical vectors using nongapped pairwise homology alignment scores against indicator peptides, can statistically quantify peptide similarity for classification.

illustrative query generic synthetic bio-basis orthogonal hyperplane
Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.

PMID 35869080 · PMC9307511 · Nature communications · 2022 · 7 claims · 4 setups

Has reproduction · 80

DiffScan is a computational framework combining a Normalization module and a Scan module to identify SVRs at nucleotide resolution from SP data.

transcripts platforms bacillus multi-subcellular simulated negative benchmark
Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

PMID 18984577 · PMC2649809 · Molecular & cellular proteomics : MCP · 2009 · 8 claims · 6 setups

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Brain-specific proteins are 1.8 times more likely to be observed in CSF than in plasma

csf brain normal 2d-dige label-free isotopic
Negative emotionality: monoamine oxidase B gene variants modulate personality traits in healthy humans.

PMID 19657584 · PMC3653168 · Journal of neural transmission (Vienna, Austria : 1996) · 2009 · 7 claims · 7 setups

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MAOB SNPs rs10521432 and rs6651806 are significantly associated with Negative Emotionality in healthy volunteers

healthy genotype maoa snp multidimensional profile
nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

PMID 15980516 · PMC1160133 · Nucleic acids research · 2005 · 6 claims · 4 setups

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nsSNPAnalyzer is a web server that predicts whether a query nsSNP is disease-associated or functionally neutral using a Random Forest classifier combining structural and evolutionary information

curated homologous structure random structural secondary
In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.

PMID 32898168 · PMC7478592 · PLoS biology · 2020 · 8 claims · 6 setups

Has reproduction · 89

SARS-CoV-2 infection induces a strong interferon-mediated antiviral response in the nasopharynx, up-regulating antiviral factors (OAS1-3, IFIT1-3, MX2, RSAD2, HERC5) and Th1 chemokines CXCL9/10/11, while down-regulating ribosomal protein transcripts.

nasopharyngeal airway patient-matched swab shotgun bulk rt-pcr
Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

PMID 19756158 · PMC2742196 · PLoS computational biology · 2009 · 8 claims · 4 setups

Full-text index only

MIP active learning is a novel active learning method that preferentially seeks informative Positive (functionally active) examples rather than only maximizing classifier accuracy.

engineered p53 computational yeast-based regional homology
Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues.

PMID 18416831 · PMC2377273 · BMC cancer · 2008 · 6 claims · 4 setups

Full-text index only

Three protein spots were significantly altered in abundance between metastase-positive and metastase-negative breast cancer patient groups

excised formalin-fixed log-normalized two-dimensional liquid immunohistochemistry

Experiments

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

p53 expression and its relationship to DNA alterations in bone and soft tissue sarcomas.

Cell clusters overlying focally disrupted mammary myoepithelial cell layers and adjacent cells within the same duct display different immunohistochemical and genetic features: implications for tumor progression and invasion.

The specificity of the FOXL2 c.402C>G somatic mutation: a survey of solid tumors.

Identification and characterisation of Pseudomonas 16S ribosomal DNA from ileal biopsies of children with Crohn's disease.

MEDUSA: A Pipeline for Sensitive Taxonomic Classification and Flexible Functional Annotation of Metagenomic Shotgun Sequences.

CGMIM: automated text-mining of Online Mendelian Inheritance in Man (OMIM) to identify genetically-associated cancers and candidate genes.

A functional map of NFkappaB signaling identifies novel modulators and multiple system controls.

Comprehensive analysis of mitophagy in HPV-related head and neck squamous cell carcinoma.

Microarray analysis: genome-scale hypothesis scanning.

SNPdetector: a software tool for sensitive and accurate SNP detection.

TPRpred: a tool for prediction of TPR-, PPR- and SEL1-like repeats from protein sequences.

Peptide bioinformatics: peptide classification using peptide machines.

Differential analysis of RNA structure probing experiments at nucleotide resolution: uncovering regulatory functions of RNA structure.

Brain-specific proteins decline in the cerebrospinal fluid of humans with Huntington disease.

Negative emotionality: monoamine oxidase B gene variants modulate personality traits in healthy humans.

nsSNPAnalyzer: identifying disease-associated nonsynonymous single nucleotide polymorphisms.

In vivo antiviral host transcriptional response to SARS-CoV-2 by viral load, sex, and age.

Predicting positive p53 cancer rescue regions using Most Informative Positive (MIP) active learning.

Two-dimensional electrophoretic comparison of metastatic and non-metastatic human breast tumors using in vitro cultured epithelial cells derived from the cancer tissues.