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 1k

System / cell line: patients ✕ Clear

Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays.

PMID 16549007 · PMC1544357 · BMC bioinformatics · 2006 · 7 claims · 2 setups

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A methodology combining Cox proportional hazards models with a compound covariate, cross-validated log partial likelihood (ACVL) for predictive accuracy, and permutation-based significance testing can identify an optimal subset of significant genes for survival prediction

simulated diffuse simulation cdna
Search for genetic variants in the p66Shc longevity gene by PCR-single strand conformational polymorphism in patients with early-onset cardiovascular disease.

PMID 16519809 · PMC1420326 · BMC genetics · 2006 · 7 claims · 2 setups

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p66Shc gene increases intracellular reactive oxygen species (ROS), affecting the rate of oxidative damage to nucleic acids

genomic pcr-single direct
The role of the multidisciplinary health care team in the management of patients with Marfan syndrome.

PMID 27843325 · PMC5098778 · Journal of multidisciplinary healthcare · 2016 · 8 claims · 1 setups

Has reproduction

A multidisciplinary health care team is a means to maximize therapeutic success for patients with Marfan syndrome (MFS)

mfs email
Evaluation of EGR1 as a candidate gene for high myopia.

PMID 18636116 · PMC2464612 · Molecular vision · 2008 · 6 claims · 1 setups

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EGR1/ZENK is upregulated to inhibit axial eye growth (STOP signal) and downregulated during axial elongation in animal models of experimentally induced myopia

genomic pcr
Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

PMID 17406619 · PMC2688820 · Nature protocols · 2007 · 8 claims · 7 setups

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Combining three human-optimized DOP-PCR primers before a secondary amino-labeled PCR increases array hybridization sensitivity and reproducibility sixfold compared to the standard 6MW DOP-PCR primer

large-insert patients test genomic array-cgh manual automated
A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis.

PMID 18667089 · PMC2533022 · BMC genomics · 2008 · 7 claims · 2 setups

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HFCC is a method/software for genome-wide epistasis detection using case-control multi-locus association analysis, combining a fast computing algorithm with flexibility to test a variety of epistatic models.

blood-derived simulated genome-wide simulation-based
Variants in LRRC7 lead to intellectual disability, autism, aggression and abnormal eating behaviors.

PMID 39256359 · PMC11387733 · Nature communications · 2024 · 8 claims · 7 setups

Has reproduction · 87

Heterozygous missense or loss-of-function variants in LRRC7 cause a dominant neurodevelopmental disorder in 33 identified individuals

genomes genematcher affected 293t genetic exome phenotype
Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

PMID 35012625 · PMC8743438 · Genome biology · 2022 · 8 claims · 9 setups

Has reproduction · 68

GENEVA (Gene Expression Variance Analysis) is a semi-automated framework that mines large-scale public RNA-seq datasets to identify conditions associated with a gene's expression variance

gtex genetic lncap heart rna-seq meta-analysis electronic
Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

PMID 36245985 · PMC9553530 · Journal of oncology · 2022 · 8 claims · 8 setups

Has reproduction

A three-class WSI cluster (C0/C1/C2) derived via mini batch K-means clustering on Inception V3-extracted image features is significantly associated with overall survival and is an independent prognostic predictor in BLCA.

tcga-blca gse32894 deep transfer machine
5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.

PMID 38277218 · PMC10911375 · Aging · 2024 · 8 claims · 8 setups

Has reproduction · 93

m5C regulators are differentially expressed between AML and normal samples and correlate with AML prognosis

tcga aml gse12417 bulk mutation methylation
Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.

PMID 40427728 · PMC12109394 · Biology · 2025 · 8 claims · 8 setups

Has reproduction · 84

A seven-gene IRG prognostic signature (LIFR, EZR, TBC1D4, NSF, RPL5, SAA1, PGK1) predicts overall survival in breast cancer across training and four validation cohorts

tcga-brca triple-negative ffpe bulk univariate kaplan-meier
High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies.

PMID 34010620 · PMC8096189 · Cell · 2021 · 8 claims · 5 setups

Has reproduction · 87

A Phage-DMS library tiling all single amino acid mutations across the SARS-CoV-2 spike ectodomain (plus D614G) was generated and validated with high sequence coverage.

phage-displayed cloned plasma spike-pseudotyped phage-dms deep elisa
Molecular genetic evidence for unifocal origin of advanced epithelial ovarian cancer and for minor clonal divergence.

PMID 7577492 · PMC2033953 · British journal of cancer · 1995 · 7 claims · 4 setups

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LOH analysis has higher sensitivity than DNA flow cytometry for detecting unifocal origin of bilateral ovarian tumors

bilateral paraffin-embedded ovarian peripheral loh flow isolation
Loss of heterozygosity at the 5,10-methylenetetrahydrofolate reductase locus in human ovarian carcinomas.

PMID 9099956 · PMC2222800 · British journal of cancer · 1997 · 8 claims · 7 setups

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No sequence mutations were found in the MTHFR gene in ovarian tumors and cell lines despite extensive SSCP screening

ovarian non-mucinous informative rt-pcr immunohistochemistry pcr-rflp
Mutational analyses of multiple target genes in histologically heterogeneous gastric cancer with microsatellite instability.

PMID 10081489 · PMC5921733 · Japanese journal of cancer research : Gann · 1998 · 7 claims · 5 setups

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MSI frequency in gastric cancers with histological heterogeneity was 35% (7/20 cases) and 28% (11/40 tumor DNAs), consistent with prior gastric cancer MSI studies.

formalin-fixed msi-positive surgically microsatellite pcr-sscp histopathological
Heterogeneity of p53 mutational status in esophageal squamous cell carcinoma.

PMID 9617346 · PMC5921814 · Japanese journal of cancer research : Gann · 1998 · 6 claims · 4 setups

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Three of 10 esophageal squamous cell carcinomas showed heterogeneous p53 mutational status, but only within the pre-invasive (carcinoma in situ) area.

esophageal paraffin-embedded genomic biotinylated immunohistochemistry microdissection nested
Mitotic checkpoint protein hsMAD2 as a marker predicting liver metastasis of human gastric cancers.

PMID 11572763 · PMC5926839 · Japanese journal of cancer research : Gann · 2001 · 8 claims · 4 setups

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No mutations were found in the coding sequence of the hsMAD2 gene in 32 primary gastric cancers

gastric cancer formalin-fixed near-diploid pcr semi-quantitative immunohistochemistry
Pharmacogenomic biomarkers.

PMID 12364812 · PMC3850811 · Disease markers · 2002 · 8 claims · 8 setups

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Development of a pharmacogenomic biomarker requires sequential steps: laboratory identification, retrospective confirmation in clinical samples, prospective clinical trial validation, and regulatory approval before patient stratification.

populations population tumor breast genetic array immunohistochemistry
Use of genomic data in risk assessment.

PMID 11983054 · PMC139345 · Genome biology · 2002 · 8 claims · 4 setups

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New genomic technologies (CGH, SNP analysis, restriction landmark genome scanning, spectral karyotyping, transcript profiling) can be applied to improve risk assessment accuracy

glioma lung animal genome sensitivity expression snp
p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.

PMID 11875738 · PMC2375302 · British journal of cancer · 2002 · 8 claims · 6 setups

Full-text index only

p53 status can be reliably determined by yeast functional assay from single frozen sections of trucut biopsies

frozen plasmids single extracted p53 sanger laser

Experiments

Predicting survival outcomes using subsets of significant genes in prognostic marker studies with microarrays.

Search for genetic variants in the p66Shc longevity gene by PCR-single strand conformational polymorphism in patients with early-onset cardiovascular disease.

The role of the multidisciplinary health care team in the management of patients with Marfan syndrome.

Evaluation of EGR1 as a candidate gene for high myopia.

Construction and use of spotted large-insert clone DNA microarrays for the detection of genomic copy number changes.

A method for detecting epistasis in genome-wide studies using case-control multi-locus association analysis.

Variants in LRRC7 lead to intellectual disability, autism, aggression and abnormal eating behaviors.

Systematic identification of ACE2 expression modulators reveals cardiomyopathy as a risk factor for mortality in COVID-19 patients.

Artificial Intelligence Meets Whole Slide Images: Deep Learning Model Shapes an Immune-Hot Tumor and Guides Precision Therapy in Bladder Cancer.

5-methylcytosine RNA modification regulators-based patterns and features of immune microenvironment in acute myeloid leukemia.

Elucidating the Prognostic and Therapeutic Implications of Insulin Resistance Genes in Breast Cancer: A Machine Learning-Powered Analysis.

High-resolution profiling of pathways of escape for SARS-CoV-2 spike-binding antibodies.

Molecular genetic evidence for unifocal origin of advanced epithelial ovarian cancer and for minor clonal divergence.

Loss of heterozygosity at the 5,10-methylenetetrahydrofolate reductase locus in human ovarian carcinomas.

Mutational analyses of multiple target genes in histologically heterogeneous gastric cancer with microsatellite instability.

Heterogeneity of p53 mutational status in esophageal squamous cell carcinoma.

Mitotic checkpoint protein hsMAD2 as a marker predicting liver metastasis of human gastric cancers.

Pharmacogenomic biomarkers.

Use of genomic data in risk assessment.

p53 as a potential predictive factor of response to chemotherapy: feasibility of p53 assessment using a functional test in yeast from trucut biopsies in breast cancer patients.