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 20

System / cell line: real ✕ Assay: regression ✕ Clear

Statistical analysis of real-time PCR data.

PMID 16504059 · PMC1395339 · BMC bioinformatics · 2006 · 8 claims · 2 setups

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Four statistical models (multiple regression, ANCOVA, t-test, Wilcoxon test) were developed to estimate ΔΔCt with associated significance/confidence intervals

real-time linear
Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation.

PMID 40674582 · PMC12502914 · Bioinformatics (Oxford, England) · 2025 · 8 claims · 3 setups

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A two-stage procedure using feature-specific and sign-specific adaptive weights shares information on feature selection, effect direction, and effect size between related regression problems.

simulated multi-task penalised adaptive hyperparameter
Associations between hepatitis B virus genotype and mutants and the risk of hepatocellular carcinoma.

PMID 18695135 · PMC2518166 · Journal of the National Cancer Institute · 2008 · 8 claims · 7 setups

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HBV genotype C is an independent risk factor for HCC compared with genotype B

plasma serum cohort epidemiological real-time direct radioimmunoassay
11q13 amplification status and human papillomavirus in relation to p16 expression defines two distinct etiologies of head and neck tumours.

PMID 17003776 · PMC2360598 · British journal of cancer · 2006 · 8 claims · 7 setups

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HPV-positive HNSCC tumours are significantly less likely to carry 11q13 amplification than HPV-negative tumours

hnscc paraffin nested hpv pyrosequencing
Genetic association study and meta-analysis of the HTR2C Cys23Ser polymorphism and migraine.

PMID 17901921 · PMC3451673 · The journal of headache and pain · 2007 · 8 claims · 3 setups

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The HTR2C Cys23Ser polymorphism is not significantly associated with migraine or migraine with aura in the case-control study

blood-derived migraine pooled allelic case-control meta-analysis
Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

PMID 23516341 · PMC3597545 · PLoS computational biology · 2013 · 8 claims · 7 setups

Has reproduction · 44

Local sequence context strongly determines position-specific polymerase kinetic rate: roughly 80% of IPD variation is explained by a 10 bp context (7 bases upstream, 2 bases downstream of the incorporation site), saturating at 7 bases upstream.

plasmid coli wild-type artificial smrt read-mixing distributional
The genomic analysis of lactic acidosis and acidosis response in human cancers.

PMID 19057672 · PMC2585811 · PLoS genetics · 2008 · 8 claims · 8 setups

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Lactic acidosis and hypoxia induce largely distinct gene expression programs in HMECs, with lactic acidosis producing a much larger and more dramatic response

mammary hmec gene breast gene real-time bayesian
Detecting imbalanced expression of SNP alleles by minisequencing on microarrays.

PMID 15500681 · PMC529269 · BMC biotechnology · 2004 · 8 claims · 7 setups

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Both microarray minisequencing formats accurately quantify SNP allele ratios, with R2 > 0.95 for the majority of regression lines

genomic huvec microarray solid-phase real-time
Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.

PMID 37012480 · PMC10172113 · Nature methods · 2023 · 8 claims · 5 setups

Has reproduction · 90

pSCoPE (prioritized precursor selection via MaxQuant.Live) increases sensitivity, data completeness, and proteome coverage more than twofold over shotgun single-cell proteomics

bulk hek293 single-cell bone prioritized single-cell spike-in
Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

PMID 19888451 · PMC2766054 · PloS one · 2009 · 7 claims · 4 setups

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Somatic mutation frequency (%MSI) of 3'UTR microsatellites in MSI-H colorectal tumors correlates significantly with microsatellite length (r=0.86, p=7.2×10−13), following an exponential growth model.

msi-h computational rb1cc1 normal pcr nonlinear real-time
Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

PMID 37853325 · PMC10583454 · Genetics, selection, evolution : GSE · 2023 · 5 claims · 6 setups

Has reproduction

SLDP selects a subset of WGS variants using GWAS prior information (P-value threshold) combined with LD pruning (r2) to improve genomic prediction accuracy.

duroc discovery training real low-coverage genome-wide genomic
TGF-β-mediated activation of fibroblasts in cervical cancer: implications for tumor microenvironment and prognosis.

PMID 40124621 · PMC11929507 · PeerJ · 2025 · 8 claims · 8 setups

Has reproduction · 79

TGF-β signaling pathway activity is significantly increased in fibroblasts from cervical cancer samples compared to normal samples and correlates with tumor proliferation and differentiation.

cervical tcga-cesc hela scrna-seq scrna-seq wgcna cox
Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

PMID 37124622 · PMC10131083 · Frontiers in genetics · 2023 · 8 claims · 8 setups

Has reproduction · 71

Two distinct RNA modification patterns exist among BCa samples with radically varying clinical outcomes and biological characteristics

meta-geo tcga-blca bca genomics unsupervised lasso weighted
Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

PMID 19844207 · PMC2797562 · Molecular psychiatry · 2010 · 8 claims · 7 setups

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rs1344706 in ZNF804A is associated with schizophrenia in the Irish ICCSS sample, replicating the original Cardiff finding

irish iccss postmortem genomic snp haplotype logistic
Association between telomere length and V(H) gene mutation status in chronic lymphocytic leukaemia: clinical and biological implications.

PMID 12592375 · PMC2377180 · British journal of cancer · 2003 · 7 claims · 5 setups

Full-text index only

Unmutated VH gene CLL cases have significantly shorter telomeres than mutated VH gene CLL cases

cll subset pcr southern real-time
Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

PMID 18053132 · PMC2254445 · BMC bioinformatics · 2007 · 6 claims · 5 setups

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The paired oligo-border kernel (POBK) combined with SVMs predicts peptide adsorption/elution in SAX-SPE and retention time in IP-RP-HPLC more accurately than existing methods.

peptides peptide sax-spe ip-rp-hplc cross-run
Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

PMID 18784189 · PMC2577347 · Nucleic acids research · 2008 · 8 claims · 6 setups

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Genomic waves are present in both Illumina and Affymetrix SNP genotyping arrays, confirming they are not platform-specific

representative illumina six snp serial concentration
CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

PMID 18577749 · PMC2483574 · Journal of the National Cancer Institute · 2008 · 7 claims · 8 setups

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CHD5 promoter is highly methylated in neuroblastoma cell lines with 1p deletion and absent CHD5 expression (NLF, IMR5)

neuroblastoma nlf athymic methylation-specific quantitative soft
Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.

PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups

Has reproduction · 74

540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed

breast colorectal lung common microarray kegg protein-protein
CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.

PMID 36072582 · PMC9441746 · Frontiers in immunology · 2022 · 8 claims · 8 setups

Has reproduction · 81

Higher stromal and ESTIMATE scores are associated with favorable prognosis in DLBCL

dlbcl ici-related degs ffpe estimate consensus differential

Experiments

Statistical analysis of real-time PCR data.

Estimating sparse regression models in multi-task learning and transfer learning through adaptive penalisation.

Associations between hepatitis B virus genotype and mutants and the risk of hepatocellular carcinoma.

11q13 amplification status and human papillomavirus in relation to p16 expression defines two distinct etiologies of head and neck tumours.

Genetic association study and meta-analysis of the HTR2C Cys23Ser polymorphism and migraine.

Detecting DNA modifications from SMRT sequencing data by modeling sequence context dependence of polymerase kinetic.

The genomic analysis of lactic acidosis and acidosis response in human cancers.

Detecting imbalanced expression of SNP alleles by minisequencing on microarrays.

Prioritized mass spectrometry increases the depth, sensitivity and data completeness of single-cell proteomics.

Screening for microsatellite instability identifies frequent 3'-untranslated region mutation of the RB1-inducible coiled-coil 1 gene in colon tumors.

Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population.

TGF-β-mediated activation of fibroblasts in cervical cancer: implications for tumor microenvironment and prognosis.

Comprehensive analysis of a novel RNA modifications-related model in the prognostic characterization, immune landscape and drug therapy of bladder cancer.

Replication of association between schizophrenia and ZNF804A in the Irish Case-Control Study of Schizophrenia sample.

Association between telomere length and V(H) gene mutation status in chronic lymphocytic leukaemia: clinical and biological implications.

Statistical learning of peptide retention behavior in chromatographic separations: a new kernel-based approach for computational proteomics.

Adjustment of genomic waves in signal intensities from whole-genome SNP genotyping platforms.

CHD5, a tumor suppressor gene deleted from 1p36.31 in neuroblastomas.

Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.

CCL8 as a promising prognostic factor in diffuse large B-cell lymphoma via M2 macrophage interactions: A bioinformatic analysis of the tumor microenvironment.