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 23

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

Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

PMID 33138797 · PMC7607642 · BMC cancer · 2020 · 8 claims · 7 setups

Has reproduction · 72

edgeR identifies 9 DEGs associated with pCR and 13 DEGs associated with relapse from 579 immune genes in a small TNBC sample set (n=55)

ffpe same nanostring training nanostring immunohistochemistry differential
Experimental identification and in silico prediction of bacterivory in green algae.

PMID 33649548 · PMC8245530 · The ISME journal · 2021 · 7 claims · 6 setups

Has reproduction · 93

Five prasinophyte strains (Pterosperma cristatum NIES626, Pyramimonas parkeae CCMP726, Pyramimonas parkeae NIES254, Nephroselmis pyriformis RCC618, Dolichomastix tenuilepis CCMP3274) ingest live fluorescently labeled bacteria, detected by microscopy and/or flow cytometry

prasinophyte same green pelagibaca flow epifluorescence gene-based
SNPdetector: a software tool for sensitive and accurate SNP detection.

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

Full-text index only

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
Detection of p53 gene mutations in aspiration biopsy specimens from suspected breast cancers by polymerase chain reaction-single strand conformation polymorphism analysis.

PMID 7730136 · PMC5920757 · Japanese journal of cancer research : Gann · 1995 · 4 claims · 4 setups

Full-text index only

Detection of p53 gene mutation by PCR-SSCP in aspirated breast biopsy specimens is a helpful method for more accurate diagnosis of suspected breast cancer

aspiration aspirated biopsy pcr-sscp flow p53
ATM variants and cancer risk in breast cancer patients from Southern Finland.

PMID 16914028 · PMC1592307 · BMC cancer · 2006 · 8 claims · 6 setups

Full-text index only

Neither 5557G>A nor ivs38-8T>C, nor any haplotype containing them, was significantly associated with breast cancer risk in any patient group

familial brca1 same genotype genotyping denaturing direct
Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

PMID 18769673 · PMC2518838 · PloS one · 2008 · 8 claims · 6 setups

Full-text index only

The protein sequence-structure map behaves as a noisy digital communication channel whose capacity C exceeds the transmission rate R for native structures, satisfying Shannon's noisy channel theorem

chains pdbselect25 same single-domain statistical channel negative
Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression.

PMID 19943934 · PMC2794290 · BMC cancer · 2009 · 8 claims · 5 setups

Full-text index only

Hundreds of genes differentiate GISTs according to KIT versus PDGFRA mutation and expression status, despite no discriminative profile for clinical/pathological parameters.

frozen genomic formalin-fixed differentially microarray sequencing quantitative
Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.

PMID 19651875 · PMC2761287 · Nucleic acids research · 2009 · 8 claims · 7 setups

Full-text index only

The LCV approach predicts HTH motifs with 93.29% accuracy, 93.93% sensitivity and 92.66% specificity using only primary sequence information

quintessentialset-88 hth same newly lcs svm traditional
A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics.

PMID 36748417 · PMC9836091 · Microbial genomics · 2022 · 8 claims · 6 setups

Has reproduction · 75

Long-read metagenomics enables isolation-independent identification and characterization of eae-positive STEC directly from raw milk.

pure enriched stec-negative extracted ont real-time artificial
A bioinformatics pipeline for a tick pathogen surveillance multiplex amplicon sequencing assay.

PMID 37247570 · PMC10878300 · Ticks and tick-borne diseases · 2023 · 7 claims · 3 setups

Full-text index only

The MPAS pipeline is a portable, reproducible Nextflow-based bioinformatics pipeline that identifies and summarizes amplicon sequences produced by the MPAS assay.

host-seeking mpas same targeted mpas clc
TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.

PMID 36699358 · PMC9710689 · Bioinformatics advances · 2022 · 6 claims · 2 setups

Has reproduction · 50

TOSCA is the first automated, open-source, end-to-end tumor-only somatic calling workflow for WES and targeted panel sequencing data.

t-cell hcc1395 targeted whole-exome
Calibration-free NGS quantitation of mutations below 0.01% VAF.

PMID 34675197 · PMC8531361 · Nature communications · 2021 · 8 claims · 6 setups

Has reproduction · 96

QBDA (Quantitative Blocker Displacement Amplification) integrates UMI molecular barcoding with BDA variant enrichment to enable calibration-free VAF quantitation

h37rv repository healthy same single-plex 10-plex 22-plex
Heterogeneity of p53 mutational status in intramucosal carcinoma of the colorectum.

PMID 11223545 · PMC5926696 · Japanese journal of cancer research : Gann · 2001 · 7 claims · 4 setups

Full-text index only

p53 gene mutations occur and diverge at the intramucosal carcinoma stage, before submucosal invasion

endoscopically same pcr-based immunohistochemistry histologic
Mutations of p53 in morphologically non-neoplastic mucosa of long-standing ulcerative colitis.

PMID 11223540 · PMC5926702 · Japanese journal of cancer research : Gann · 2001 · 8 claims · 4 setups

Full-text index only

MNNM-p53OE shares identical p53 mutations with the coexisting/adjoining carcinoma and/or dysplasia, indicating a common clonal origin

colectomy microdissected same immunohistochemistry nested
Abnormality of the DNA double-strand-break checkpoint/repair genes, ATM, BRCA1 and TP53, in breast cancer is related to tumour grade.

PMID 15138484 · PMC2409464 · British journal of cancer · 2004 · 8 claims · 4 setups

Full-text index only

High-grade breast tumours show a high frequency of LOH and/or abnormal expression of ATM, BRCA1 and TP53

early-onset same peripheral breast allelotyping immunohistochemistry direct
Prevalence of von Hippel-Lindau gene mutations in sporadic renal cell carcinoma: results from The Netherlands cohort study.

PMID 15932632 · PMC1177929 · BMC cancer · 2005 · 7 claims · 4 setups

Full-text index only

VHL mutations were detected in 61% (114/187) of sporadic clear-cell RCC patients

archival subset flanking paraffin-embedded pcr-sscp feasibility histopathological
Detection of venous thromboembolism by proteomic serum biomarkers.

PMID 17579716 · PMC1891085 · PloS one · 2007 · 5 claims · 8 setups

Full-text index only

A neural network-based classifier built from direct MALDI-TOF MS serum protein expression profiles can diagnose VTE with sensitivity/specificity that exceeds D-dimer assays

serum anova-selected citrated depleted direct artificial d-dimer
Metabolomic profiling in LRRK2-related Parkinson's disease.

PMID 19847307 · PMC2761616 · PloS one · 2009 · 7 claims · 3 setups

Full-text index only

Metabolomic profiles of both idiopathic PD and LRRK2 PD are clearly separated from controls

plasma preprocessed untargeted targeted pls-da
Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.

PMID 27092297 · PMC4820441 · Frontiers in cellular and infection microbiology · 2016 · 7 claims · 7 setups

Has reproduction · 89

STEC are prevalent in surface waters of four Lower Mainland BC watersheds, recovered from 21.6, 23.2, 19.5, and 9.2% of samples across sites, with seasonal variation (13.3% in fall to 34.3% in winter).

surface coli presumptive confirmed hydrophobic sandwich monoplex
Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis.

PMID 11161385 · PMC2363700 · British journal of cancer · 2001 · 8 claims · 6 setups

Full-text index only

PDC shows frequent alterations of K-ras, p53, p16 and DPC4, confirming these as the core molecular fingerprint of ductal cancer

pancreatic same tumor pet sscp methylation-specific microsatellite

Experiments

Prediction of prognostic signatures in triple-negative breast cancer based on the differential expression analysis via NanoString nCounter immune panel.

Experimental identification and in silico prediction of bacterivory in green algae.

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

Detection of p53 gene mutations in aspiration biopsy specimens from suspected breast cancers by polymerase chain reaction-single strand conformation polymorphism analysis.

ATM variants and cancer risk in breast cancer patients from Southern Finland.

Random amino acid mutations and protein misfolding lead to Shannon limit in sequence-structure communication.

Functional features of gene expression profiles differentiating gastrointestinal stromal tumours according to KIT mutations and expression.

Local combinational variables: an approach used in DNA-binding helix-turn-helix motif prediction with sequence information.

A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics.

A bioinformatics pipeline for a tick pathogen surveillance multiplex amplicon sequencing assay.

TOSCA: an automated Tumor Only Somatic CAlling workflow for somatic mutation detection without matched normal samples.

Calibration-free NGS quantitation of mutations below 0.01% VAF.

Heterogeneity of p53 mutational status in intramucosal carcinoma of the colorectum.

Mutations of p53 in morphologically non-neoplastic mucosa of long-standing ulcerative colitis.

Abnormality of the DNA double-strand-break checkpoint/repair genes, ATM, BRCA1 and TP53, in breast cancer is related to tumour grade.

Prevalence of von Hippel-Lindau gene mutations in sporadic renal cell carcinoma: results from The Netherlands cohort study.

Detection of venous thromboembolism by proteomic serum biomarkers.

Metabolomic profiling in LRRK2-related Parkinson's disease.

Phenotypic and Genotypic Characteristics of Shiga Toxin-Producing Escherichia coli Isolated from Surface Waters and Sediments in a Canadian Urban-Agricultural Landscape.

Pancreatic tumours: molecular pathways implicated in ductal cancer are involved in ampullary but not in exocrine nonductal or endocrine tumorigenesis.