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 19

System / cell line: type ✕ Assay: ffpe ✕ Clear

Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

PMID 41029822 · PMC12486589 · Journal of translational medicine · 2025 · 8 claims · 5 setups

Has reproduction · 67

fRNA-seq transcript counts are best fit by the negative binomial distribution, with little evidence supporting zero-inflated extensions

compendium frna-seq nb-generated breast ffpe distribution synthetic
'Classical' but not 'other' mutations of EGFR kinase domain are associated with clinical outcome in gefitinib-treated patients with non-small cell lung cancer.

PMID 18000506 · PMC2360265 · British journal of cancer · 2007 · 8 claims · 4 setups

Full-text index only

'Classical' EGFR mutations (exon 18 G719X, exon 19 DEL19, exon 21 L858R) are associated with better clinical outcome (disease control) with gefitinib

microdissected genomic ffpe advanced direct nested immunohistochemistry
High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies.

PMID 18495026 · PMC2408599 · BMC cancer · 2008 · 8 claims · 4 setups

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HRM correctly identified all 73 EGFR-mutation-positive FFPE samples previously found by sequencing, giving 100% sensitivity and 90% specificity

ffpe single high direct hrm
Targeted KRAS mutation assessment on patient tumor histologic material in real time diagnostics.

PMID 19888477 · PMC2768905 · PloS one · 2009 · 8 claims · 5 setups

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Q-PCR methods yield informative KRAS mutation results even on very fragmented FFPE-DNA where dideoxy-sequencing fails (p<0.0001)

ffpe dideoxy-sequencing taqman-mgb dxs-kras
Rapid detection of SMARCB1 sequence variation using high resolution melting.

PMID 20003390 · PMC2801682 · BMC cancer · 2009 · 8 claims · 6 setups

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HRM screening of SMARCB1 amplicons has a zero false negative rate compared to direct sequencing

genomic same tumor rhabdoid high direct hrm
Association between cigarette smoking, APC mutations and the risk of developing sporadic colorectal adenomas and carcinomas.

PMID 16545110 · PMC1475604 · BMC cancer · 2006 · 8 claims · 4 setups

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Smoking is associated with adenoma and CRC development, with the association strongest in tumors lacking APC truncation mutations

formalin-fixed ffpe paired study direct pcr restriction
Correlation between KIT expression and KIT mutation in melanoma: a study of 173 cases with emphasis on the acral-lentiginous/mucosal type.

PMID 19718013 · PMC4120323 · Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc · 2009 · 8 claims · 2 setups

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Immunohistochemical KIT expression is significantly associated with KIT mutation status in acral lentiginous/mucosal melanoma

melanoma immunohistochemistry pcr
An integrated single-cell and spatial proteotranscriptomics atlas of fibroblast-driven immunoregulation within the human adult oral cavity.

PMID 42147490 · PMC13179517 · Cell press blue · 2026 · 8 claims · 8 setups

Has reproduction · 85

Fibroblasts act as central regulators of structural immunity in the human oral cavity, forming peri-epithelial hubs enriched in effector cytokines

oral ffpe scrna-seq integrated scrna-seq spatial ligand-receptor
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
Single-cell dissection of chronic lung allograft dysfunction reveals convergent and distinct fibrotic mechanisms.

PMID 41122970 · PMC12581678 · JCI insight · 2025 · 8 claims · 7 setups

Has reproduction · 75

CLAD harbors disease-specific cellular subsets including Fibro.AT2 cells, exhausted CD8+ T cells, and superactivated macrophages

clad covid-19 ffpe end-stage single-cell single-nucleus integrative
Expression of neurofibromin 1 in colorectal cancer and cetuximab resistance.

PMID 34779495 · PMC8611403 · Oncology reports · 2022 · 8 claims · 8 setups

Has reproduction · 73

NF1 is highly expressed in cetuximab-sensitive CRC cell lines and minimally expressed in cetuximab-resistant ones

crc cetuximab-sensitive sirna ffpe western growth colony
FRMD8 inhibits tumor metastasis in BRCA1-associated TNBC by negatively regulating tmTNF-α.

PMID 40619383 · PMC12229025 · Cellular & molecular biology letters · 2025 · 8 claims · 8 setups

Has reproduction · 73

Low FRMD8 expression in BRCA1-mutant breast cancer cells significantly enhances metastatic potential to various organs

tnbc geo breast frmd8 bulk meta-analysis single-cell
TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival.

PMID 16229746 · PMC1276789 · BMC cancer · 2005 · 8 claims · 4 setups

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Survival for BRCA1-familial ovarian cancer cases with TP53 mutations was not significantly different from familial cases without TP53 mutations (p=0.25, RR=1.64)

ovarian sporadic paraffin-embedded mutation survival extraction
Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

PMID 18418848 · PMC6668724 · Genes, chromosomes & cancer · 2008 · 6 claims · 5 setups

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Emulsion PCR combined with picotiter plate pyrosequencing (454 sequencing) enables high-resolution, high-throughput detection of low-frequency sequence variants among the many individual copies of an amplified gene.

erbb2-amplified erbb2-positive plasmid cos-7 emulsion serial immune-complex
Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.

PMID 38358352 · PMC10903300 · Cancer research communications · 2024 · 8 claims · 7 setups

Has reproduction · 64

Two main neutrophil subtypes exist in primary tumors: an activated subtype sharing transcriptomic signatures with healthy neutrophils, and a tumor-specific subtype.

colorectal sorted integrated neutrophil scrna-seq bulk immunohistochemistry
A novel oxidative stress-related gene signature as an indicator of prognosis and immunotherapy responses in HNSCC.

PMID 38157249 · PMC10781479 · Aging · 2023 · 6 claims · 7 setups

Has reproduction · 85

A nine-gene oxidative stress-related scoring (OSRS) model (AREG, CES1, CSTA, FDCSP, JCHAIN, IFFO2, PGLYRP4, SPOCK2, SPINK6) predicts overall survival in HNSCC.

tcga-hnscc gse41613 gse103322 prjeb23709 bulk single-cell immunotherapy
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
Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

PMID 19010816 · PMC6953412 · Molecular cancer research : MCR · 2008 · 8 claims · 8 setups

Full-text index only

Activating RAS-MAPK pathway mutations are present in >70% of serous LMP tumors versus ~12.5% of serous ovarian carcinomas

serous same lmp braf-mutant gene hotspot erbb2
Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.

PMID 19811662 · PMC2766370 · Molecular cancer · 2009 · 7 claims · 6 setups

Full-text index only

LCN-HRM enables detection and sequencing-based characterisation of low-level mutations that are undetectable by direct sequencing alone

hct116 ffpe genomic tx84 dideoxynucleotide high lcn-hrm

Experiments

'Classical' but not 'other' mutations of EGFR kinase domain are associated with clinical outcome in gefitinib-treated patients with non-small cell lung cancer.

High resolution melting analysis for rapid and sensitive EGFR and KRAS mutation detection in formalin fixed paraffin embedded biopsies.

Targeted KRAS mutation assessment on patient tumor histologic material in real time diagnostics.

Rapid detection of SMARCB1 sequence variation using high resolution melting.

Association between cigarette smoking, APC mutations and the risk of developing sporadic colorectal adenomas and carcinomas.

Correlation between KIT expression and KIT mutation in melanoma: a study of 173 cases with emphasis on the acral-lentiginous/mucosal type.

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

TP53 mutations in ovarian carcinomas from sporadic cases and carriers of two distinct BRCA1 founder mutations; relation to age at diagnosis and survival.

Direct resequencing of the complete ERBB2 coding sequence reveals an absence of activating mutations in ERBB2 amplified breast cancer.

Mutation of ERBB2 provides a novel alternative mechanism for the ubiquitous activation of RAS-MAPK in ovarian serous low malignant potential tumors.

Limited copy number-high resolution melting (LCN-HRM) enables the detection and identification by sequencing of low level mutations in cancer biopsies.