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 832

System / cell line: cancer ✕ Clear

Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.

PMID 41579861 · PMC12923976 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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oncRNA binary presence-absence patterns constitute digital molecular barcodes that capture cancer type and subtype identity

tcga exrna cptac mda-mb-231 small machine atac-seq
FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity.

PMID 41621066 · PMC13050545 · Cell reports · 2026 · 8 claims · 8 setups

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FOXA1 mutations in a 874-tumor cohort cluster into missense, in-frame indel, and truncation subgroups, with indels concentrated at residues M253/E255

prostate targeted single-nucleus scatac-seq
CAF-enriched COL4A6 promotes gastric cancer progression and stromal remodeling despite an inverse association in bulk transcriptomes.

PMID 41735371 · PMC13031391 · Scientific reports · 2026 · 7 claims · 7 setups

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COL4A6 carries an inverse association (OR<1) in bulk transcriptome-based risk models despite being markedly upregulated and predominantly localized to the CAF compartment in clinical specimens

tcga-stad gse66229 gse183904 paired bulk microarray scrna-seq
Splice-switching of the oncogenic BCS1L isoform suppresses ovarian cancer progression by disrupting mitochondrial function.

PMID 41771836 · PMC13039997 · Cell death & disease · 2026 · 7 claims · 8 setups

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BCS1L is alternatively spliced into a full-length isoform (BCS1L-L) and an exon 2-skipped short isoform (BCS1L-S)

tcga-ov ovarian clinical fte187 gsea single-cell qpcr
Exploring the mechanism of action of abemaciclib in breast cancer through circulating chromatin fragments.

PMID 41845059 · PMC13149665 · Communications medicine · 2026 · 8 claims · 5 setups

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cfDNA concentrations are significantly higher in breast cancer patients than healthy donors and decline following abemaciclib therapy

serum t47d edger-normalized cfdna proliferation pathway
Dynamic changes of the immune microenvironment in ovarian cancer following neoadjuvant chemotherapy.

PMID 41872134 · PMC13039919 · Cell death discovery · 2026 · 8 claims · 8 setups

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Prostaglandin-mediated immunosuppressive microenvironment formation is a critical contributor to chemotherapy resistance following cisplatin treatment

high-grade hgsoc bone bmdms scrna-seq cell-cell tensor
scComm: a contrastive learning framework for deciphering cell-cell communications at single-cell resolution.

PMID 41877186 · PMC13134144 · Genome biology · 2026 · 8 claims · 7 setups

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scComm infers cell-cell communications at single-cell resolution using a data-adaptive L-R weighting module and supervised contrastive learning (SupCon loss) to distinguish significant CCC events from background noise

simulated spatial liver single-cell simulated spatial scrna-seq
Quemliclustat and chemotherapy with or without zimberelimab in metastatic pancreatic adenocarcinoma: a randomized phase 1 trial.

PMID 41912809 · PMC13099643 · Nature medicine · 2026 · 7 claims · 8 setups

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Quemliclustat combined with gemcitabine/nab-paclitaxel (G/nP) with or without zimberelimab has a safety profile consistent with G/nP alone across dose-escalation and dose-expansion phases

mia hct-116 patients randomized rna-seq rt-pcr phase
Targeting KIFC1 to disrupt centrosome clustering and trigger anaphase catastrophe in small-cell lung cancer.

PMID 41948931 · PMC13134724 · JCI insight · 2026 · 8 claims · 8 setups

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KIFC1 is overexpressed in SCLC compared with normal tissues and other cancer types

sclc h146 clinical cancer immunofluorescence viability flow
Nonsense-mediated mRNA decay inhibition reshapes the cancer immunopeptidome.

PMID 41956098 · PMC7619149 · Immunity · 2026 · 8 claims · 8 setups

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Reduced NMD activity (lower NMD score) predicts improved CPI response across >1,000 patients, independent of TMB or tumor type

tcga a375 reporter patient-derived multi-omics crispr-cas9 sirna
A transcriptomic-based model associated with PARP inhibitor sensitivity and immunogenic signatures in ovarian cancer.

PMID 42014663 · PMC13230468 · Discover oncology · 2026 · 8 claims · 8 setups

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A 23-gene PARPi-sensor transcriptomic model stratifies ovarian cancer patients into high- and low-risk groups with significantly different overall survival, validated in TCGA and ICGC cohorts

pdx tcga prognostic tcia bulk non-negative univariate
Functional germline variants together with somatic mutations alter the integrity of cancer hallmark regulatory networks.

PMID 42057121 · PMC13151107 · Genome medicine · 2026 · 8 claims · 6 setups

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Combined germline and somatic alterations disturb cancer hallmark pathway integrity in individual-specific ways, potentially explaining unique clinical behavior of each cancer.

tcga cancer individual biological germline somatic crispr
Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

PMID 20003409 · PMC2799438 · BMC medicine · 2009 · 8 claims · 5 setups

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A panel of 48 genomically characterized breast cancer cell lines can model patient tumour heterogeneity to identify biomarkers predicting response to PG-11047

panel breast 250-gene candidate genome growth pathway
iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.

PMID 42108258 · PMC13158306 · Signal transduction and targeted therapy · 2026 · 8 claims · 5 setups

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iS2C2 integrates the S2C2 cell-cell communication algorithm with LLMs to generate biologically interpretable hypotheses from scRNA-seq and spatial transcriptomics data

single-cell algorithm domain scrna-seq single-cell perturbation llm-based
Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.

PMID 19903341 · PMC2810663 · Genome biology · 2009 · 7 claims · 3 setups

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GAP is a method for automatic detection of absolute segmental copy number and genotype status from SNP-array cancer genome profiles

breast snp flow karyotyping
Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

PMID 19835606 · PMC2784330 · Genome biology · 2009 · 7 claims · 2 setups

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Hybrid selection of cDNA dramatically increases the specificity of sequencing reads mapping to targeted cancer-related transcripts.

k-562 targeted sanger
Identification of biomarkers from mass spectrometry data using a "common" peak approach.

PMID 16869977 · PMC1550264 · BMC bioinformatics · 2006 · 8 claims · 1 setups

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"Common" peaks—those exhibited by many subjects—can be identified and used as biomarkers in high-dimensional mass spectrometry data

serum mass
Enhancing cell subpopulation discovery in cancer by integrating single-cell transcriptome and expressed variants.

PMID 41647537 · PMC12869734 · Fundamental research · 2026 · 6 claims · 3 setups

Has reproduction · 68

scCluster, an end-to-end deep clustering model integrating gene expression and expressed variant (eSNP) features, stratifies cell subpopulations in cancer scRNA-seq data.

raw real-world expressed gene deep
Glycomic analysis: an array of technologies.

PMID 19728746 · PMC3443568 · ACS chemical biology · 2009 · 8 claims · 8 setups

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Glycosylation is the most prevalent protein post-translational modification, occurring on at least 50% of all proteins

sera t-cells serum glycoproteins lectin hydrazide bioorthogonal
Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.

PMID 38482016 · PMC10933018 · Frontiers in immunology · 2024 · 8 claims · 8 setups

Has reproduction · 80

C3 PLP2+ Tumor Epithelial Progenitor Cells are a noteworthy subpopulation exerting a pivotal influence on CC differentiation and progression

cervical tcga siha scrna-seq bulk rt-qpcr

Experiments

Systematic annotation of orphan RNAs reveals blood-accessible molecular barcodes of cancer identity and cancer-emergent oncogenic drivers.

FOXA1 mutations co-opt nascent transcription factor networks in partnership with androgen receptor to enhance prostate tumorigenicity.

CAF-enriched COL4A6 promotes gastric cancer progression and stromal remodeling despite an inverse association in bulk transcriptomes.

Splice-switching of the oncogenic BCS1L isoform suppresses ovarian cancer progression by disrupting mitochondrial function.

Exploring the mechanism of action of abemaciclib in breast cancer through circulating chromatin fragments.

Dynamic changes of the immune microenvironment in ovarian cancer following neoadjuvant chemotherapy.

scComm: a contrastive learning framework for deciphering cell-cell communications at single-cell resolution.

Quemliclustat and chemotherapy with or without zimberelimab in metastatic pancreatic adenocarcinoma: a randomized phase 1 trial.

Targeting KIFC1 to disrupt centrosome clustering and trigger anaphase catastrophe in small-cell lung cancer.

Nonsense-mediated mRNA decay inhibition reshapes the cancer immunopeptidome.

A transcriptomic-based model associated with PARP inhibitor sensitivity and immunogenic signatures in ovarian cancer.

Functional germline variants together with somatic mutations alter the integrity of cancer hallmark regulatory networks.

Integrating complex genomic datasets and tumour cell sensitivity profiles to address a 'simple' question: which patients should get this drug?

iS2C2: a cointelligent platform for mechanistic discovery of disease cellular crosstalk.

Genome Alteration Print (GAP): a tool to visualize and mine complex cancer genomic profiles obtained by SNP arrays.

Targeted next-generation sequencing of a cancer transcriptome enhances detection of sequence variants and novel fusion transcripts.

Identification of biomarkers from mass spectrometry data using a "common" peak approach.

Enhancing cell subpopulation discovery in cancer by integrating single-cell transcriptome and expressed variants.

Glycomic analysis: an array of technologies.

Decoding the tumor microenvironment and molecular mechanism: unraveling cervical cancer subpopulations and prognostic signatures through scRNA-Seq and bulk RNA-seq analyses.