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 24

System / cell line: metastatic ✕ Assay: model ✕ Clear

A pan-cancer single-cell transcriptomic atlas of human bone metastases.

PMID 41619722 · PMC12923970 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

Full-text index only

Constructed a pan-cancer single-cell transcriptomic atlas of 62 human bone metastases (predominantly spinal) across 13 primary cancer types, with paired primary tumor and normal bone marrow samples.

bone paired plasmacytoma malignant scrna-seq ihc infercnv
Targeting the Lipid Metabolism Proteins FASN and GPAM in Alveolar Type II Cells Decreases Lung Metastasis.

PMID 41778850 · PMC7619144 · Cancer discovery · 2026 · 7 claims · 8 setups

Full-text index only

AT2 cells and surfactant lipids (e.g., PC, PE, PI, PG) are enriched in the vicinity of breast cancer lung metastases in both patients and mice

postmortem lungs lung at2 immunohistochemistry maldi-msi longitudinal
Can we find the genes involved in complex traits?

PMID 15461809 · PMC545590 · Genome biology · 2004 · 8 claims · 8 setups

Full-text index only

Large regions of the mouse genome exist in linkage disequilibrium (LD), including a 40 Mb region on the X chromosome, reflecting selection against recombination to preserve allelic combinations.

inbred strains 000-strain recombinant snp expression eqtl
ISG15-driven immune modulation and tumor progression in breast cancer metastasis: insights from single-cell and spatial transcriptomics.

PMID 41639695 · PMC12958617 · BMC medicine · 2026 · 8 claims · 8 setups

Full-text index only

CSC proportion is elevated in lymph node metastatic tumor tissue (BRCA_LNMT) compared to primary tumor (BRCA_PT)

4t1 brca tcga-brca top single-cell spatial bulk
The Ly6g(high) Neutrophil Subset Dictates Breast Cancer Lung Metastasis via CD8(+) T Cell Death.

PMID 41625479 · PMC12857760 · Cancer communications (London, England) · 2026 · 8 claims · 8 setups

Full-text index only

Neutrophils in the lung metastatic niche comprise two functionally distinct subsets, Ly6g^high and Ly6g^low, based on Ly6g expression level

lung cramp cd8+ neutrophils single-cell flow genetic
Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

PMID 15258335 · PMC3851082 · Disease markers · 2003 · 8 claims · 8 setups

Full-text index only

Proteomic pattern analysis of serum mass spectra, without identifying the underlying proteins, can distinguish cancer patients from healthy controls with high sensitivity and specificity.

serum frozen ig-depleted clinical seldi-tof maldi lc-ms
A Plastic EMP1+ to LGR5+ Cell State Conversion as a Bypass to KRASG12D Pharmacologic Inhibition in Metastatic Colorectal Cancer.

PMID 41128661 · PMC12877754 · Cancer discovery · 2026 · 8 claims · 8 setups

Full-text index only

RMC-9945 exerts durable antitumor activity in early-stage liver metastasis but has diminished therapeutic effect in advanced metastatic disease

aktp colorectal drug single-cell rnascope
A hormetic transcriptional program coregulates invasion, proliferation and dormancy to define metastatic potential.

PMID 41781391 · PMC13077004 · Nature communications · 2026 · 8 claims · 7 setups

Full-text index only

Prrx1 is a master regulator of dissemination that, beyond promoting invasion, represses proliferation (via Ccnd1/2, Cdkn2a/b/c) and activates a dormancy program (Gas6, Mme, Ogn)

infiltrating metabric facs-sorted pymt immunohistochemistry bioinformatic rt-qpcr
Single-cell profiling reveals distinct populations of tumor-associated macrophages and metastatic tumor cells in breast cancer brain metastasis.

PMID 42034645 · PMC13247122 · Cell death & disease · 2026 · 8 claims · 8 setups

Full-text index only

Single-cell profiling of BCBM identifies 12 tumor-associated macrophage (TAM) subtypes and 5 metastatic tumor cell (MTC) subtypes with distinct transcriptional profiles

brain breast scrna-seq tams scrna-seq bulk copy
Anti-CSF-1R therapy with combined immuno-chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched triple negative breast cancers.

PMID 41484081 · PMC12858953 · Nature communications · 2026 · 8 claims · 8 setups

Full-text index only

Combined low-dose CTX + anti-CSF-1R (SNDX-ms6352) is highly effective against aggressive metastatic Trp53-null TNBC models with high macrophage infiltration, producing complete tumor regression in claudin-low models.

trp53-null complete t12 cell-deficient imaging survival tumor
Development and validation of an oxidative phosphorylation based prognostic model revealing tumor progression and immune microenvironment in lung adenocarcinoma.

PMID 41670771 · PMC12996521 · Discover oncology · 2026 · 8 claims · 8 setups

Full-text index only

OXPHOS activity is significantly elevated in LUAD tumor tissue compared to adjacent normal tissue

tcga-luad geo lung single-cell bulk ssgsea cibersort
Glutamine-mediated crosstalk between M2 macrophages and tumor cells via the SLC38A5/FOXM1/CNIH4 axis promotes oral squamous cell carcinoma progression.

PMID 41715179 · PMC13020291 · Journal of translational medicine · 2026 · 8 claims · 8 setups

Full-text index only

Glutamine secretion from M2 macrophages to tumor cells via SLC38A5 is the core mCCC pathway upregulated in metastatic OSCC lesions compared to primary lesions.

oscc epithelial tcga-oscc hsc-3 scrna-seq hdwgcna bulk
From the gamma-glutamyl cycle to the glycan cycle: a road with many turns and pleasant surprises.

PMID 19840938 · PMC2787308 · The Journal of biological chemistry · 2009 · 8 claims · 8 setups

Full-text index only

γ-Glutamyl transpeptidase (GGT) activity in rat liver shows biphasic changes during azo dye-induced hepatocarcinogenesis, mirroring the oncofetal expression pattern of α-fetoprotein

liver tissues ascites hepatoma spectrophotometric enzyme glycan
geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.

PMID 33952321 · PMC8097837 · Genome biology · 2021 · 8 claims · 6 setups

Has reproduction · 75

geneshot identifies microbial genomic islands consistently associated with ICI response across independent cohorts

stool deduplicated cag reference gene-level novo co-abundance
Protocol for quantifying interaction patterns among genomic alterations in cancer.

PMID 41686643 · PMC12915222 · STAR protocols · 2026 · 6 claims · 5 setups

Full-text index only

Background-aware permutation strategies that constrain permutation per gene and per sample enable robust, scalable inference of condition-specific (context-aware) genetic interactions across cancer cohorts

msk-met somatic copy-number binary
Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN.

PMID 41547856 · PMC12917120 · Nature communications · 2026 · 8 claims · 8 setups

Full-text index only

GARDEN identifies and characterizes rare pathogenic cell populations/regions in spatial omics by embedding graph-based dynamic attention into a spatially-aware graph fusion contrastive model

breast anterior brain olfactory 10x starmap slide-seqv2
Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.

PMID 33086062 · PMC7649750 · Cell reports · 2020 · 8 claims · 8 setups

Has reproduction · 59

KMT2D is a potent tumor suppressor in melanoma

hmel-brafv600e tyr-creert2 tma kmt2d pooled xenograft genetically
Generative and integrative modeling for transcriptomics with formalin fixed paraffin embedded material.

PMID 41029822 · PMC12486589 · Journal of translational medicine · 2025 · 8 claims · 6 setups

Has reproduction · 67

The negative binomial distribution best fits fRNA-seq transcript counts, with little evidence supporting zero-inflated extensions

compendium ffpe simulated frna-seq statistical bulk integrity
The genomic analysis of lactic acidosis and acidosis response in human cancers.

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

Full-text index only

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
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

Experiments

A pan-cancer single-cell transcriptomic atlas of human bone metastases.

Targeting the Lipid Metabolism Proteins FASN and GPAM in Alveolar Type II Cells Decreases Lung Metastasis.

Can we find the genes involved in complex traits?

ISG15-driven immune modulation and tumor progression in breast cancer metastasis: insights from single-cell and spatial transcriptomics.

The Ly6g(high) Neutrophil Subset Dictates Breast Cancer Lung Metastasis via CD8(+) T Cell Death.

Diagnostic proteomics: serum proteomic patterns for the detection of early stage cancers.

A Plastic EMP1+ to LGR5+ Cell State Conversion as a Bypass to KRASG12D Pharmacologic Inhibition in Metastatic Colorectal Cancer.

A hormetic transcriptional program coregulates invasion, proliferation and dormancy to define metastatic potential.

Single-cell profiling reveals distinct populations of tumor-associated macrophages and metastatic tumor cells in breast cancer brain metastasis.

Anti-CSF-1R therapy with combined immuno-chemotherapy coordinate an adaptive immune response to eliminate macrophage enriched triple negative breast cancers.

Development and validation of an oxidative phosphorylation based prognostic model revealing tumor progression and immune microenvironment in lung adenocarcinoma.

Glutamine-mediated crosstalk between M2 macrophages and tumor cells via the SLC38A5/FOXM1/CNIH4 axis promotes oral squamous cell carcinoma progression.

From the gamma-glutamyl cycle to the glycan cycle: a road with many turns and pleasant surprises.

geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response.

Protocol for quantifying interaction patterns among genomic alterations in cancer.

Robust characterization and interpretation of rare pathogenic cell populations from spatial omics using GARDEN.

Enhancer Reprogramming Confers Dependence on Glycolysis and IGF Signaling in KMT2D Mutant Melanoma.

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

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

Characterizing Neutrophil Subtypes in Cancer Using scRNA Sequencing Demonstrates the Importance of IL1β/CXCR2 Axis in Generation of Metastasis-specific Neutrophils.