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: interaction ✕ Assay: copy ✕ Clear

Protocol for quantifying interaction patterns among genomic alterations in cancer.

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

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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
Single-Cell RNA Analysis of Murine Osteosarcoma Uncovers Skp2 Function in Metastasis, Genomic Instability, and Immune Activation and Reveals Additional Target Pathways.

PMID 41877584 · PMC13103941 · Cancer research communications · 2026 · 8 claims · 6 setups

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Skp2 KO improves survival, drives apoptosis, and induces antitumor immunity in Rb1/Trp53-deficient murine osteosarcoma

tumors same osteosarcoma skp2 scrna-seq mutation copy-number
Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

PMID 39759507 · PMC11695424 · Frontiers in immunology · 2024 · 8 claims · 8 setups

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A malignant cell subtype in PCa with high expression of NEFH was identified, located at the differentiation terminal, showing higher malignancy and association with advanced tumor lesions.

pca malignant tcga mda single-cell infercnv pseudotime
Single-cell transcriptomic analysis reveals intra-tumoral heterogeneity and immunotherapy strategies in high-grade serous ovarian cancer.

PMID 41907410 · PMC13018870 · iScience · 2026 · 8 claims · 8 setups

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scRNA-seq of 17 HGSOC tissue samples reveals seven major cell types and extensive intra-tumoral heterogeneity

hgsoc epithelial tcga gse165897 single-cell copy kegg
Wnt3-mediated fibrosis and carcinogenesis of lung squamous cell carcinoma in idiopathic pulmonary fibrosis.

PMID 42063567 · PMC13127482 · iScience · 2026 · 8 claims · 8 setups

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LUSC arising within UIP originates from AT2-derived metaplastic basal cells

fresh-frozen same scrna-seq paired single-cell copy ligand-receptor
A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

PMID 41844817 · PMC13111741 · Discover oncology · 2026 · 8 claims · 8 setups

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MTRNR2L8 is markedly upregulated in RCRC tumor cells and is associated with poorer patient survival

crc epithelial rcrc tcga-read scrna-seq copy gene
Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

PMID 42043480 · PMC13115984 · Cancer medicine · 2026 · 8 claims · 8 setups

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EGFRI eligibility (defined by left-sidedness, RAS/BRAF wild-type, MSS) stratifies cancer cell transcriptomic characteristics more strongly than sidedness alone.

crc epcam+ aggregated cancer scrna-seq copy pseudobulk
Nutrigenomics: the genome--food interface.

PMID 18087577 · PMC2137135 · Environmental health perspectives · 2007 · 8 claims · 8 setups

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Nutrigenomics integrates genomic science with nutrition to study how dietary components affect gene expression, the proteome, and the metabolome.

general humans lymphocytes healthy snp controlled micronucleus
Protein co-evolution, co-adaptation and interactions.

PMID 18818697 · PMC2556093 · The EMBO journal · 2008 · 8 claims · 6 setups

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The mirrortree method predicts protein-protein interactions by detecting pairs of protein families with similar phylogenetic trees (quantified as Pearson correlation of sequence similarity matrices).

nuoe intra-protein coli interacting phylogenetic correlated domain-restricted
Sequencing the regulatory genome.

PMID 18598374 · PMC2481419 · Genome biology · 2008 · 8 claims · 8 setups

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Nuclear-lamina-associated domains (LADs) define chromatin regions with distinct transcriptional characteristics (fewer, lower-expressed genes, low RNA Pol II occupancy, H3K27me3-enriched borders)

interphase nine beta-globin drosophila nuclear digital chip
Single-cell RNA sequencing of adenoid cystic carcinoma of the breast reveals cellular heterogeneity and tumor microenvironment features.

PMID 41761191 · PMC13041279 · BMC medical genomics · 2026 · 8 claims · 7 setups

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H19+ myoepithelial cells (H19+myoEpC) represent the dominant malignant subpopulation in ACCB, characterized by the majority of large-scale CNVs and high expression of oncogenic pathway genes and ligands (e.g., LAMB1, WNT6)

tumor hnacc epithelial accb single-cell scrna-seq copy
Dissecting tumor heterogeneity in colorectal cancer: uncovering the role of BCL2L1(+) cells through single-cell analysis.

PMID 41958675 · PMC13056825 · Frontiers in immunology · 2026 · 8 claims · 8 setups

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scRNA-seq identifies five CRC tumor cell subtypes, with the C4 BCL2L1+ subtype predominantly enriched in liver metastases and showing enhanced proliferation, metabolic reprogramming, and anti-apoptotic activity

crc epcs malignant tcga scrna-seq infercnv cytotrace
Dissecting origin factors of lymph node metastasis in non-small cell lung cancer via multimodal omics.

PMID 41975179 · PMC13250061 · Nature communications · 2026 · 8 claims · 8 setups

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Epithelial cells in mLNs and matched mLN+ primary tumors (mLN+PTs) show enhanced cancer stemness (higher CytoTRACE scores) compared to mLN-negative and normal samples.

patient-matched mln epithelial tcga-luad scrna-seq spatial cytotrace
Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).

PMID 39578472 · PMC11584678 · Scientific data · 2024 · 8 claims · 8 setups

Has reproduction · 90

Two T2T gap-free haplotype assemblies of C. sonnerati (YSFRI_Csonn_HA_1.0 and YSFRI_Csonn_HB_1.0) were successfully generated, each spanning 24 chromosomes with no gaps.

cephalopholis analysis next-generation pacbio ont
Genome-wide signatures of convergent evolution in echolocating mammals.

PMID 24005325 · PMC3836225 · Nature · 2013 · 8 claims · 8 setups

Has reproduction

Genome-wide convergent sequence evolution between echolocating lineages is not rare but widespread and continuously distributed, with signatures consistent with convergence in nearly 200 loci out of 2,326 examined.

four raw orthologous mammalian whole-genome novo homology-based
The potential of optical proteomic technologies to individualize prognosis and guide rational treatment for cancer patients.

PMID 19756916 · PMC2778706 · Targeted oncology · 2009 · 8 claims · 5 setups

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Genomic/gene expression profiling alone is insufficient to identify tumors with molecular pathway changes predictive of treatment outcome; protein-level functional assessment (activation states, PTMs, interactions) is also required

microarray ffpe models cancer immunohistochemistry fret fret-flim
Chromosome-Level Genome Assembly and Annotation of Piptanthus nepalensis (Hook.) Sweet.

PMID 41912568 · PMC13199499 · Scientific data · 2026 · 7 claims · 8 setups

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A chromosome-scale genome assembly of P. nepalensis was generated by integrating PacBio HiFi long reads, Illumina short reads, and Hi-C chromatin interaction data.

nepalensis assembled illumina whole-genome hi-c rna-seq
Cross-tissue atlas of mucosa-associated lymphoid tissue lymphomas reveals intratumoral heterogeneity and microenvironmental subtypes.

PMID 42066772 · PMC13198276 · Cell reports. Medicine · 2026 · 8 claims · 8 setups

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Integrative bulk, single-nucleus, and spatial RNA-seq analysis identifies three LME subtypes in MALT lymphoma: LME1 (mesenchymal), LME2 (inflammatory), and LME3 (depleted).

malt ffpe snrna-seq-derived snrna-seq bulk single-nucleus spatial
Single-Cell Sequencing Reveals γδT Cell Heterogeneity Under Distinct Microsatellite Statuses as a Potential Biomarker for Immunotherapy and Prognosis in Colorectal Cancer.

PMID 42074506 · PMC13116210 · Genes · 2026 · 7 claims · 8 setups

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γδT cells in colorectal cancer form five distinct subsets (C0_FCER1G, C1_IL7R, C2_CD81, C3_TOP2A, C4_CXCL13) with distinct marker genes and functional states

crc γδt epithelial c4_cxcl13 single-cell differential pseudotime
Whither genomics?

PMID 11104516 · PMC138820 · Genome biology · 2000 · 8 claims · 8 setups

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Genomics is both a science (understanding genome structure/evolution) and a tool (learning gene function) that collects comprehensive data on all genes, in contrast to genetics which studies a few genes controlling a phenotype

mammalian budding yeast general expression genome-wide synthetic

Experiments

Protocol for quantifying interaction patterns among genomic alterations in cancer.

Single-Cell RNA Analysis of Murine Osteosarcoma Uncovers Skp2 Function in Metastasis, Genomic Instability, and Immune Activation and Reveals Additional Target Pathways.

Unveiling the NEFH+ malignant cell subtype: Insights from single-cell RNA sequencing in prostate cancer progression and tumor microenvironment interactions.

Single-cell transcriptomic analysis reveals intra-tumoral heterogeneity and immunotherapy strategies in high-grade serous ovarian cancer.

Wnt3-mediated fibrosis and carcinogenesis of lung squamous cell carcinoma in idiopathic pulmonary fibrosis.

A differential single-cell transcriptome atlas of left-sided and right-sided colorectal cancer.

Multi-Transcriptomic Analysis Reveals That EREG-Driven TME Crosstalk Defines Anti-EGFR Response in Colorectal Cancer.

Nutrigenomics: the genome--food interface.

Protein co-evolution, co-adaptation and interactions.

Sequencing the regulatory genome.

Single-cell RNA sequencing of adenoid cystic carcinoma of the breast reveals cellular heterogeneity and tumor microenvironment features.

Dissecting tumor heterogeneity in colorectal cancer: uncovering the role of BCL2L1(+) cells through single-cell analysis.

Dissecting origin factors of lymph node metastasis in non-small cell lung cancer via multimodal omics.

Gap-free telomere-to-telomere haplotype assembly of the tomato hind (Cephalopholis sonnerati).

Genome-wide signatures of convergent evolution in echolocating mammals.

The potential of optical proteomic technologies to individualize prognosis and guide rational treatment for cancer patients.

Chromosome-Level Genome Assembly and Annotation of Piptanthus nepalensis (Hook.) Sweet.

Cross-tissue atlas of mucosa-associated lymphoid tissue lymphomas reveals intratumoral heterogeneity and microenvironmental subtypes.

Single-Cell Sequencing Reveals γδT Cell Heterogeneity Under Distinct Microsatellite Statuses as a Potential Biomarker for Immunotherapy and Prognosis in Colorectal Cancer.

Whither genomics?