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 201

Assay: subtype ✕ Clear

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

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

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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
A unified framework for correcting batch effects and integrating multi-omics data.

PMID 41786846 · PMC13079841 · Scientific reports · 2026 · 7 claims · 6 setups

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MoDAmix, a four-stage domain adaptation framework (pre-training, single-omics adversarial adaptation, multi-omics adversarial alignment, semi-supervised class alignment), unifies batch correction across multiple omics layers.

brain aml same single-cell bulk k-means
Shared patterns of dysregulated gene expression across squamous cell carcinomas unveil predictors for prognosis and drug sensitivity.

PMID 41803163 · PMC13096486 · Scientific reports · 2026 · 8 claims · 6 setups

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SCCs from head and neck (HNSC), esophagus (ESCC), and cervix (CESC) share highly similar dysregulated gene expression patterns (DGEPs), whereas lung (LUSC) and skin (CSCC) SCCs are more molecularly distinct

tumor combined tcga differential sequencing weighted
A Soft Matrix Microenvironment Promotes Laterally Spreading Tumors via Oxidative Phosphorylation-Dependent Cell Adhesion.

PMID 41833005 · PMC13248847 · Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026 · 7 claims · 8 setups

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LSTs exhibit a more malignant phenotype than PAs, with higher inferred CNV scores, stronger genetic correlation with colorectal cancer, and downregulation of adhesion molecules

patients bulk colorectal epithelial clinical bulk single-cell
A cross-scale multimodal framework identifies clinically actionable immunotherapy biomarkers in melanoma through bulk to single-cell and spatial transcriptomics integration.

PMID 41840725 · PMC13104449 · Human genomics · 2026 · 7 claims · 8 setups

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Multi-omics consensus clustering (MOVICS) identifies two distinct SKCM molecular subtypes, CS1 and CS2

tcga-skcm meta-geo gtex melanoma multi-omics bulk transcriptome-wide
Single-cell transcriptomics reveals heterogeneous neutrophil populations and diagnostic biomarkers in atherosclerosis.

PMID 41847341 · PMC12989409 · Frontiers in physiology · 2026 · 8 claims · 8 setups

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Integration of scRNA-seq data from six human carotid samples identified 16 distinct cell subtypes after batch effect correction with Harmony

carotid neutrophil bulk c57bl scrna-seq hdwgcna lasso
Ectopic NMDAR expression in cancer unmasks germline-encoded autoimmunity.

PMID 41882353 · PMC13216075 · Nature · 2026 · 8 claims · 8 setups

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GluN1 and GluN2B NMDAR subunits are ectopically expressed in cancer cells of human TNBC tumours

breast tnbc 4t1-nmdar orthotopic bulk spatial immunofluorescence
Therapeutic manipulation and spatial quantification of the tumor microenvironment in colorectal cancer.

PMID 41907400 · PMC13018967 · iScience · 2026 · 8 claims · 8 setups

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Colorectal cancer fibroblast heterogeneity can be distilled into two overarching, transcriptomically distinct CAF populations marked by PDGFRA+ and ACTA2+ expression

crc colonic gemm scrna-seq multiplex bulk
Single-cell and spatial profiling of peripheral blood and synovium unveils pro-arthritis CNBP(+) myeloid cells.

PMID 41928282 · PMC13169754 · Journal of translational medicine · 2026 · 8 claims · 8 setups

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Peripheral CNBP+ monocytes are expanded and show elevated 'inflammatory response' pathway scores in arthritis patients

peripheral blood synovial arthritis single-cell bulk immunofluorescence
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
NuRepress: Inferring Transcriptional Repressors from Phased Nucleosome Architecture.

PMID 42074600 · PMC13115820 · Genes · 2026 · 7 claims · 8 setups

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NuRepress is a computational framework that predicts candidate transcriptional repressors by integrating repressive chromatin architecture, functional (accessibility) signatures, and transcriptional outcomes

pancreatic patski well-phased chip-seq atac-seq rna-seq
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
Emerging translational bioinformatics: knowledge-guided biomarker identification for cancer diagnostics.

PMID 19964620 · PMC5003034 · Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Annual International Conference · 2009 · 8 claims · 3 setups

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omniBiomarker, a web-based application, uses prior biological knowledge to identify the most biologically relevant gene ranking metric for a given clinical problem

renal microarray qrt-pcr computational
Clinical and genotypic findings in HIV-infected patients with the K65R mutation failing first-line antiretroviral therapy in Nigeria.

PMID 19644383 · PMC2815152 · Journal of acquired immune deficiency syndromes (1999) · 2009 · 8 claims · 3 setups

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K65R mutation is present in a substantial proportion (10.9%) of Nigerian patients failing first-line ART, including many with no prior tenofovir exposure

plasma k65r-positive hiv-1 comparative clinical
Social and ethical implications of genomics, race, ethnicity, and health inequities.

PMID 19000599 · PMC2892396 · Seminars in oncology nursing · 2008 · 8 claims · 5 setups

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Race and ethnicity are increasingly viewed as genetic surrogates for predicting disease risk and treatment response, though directly assessing genomic and environmental factors is more accurate.

population prostate non-small-cell breast genome-wide gene somatic
Endothelial Adgrl2 Expression and Alternative Splicing Controls the Cerebrovasculature.

PMID 41876233 · PMC13108381 · The Journal of neuroscience : the official journal of the Society for Neuroscience · 2026 · 8 claims · 5 setups

Has reproduction · 75

Endothelial cell-specific deletion of Adgrl2 impairs cerebrovascular integrity in mice

wild-type cortex brain single-molecule single-cell immunohistochemistry
Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics.

PMID 31918046 · PMC6992905 · iScience · 2020 · 8 claims · 8 setups

Has reproduction · 96

Assembled the largest reference blood gene expression profiling (GEP) dataset for AML to date: 12,029 samples from 105 studies across three platforms.

peripheral datasets hg-u133 disjoint bulk machine deep
DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.

PMID 34261540 · PMC8281595 · Genome medicine · 2021 · 8 claims · 7 setups

Has reproduction · 84

DeepProg is a novel ensemble framework of deep-learning and machine-learning approaches that robustly predicts patient survival subtypes using multi-omics data

cancer breast hepatocarcinoma tcga multi-omics gene rna-seq
Integrating multi-omics data reveals the antitumor role and clinical benefits of gamma-delta T cells in triple-negative breast cancer.

PMID 40197136 · PMC11974128 · BMC cancer · 2025 · 8 claims · 8 setups

Has reproduction · 59

High γδT cell infiltration is associated with favorable prognosis in TNBC but not in HR-positive or HER2-positive breast cancer

tnbc tcga-brca metabric single-cell bulk immunohistochemistry
Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.

PMID 38322112 · PMC10846924 · International journal of clinical practice · 2024 · 8 claims · 8 setups

Has reproduction · 71

AML cases can be categorized into two distinct PANRG (PANoptosis-related gene) clusters with differentially expressed prognostic genes (PRDEGs)

aml hovon cancer tcga bulk consensus machine

Experiments

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

A unified framework for correcting batch effects and integrating multi-omics data.

Shared patterns of dysregulated gene expression across squamous cell carcinomas unveil predictors for prognosis and drug sensitivity.

A Soft Matrix Microenvironment Promotes Laterally Spreading Tumors via Oxidative Phosphorylation-Dependent Cell Adhesion.

A cross-scale multimodal framework identifies clinically actionable immunotherapy biomarkers in melanoma through bulk to single-cell and spatial transcriptomics integration.

Single-cell transcriptomics reveals heterogeneous neutrophil populations and diagnostic biomarkers in atherosclerosis.

Ectopic NMDAR expression in cancer unmasks germline-encoded autoimmunity.

Therapeutic manipulation and spatial quantification of the tumor microenvironment in colorectal cancer.

Single-cell and spatial profiling of peripheral blood and synovium unveils pro-arthritis CNBP(+) myeloid cells.

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

NuRepress: Inferring Transcriptional Repressors from Phased Nucleosome Architecture.

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

Emerging translational bioinformatics: knowledge-guided biomarker identification for cancer diagnostics.

Clinical and genotypic findings in HIV-infected patients with the K65R mutation failing first-line antiretroviral therapy in Nigeria.

Social and ethical implications of genomics, race, ethnicity, and health inequities.

Endothelial Adgrl2 Expression and Alternative Splicing Controls the Cerebrovasculature.

Scalable Prediction of Acute Myeloid Leukemia Using High-Dimensional Machine Learning and Blood Transcriptomics.

DeepProg: an ensemble of deep-learning and machine-learning models for prognosis prediction using multi-omics data.

Integrating multi-omics data reveals the antitumor role and clinical benefits of gamma-delta T cells in triple-negative breast cancer.

Machine Learning-Based Integrated Analysis of PANoptosis Patterns in Acute Myeloid Leukemia Reveals a Signature Predicting Survival and Immunotherapy.