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 34

System / cell line: prognosis ✕ Clear

Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.

PMID 38601155 · PMC11005030 · Frontiers in immunology · 2024 · 8 claims · 8 setups

Has reproduction · 71

Mitophagy-related genes associated with immune infiltration have diagnostic/prognostic significance in ALS

blood als microarray spearman univariate
Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.

PMID 35509605 · PMC9058021 · International journal of general medicine · 2022 · 8 claims · 8 setups

Has reproduction · 59

NSCLC samples can be classified into two molecular subtypes (C1 and C2) based on hypoxia-related gene expression via consensus clustering

tcga-nsclc geo bulk microarray unsupervised
Microarray analysis: genome-scale hypothesis scanning.

PMID 14551912 · PMC212694 · PLoS biology · 2003 · 8 claims · 5 setups

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Microarrays can be used to both test and generate hypotheses, not merely to fish for candidate genes.

drosophila yeast diffuse breast microarray integrated gene
Molecular tumor profiling: translating genomic insights into clinical advances.

PMID 15287965 · PMC507868 · Genome biology · 2004 · 8 claims · 8 setups

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Gene-expression profiling can distinguish BRCA1- and BRCA2-linked breast tumors from sporadic breast tumors with similar hormone-receptor status

breast ovarian panel tumor gene-expression candidate-gene large-scale
Using random walks to identify cancer-associated modules in expression data.

PMID 24128261 · PMC4015830 · BioData mining · 2013 · 8 claims · 8 setups

Has reproduction

Walktrap-GM, a random-walk community detection algorithm adapted with stopping criteria (maximum modularity, maximum size, maximum module score), identifies modules significantly enriched with cancer genes in expression-weighted interaction networks.

hepatocellular breast sporadic geo gene differential interaction
Thirty years into the genomics era: tumor viruses led the way.

PMID 17940630 · PMC1994808 · The Yale journal of biology and medicine · 2006 · 8 claims · 8 setups

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Restriction endonuclease-based analysis and sequencing of small tumor virus genomes (SV40, phiX174) established the technical framework later used to sequence bacterial and human genomes

sv40 bacteriophage epstein-barr aids-associated restriction recombinant sequencing
Prospective health care: the second transformation of medicine.

PMID 16522218 · PMC1431721 · Genome biology · 2006 · 8 claims · 7 setups

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Predictive biomarkers (genomic, proteomic, metabolomic) will enable quantification of disease risk and anticipation of onset before pathological damage occurs.

cancer circulating breast population gene-expression proteomic 21-gene
A P4HA2 hypoxia signature derived from single cell atlas stratifies conserved subtypes with prognostic significance in cervical squamous cell carcinoma.

PMID 41559646 · PMC12910786 · BMC cancer · 2026 · 6 claims · 8 setups

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A tumor cell metaprogram (MP7) identified from scRNA-seq of CSCC shows elevated hypoxia, invasion, metastasis, proliferation, and angiogenesis scores compared to other metaprograms.

cscc tcga-cscc mp7 siha single-cell bulk gene
PD-1 antibody-bound progenitor-exhausted CD8(+) T cells in lymph nodes boost PD-1-blockade anti-tumor immunity in gastrointestinal cancer.

PMID 41951588 · PMC13237225 · Nature communications · 2026 · 8 claims · 6 setups

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Progenitor-exhausted CD8+ T cells (CD8-Tpex, TCF7+PDCD1+) are enriched in proximal lymph nodes and proliferate at a high rate after ICI treatment

esophagogastric cancer surgically tcga scrna-seq scrna reanalysis
Mass spectrometry group has mass appeal.

PMID 15598607 · PMC1247668 · Environmental health perspectives · 2004 · 7 claims · 4 setups

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Mass spectrometry can identify proteins and their post-translational modifications with high specificity and sensitivity, making it central to toxicoproteomics.

sf9 experimental general mass proteomics combined
Have microarrays failed to deliver for developmental biology?

PMID 12225576 · PMC139405 · Genome biology · 2002 · 8 claims · 8 setups

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Despite predictions that microarrays would transform biology, very few published developmental biology microarray studies have generated novel insights.

drosophila caenorhabditis developing xenopus cdna genome-wide microarray
scSurv: a deep generative model for single-cell survival analysis.

PMID 41429574 · PMC12797213 · Bioinformatics (Oxford, England) · 2026 · 8 claims · 6 setups

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scSurv combines a Cox proportional hazards model with a deep generative model (VAE) of single-cell transcriptomes to estimate individual cellular contributions to clinical outcomes

simulated tcga melanoma renal scrna-seq bulk single-cell
Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

PMID 17625512 · PMC1948102 · Molecular systems biology · 2007 · 8 claims · 5 setups

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Current syndromic disease classification lacks specificity despite historically serving clinicians well

prostate neurodegenerative experimental genetic reverse-engineered protein-protein gene
A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.

PMID 41501133 · PMC12886967 · NPJ precision oncology · 2026 · 8 claims · 8 setups

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CSRGPS is a robust, machine-learning-derived prognostic signature that outperforms existing glioma prognostic models across multiple cohorts

tcga-gbm glioma meta consensus wgcna machine

Experiments

Developing a novel immune infiltration-associated mitophagy prediction model for amyotrophic lateral sclerosis using bioinformatics strategies.

Identifying Molecular Subtypes and 6-Gene Prognostic Signature Based on Hypoxia for Optimizing Targeted Therapies in Non-Small Cell Lung Cancer.

Microarray analysis: genome-scale hypothesis scanning.

Molecular tumor profiling: translating genomic insights into clinical advances.

Using random walks to identify cancer-associated modules in expression data.

Thirty years into the genomics era: tumor viruses led the way.

Prospective health care: the second transformation of medicine.

A P4HA2 hypoxia signature derived from single cell atlas stratifies conserved subtypes with prognostic significance in cervical squamous cell carcinoma.

PD-1 antibody-bound progenitor-exhausted CD8(+) T cells in lymph nodes boost PD-1-blockade anti-tumor immunity in gastrointestinal cancer.

Mass spectrometry group has mass appeal.

Have microarrays failed to deliver for developmental biology?

scSurv: a deep generative model for single-cell survival analysis.

Human disease classification in the postgenomic era: a complex systems approach to human pathobiology.

A machine learning-defined cellular senescence signature systematically enhances prognostication and guides immunotherapy strategies for the treatment of gliomas.