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).

• COVID-19 lung disease shares driver AT2 cytopathic features with Idiopathic pulmonary fibrosis.

  PMID 35870428 · PMC9297827 · EBioMedicine · 2022 · 8 claims · 8 setups

  Has reproduction · 85

  COVID-19 lung disease resembles IPF at a fundamental level, recapitulating ViP/IPF gene expression patterns, an IL15-centric cytokine storm, and AT2 cytopathic changes (injury, DNA damage, transient progenitor-state arrest, senescence/SASP).

  lung covid-19 interaction pre-clinical composite single-cell kaplan-meier

• Use of functional genomics to understand influenza-host interactions.

  PMID 17765704 · PMC7112328 · Advances in virus research · 2007 · 8 claims · 8 setups

  Full-text index only

  Functional genomics/microarray analysis provides a global view of host response to influenza infection that reveals virus-host interaction mechanisms not accessible by conventional techniques

  hela a549 lung texas cdna microarray infection

• Asthma investigators begin to reap the fruits of genomics.

  PMID 14611649 · PMC329104 · Genome biology · 2003 · 7 claims · 8 setups

  Full-text index only

  Microarray profiling of animal models of allergic asthma can identify novel differentially expressed candidate genes involved in inflammation and airway remodeling.

  monkey models lung inbred cdna oligonucleotide northern

• PulmonDB: a curated lung disease gene expression database.

  PMID 31949184 · PMC6965635 · Scientific reports · 2020 · 6 claims · 6 setups

  Has reproduction · 53

  PulmonDB is a curated, web-based gene expression database and R package integrating microarray and RNA-seq data for COPD and IPF with manually curated controlled-vocabulary annotation.

  lung ipf copd curated hierarchical differential

• Predicting survival within the lung cancer histopathological hierarchy using a multi-scale genomic model of development.

  PMID 16800721 · PMC1483910 · PLoS medicine · 2006 · 8 claims · 8 setups

  Full-text index only

  Multi-scale genomic similarities exist between four human lung cancer subtypes and the developing mouse lung, and these similarities are prognostically meaningful.

  perfused lung microarray principal wilcoxon

• Science review: searching for gene candidates in acute lung injury.

  PMID 15566614 · PMC1065043 · Critical care (London, England) · 2004 · 8 claims · 8 setups

  Full-text index only

  The candidate gene approach combined with an ortholog gene database and gene ontology analysis identifies ALI candidate genes, with blood coagulation and inflammation ontologies most highly represented

  lung canine pulmonary alveolar microarray gene immunoassay

• Systems biology and the host response to viral infection.

  PMID 18066032 · PMC7097743 · Nature biotechnology · 2007 · 8 claims · 8 setups

  Full-text index only

  Systems biology integration of 'omics data (transcriptomics, proteomics, genomics) with computational modeling is needed to fully understand virus-host interactions and identify novel antiviral targets

  lung cd4 rhesus kshv microarray quantitative genomic

• Interactome-transcriptome analysis reveals the high centrality of genes differentially expressed in lung cancer tissues.

  PMID 16188928 · PMC4631381 · Bioinformatics (Oxford, England) · 2005 · 7 claims · 4 setups

  Full-text index only

  Genes upregulated in squamous cell lung cancer are highly connected (well-connected) nodes in the protein interactome

  squamous ophid degs oligonucleotide interaction connectivity

• Cancer genomics identifies regulatory gene networks associated with the transition from dysplasia to advanced lung adenocarcinomas induced by c-Raf-1.

  PMID 19812696 · PMC2754338 · PloS one · 2009 · 8 claims · 5 setups

  Full-text index only

  Comparison of tumor, transgenic, and non-transgenic lung cells reveals distinct and overlapping regulatory gene networks associated with progression to adenocarcinoma.

  lung gene differentially significantly laser histology principal

• Developing prognostic gene panel of survival time in lung adenocarcinoma patients using machine learning.

  PMID 35117753 · PMC8799101 · Translational cancer research · 2020 · 7 claims · 4 setups

  Has reproduction · 32

  A panel of 22 genetic features with Naïve Bayes can predict whether lung adenocarcinoma patient survival time is >3 years (accuracy=75%, AUC=0.81).

  tcga-luad geo bulk expression methylation

• Autoencoder Networks Decipher the Association between Lung Cancer and Alzheimer's Disease.

  PMID 36518809 · PMC9744611 · Computational intelligence and neuroscience · 2022 · 7 claims · 6 setups

  Has reproduction · 74

  Autoencoder networks based on 266 shared DEGs reveal a comorbidity (positive) relationship between Alzheimer's disease and lung cancer.

  brain lung integrated shared microarray differential autoencoder

• Comprehensive analysis of transcriptomics and radiomics revealed the potential of TEDC2 as a diagnostic marker for lung adenocarcinoma.

  PMID 39553728 · PMC11569783 · PeerJ · 2024 · 8 claims · 8 setups

  Has reproduction · 80

  WGCNA identified 214 key genes in the blue module most correlated with LUAD

  tcga-luad merged tedc2-associated a549 wgcna differential machine

• The field of tissue injury in the lung and airway.

  PMID 19138985 · PMC2705781 · Cancer prevention research (Philadelphia, Pa.) · 2008 · 8 claims · 8 setups

  Full-text index only

  Field cancerization and the field of injury reflect molecular changes (genomic, epigenomic, transcriptomic, proteomic) present in histologically normal-appearing tissue distant from and independent of a tumor, throughout the carcinogen-exposed respiratory epithelium

  bronchial saliva resected paraffin-embedded whole-genome mtdna methylation-specific

• Partial correlation network analysis identifies coordinated gene expression within a regional cluster of COPD genome-wide association signals.

  PMID 39418301 · PMC11521246 · PLoS computational biology · 2024 · 7 claims · 4 setups

  Has reproduction · 23

  COPD GWAS loci are more spatially clustered across the genome than expected by chance, with significant enrichment on chromosome 4q.

  lung sakornsakolpat string bulk microarray gwas

• Digital sorting of complex tissues for cell type-specific gene expression profiles.

  PMID 23497278 · PMC3626856 · BMC bioinformatics · 2013 · 8 claims · 8 setups

  Has reproduction · 85

  The Digital Sorting Algorithm (DSA) deconvolves mixed tissue expression into cell type-specific profiles using only marker genes, without requiring prior knowledge of cell type frequencies or in vitro pure-cell profiles.

  liver im-9 immune deconvolved microarray simulation roc

• Identification and validation of a metabolic-related gene risk model predicting the prognosis of lung, colon, and breast cancers.

  PMID 39779736 · PMC11711664 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 74

  540 DEGs overlap across breast, colorectal, and lung cancers out of 11,384 DEGs analyzed

  breast colorectal lung common microarray kegg protein-protein

• Expression analysis of secreted and cell surface genes of five transformed human cell lines and derivative xenograft tumors.

  PMID 15836779 · PMC1112590 · BMC genomics · 2005 · 8 claims · 3 setups

  Full-text index only

  A custom 60-mer oligonucleotide microarray covering 3531 secreted and cell surface genes was designed to profile 5 transformed human cell lines and their derivative xenograft tumors.

  carcinoma derivative xenograft custom quantitative

• Integrated bioinformatics analysis screened the key genes and pathways of idiopathic pulmonary fibrosis.

  PMID 40280949 · PMC12032202 · Scientific reports · 2025 · 8 claims · 8 setups

  Has reproduction · 93

  5328 differentially expressed transcripts (4083 genes) were identified in GSE173355 by limma, with 4012 transcripts (3206 genes) confirmed by both limma and edgeR (logFC>1, FDR<0.05)

  ipf degs differentially bleomycin-induced bulk methylation kegg

• Transcriptome analysis reveals differential splicing events in IPF lung tissue.

  PMID 24647608 · PMC3960165 · PloS one · 2014 · 8 claims · 6 setups

  Has reproduction · 81

  873 genes are differentially expressed in IPF lung tissue versus healthy controls at FDR<5%, with more up-regulated than down-regulated genes.

  lung discovery gene gse24206 sequencing rna-seq real-time

• SurvConvMixer: robust and interpretable cancer survival prediction based on ConvMixer using pathway-level gene expression images.

  PMID 38539106 · PMC10967213 · BMC bioinformatics · 2024 · 7 claims · 6 setups

  Has reproduction · 77

  SurvConvMixer reformats KEGG Pathways-in-Cancer gene expression values into pathway-level 2D gene expression images and applies a ConvMixer-based model for overall survival prediction

  luad lung bulk gene machine