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 28

Assay: pulmonary ✕ Clear

RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

PMID 24643046 · PMC3958415 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 41

Infection of PAMs with either LV or Lena affects signaling pathways directly linked to the innate immune response, including IRF activation, RIG1-like receptors, TLRs and PKR pathways.

pulmonary prrsv-infected lena-infected 3-week-old rna-seq immunoperoxidase quantitative
Autophagy gene variant IRGM -261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains.

PMID 19750224 · PMC2735778 · PLoS pathogens · 2009 · 7 claims · 5 setups

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The IRGM −261TT genotype is negatively associated with (protective against) pulmonary TB caused by M. tuberculosis

pulmonary tuberculosis reporter genotyped case-control gene spoligotyping
Comprehensive analysis of the causal risk factor from hypertension associated with prognosis and therapeutic response in renal cell carcinoma by multi-omics analysis and validation.

PMID 41680825 · PMC12998095 · Biology direct · 2026 · 8 claims · 8 setups

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A 48-gene cross-species hypertension (HTN) gene module identified from human and SHR rat scRNA-seq can classify ccRCC patients into two molecular subgroups with distinct survival and targeted therapy response

aortic spontaneously tcga icgc single-cell bulk summary-data-based
Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.

PMID 35025971 · PMC8846506 · PLoS pathogens · 2022 · 8 claims · 8 setups

Has reproduction · 95

Acod1 expression and itaconate synthesis are induced in mouse lung during IAV infection and correlate with inflammation and disease severity

lung c57bl pbmcs macrophages bulk metabolomics histopathology
Proteomics technologies and challenges.

PMID 17893073 · PMC5054093 · Genomics, proteomics & bioinformatics · 2007 · 8 claims · 8 setups

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The proteome reflects the dynamic state of a cell, tissue, or organism more accurately than the genome, so proteomics is expected to yield better disease markers for diagnosis and therapy monitoring.

serum myeloid formalin-fixed general maldi-tof phage maldi
Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

PMID 39462326 · PMC11513636 · Molecular medicine (Cambridge, Mass.) · 2024 · 8 claims · 8 setups

Has reproduction · 81

scRNA-seq of PAH and control lung tissue identifies nine distinct cell populations with high heterogeneity in composition, function, distribution, and communication

lung pah scrna-seq-derived endothelial scrna-seq bulk cell-cell
Vγ1 γδ T cells steer airway macrophages toward a profibrotic response in an autochthonous lung cancer mouse model.

PMID 41779856 · PMC12959402 · Science advances · 2026 · 7 claims · 6 setups

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Lung tumors drive expansion of both CD27+ and CD27- pulmonary γδ T cells, which acquire distinct spatial and phenotypic changes in the tumor microenvironment

spc-cre+ microdissected sorted merged flow confocal single-cell
PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

PMID 41790620 · PMC12965534 · PloS one · 2026 · 7 claims · 7 setups

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PAH-former, a Geneformer model fine-tuned on public PAH scRNA-seq data, can perform in silico perturbation to identify and rank candidate PAH disease-associated genes

pah scrna-seq pah-former candidate scrna-seq transfer perturbation
Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

PMID 37666859 · PMC10477296 · Scientific reports · 2023 · 8 claims · 8 setups

Has reproduction · 20

AM and RPR (Huangqi-Chishao decoction) alleviate bleomycin-induced pathological lung fibrotic damage in rats

ipf common key rats microarray network protein-protein
Genetics and proteomics: deciphering gene association studies in critical illness.

PMID 16934133 · PMC1750993 · Critical care (London, England) · 2006 · 8 claims · 8 setups

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Most critical illnesses are complex traits (multifactorial), unlike single-gene Mendelian diseases.

severe families caucasian tnf genetic linkage microarray
Science review: searching for gene candidates in acute lung injury.

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

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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
Understanding the mechanisms of drug-associated interstitial lung disease.

PMID 15340376 · PMC2750813 · British journal of cancer · 2004 · 8 claims · 7 setups

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Apoptosis of alveolar/bronchial epithelial cells via Fas-FasL and mitochondrial (cytochrome c/caspase-9) pathways is a key mechanism underlying drug-, chemotherapy-, and radiation-associated lung injury and fibrosis

bronchial lung swiss mice immunohistochemistry toxicology pulmonary
FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

PMID 23768108 · PMC3691734 · BMC bioinformatics · 2013 · 8 claims · 8 setups

Has reproduction · 65

FusionQ is a novel tool that detects gene fusions, constructs chimerical transcript structures, and estimates their abundances from paired-end RNA-Seq data.

simulated four rna-seq randomly simulated paired-end read-mappability
Variants in the vitamin D receptor gene and asthma.

PMID 15651992 · PMC546000 · BMC genetics · 2005 · 8 claims · 6 setups

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VDR gene variants are candidate risk factors for asthma/allergy because vitamin D effects are mediated through the VDR and VDR maps to the 12q asthma linkage region

individuals children parents transmission bronchial pulmonary
Report of a Korean patient with cystic fibrosis, carrying Q98R and Q220X mutations in the CFTR gene.

PMID 16778407 · PMC2729969 · Journal of Korean medical science · 2006 · 7 claims · 8 setups

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The patient was diagnosed with cystic fibrosis based on elevated sweat chloride concentration and identification of two CFTR mutations.

korean forearm patient's lungs direct quantitative family
A spectrum of severe familial liver disorders associate with telomerase mutations.

PMID 19936245 · PMC2775683 · PloS one · 2009 · 7 claims · 8 setups

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Heterozygous telomerase loss-of-function mutations associate with, but are not deterministic of, a broad spectrum of hematologic and severe liver abnormalities.

leukocyte leukocytes reconstitution liver sanger flow telomerase
Causal models in epidemiology: past inheritance and genetic future.

PMID 16859537 · PMC1557493 · Environmental health : a global access science source · 2006 · 8 claims · 3 setups

Full-text index only

Interaction is a fundamental characteristic of any causal process involving probabilistic steps, not a second-order phenomenon identified after accounting for main effects

smokers population cohort observational biomarker pulmonary
Schistosoma mansoni secretes a chemokine binding protein with antiinflammatory activity.

PMID 16301741 · PMC2212990 · The Journal of experimental medicine · 2005 · 8 claims · 8 setups

Full-text index only

S. mansoni eggs secrete a chemokine binding protein (smCKBP) that binds certain chemokines and inhibits their interaction with host chemokine receptors and biological activity

mansoni u937 native baculovirus chemokine mass recombinant
Getting it right: being smarter about clinical trials.

PMID 16608383 · PMC1435786 · PLoS medicine · 2006 · 9 claims · 8 setups

Full-text index only

Bias and confounding in observational studies can produce misleading associations that are overturned by randomized trials (e.g., HRT).

postmenopausal general patients men randomized population-based large
RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.

PMID 24926665 · PMC4057123 · PloS one · 2014 · 8 claims · 8 setups

Has reproduction · 87

Dexamethasone treatment (1 µM, 18 h) of primary human ASM cells differentially regulates 316 genes, including both known and previously uninvestigated glucocorticoid-responsive genes.

airway asm most single rna-seq quantitative qrt-pcr

Experiments

RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence.

Autophagy gene variant IRGM -261T contributes to protection from tuberculosis caused by Mycobacterium tuberculosis but not by M. africanum strains.

Comprehensive analysis of the causal risk factor from hypertension associated with prognosis and therapeutic response in renal cell carcinoma by multi-omics analysis and validation.

Itaconate and derivatives reduce interferon responses and inflammation in influenza A virus infection.

Proteomics technologies and challenges.

Assessing personalized molecular portraits underlying endothelial-to-mesenchymal transition within pulmonary arterial hypertension.

Vγ1 γδ T cells steer airway macrophages toward a profibrotic response in an autochthonous lung cancer mouse model.

PAH-former: Transfer learning for efficient discovery of pulmonary arterial hypertension-associated genes.

Exploring the role and mechanism of Astragalus membranaceus and radix paeoniae rubra in idiopathic pulmonary fibrosis through network pharmacology and experimental validation.

Genetics and proteomics: deciphering gene association studies in critical illness.

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

Understanding the mechanisms of drug-associated interstitial lung disease.

FusionQ: a novel approach for gene fusion detection and quantification from paired-end RNA-Seq.

Variants in the vitamin D receptor gene and asthma.

Report of a Korean patient with cystic fibrosis, carrying Q98R and Q220X mutations in the CFTR gene.

A spectrum of severe familial liver disorders associate with telomerase mutations.

Causal models in epidemiology: past inheritance and genetic future.

Schistosoma mansoni secretes a chemokine binding protein with antiinflammatory activity.

Getting it right: being smarter about clinical trials.

RNA-Seq transcriptome profiling identifies CRISPLD2 as a glucocorticoid responsive gene that modulates cytokine function in airway smooth muscle cells.