Cytoscape Publications

Showcase for publications using Cytoscape or describing Cytoscape apps. www.cytoscape.org

[cytoscape-publications]

Semantic Annotation of Experimental Methods in Analytical Chemistry Palmblad et al., Anal Chem. doi: 10.1021/acs.analchem.2c03565.

[cytoscape-publications]

Identification of hub ferroptosis-related genes and immune infiltration in lupus nephritis using bioinformatics. Hu, et al., Scientific reports doi: 10.1038/s41598-022-23730-8.

Cytoscape cited!

[cytoscape-publications]

Lymphatic metastasis-associated circRNA‒miRNA‒mRNA network for exploring the pathogenesis and therapeutic target of triple negative breast cancer based on whole-transcriptome sequencing analysis: an experimental verification study. Luo, et al., Journal of translational medicine doi: 10.1186/s12967-022-03728-6.

[cytoscape-publications]

Single-cell profiling reveals distinct adaptive immune hallmarks in MDA5+ dermatomyositis with therapeutic implications. Ye, et al., Nature communications doi: 10.1038/s41467-022-34145-4.

[cytoscape-publications]

Integrated network pharmacology and experimental analysis unveil multi-targeted effect of 18α- glycyrrhetinic acid against non-small cell lung cancer. Irshad, et al., Frontiers in pharmacology doi: 10.3389/fphar.2022.1018974.

cytoHubba is available from the Cytoscape App Store.

Cytoscape cited!

[cytoscape-publications]

Systematic analysis of circRNA biomarkers for diagnosis, prognosis and therapy in colorectal cancer. Xiao, et al., Frontiers in genetics doi: 10.3389/fgene.2022.938672.

Cytoscape cited!

[cytoscape-publications]

Bioinformatics analysis constructs potential ferroptosis-related ceRNA network involved in the formation of intracranial aneurysm. Zhu, et al., Frontiers in cellular neuroscience doi: 10.3389/fncel.2022.1016682.

[cytoscape-publications]

Identification of DNA methylation-regulated differentially expressed genes in RA by integrated analysis of DNA methylation and RNA-Seq data. Zhang, et al., Journal of translational medicine doi: 10.1186/s12967-022-03664-5.

ReactomeFIPlugIn is available from the Cytoscape App Store.

[cytoscape-publications]

A proteome-scale map of the SARS-CoV-2–human contactome. Kim et al., Nat Biotechnol. 2023; 41(1): 140–149.

[cytoscape-publications]

Inhibition of mTOR signaling protects human glioma cells from hypoxia-induced cell death in an autophagy-independent manner. Divé, et al., Cell death discovery doi: 10.1038/s41420-022-01195-y.

The WikiPathways app is available from the Cytoscape App Store.

Cytoscape cited!

[cytoscape-publications]

Characterization of serum protein expression profiles in the early sarcopenia older adults with low grip strength: a cross-sectional study. Wu, et al., BMC musculoskeletal disorders doi: 10.1186/s12891-022-05844-2.

cytoHubba is available from the Cytoscape App Store.

Cytoscape cited!

[cytoscape-publications]

Transcriptomic analysis of paternal behaviors in prairie voles. Duclot, et al., BMC genomics doi: 10.1186/s12864-022-08912-y.

EnrichmentMap is available from the Cytoscape App Store.

Cytoscape cited!

[cytoscape-publications]

Effect and mechanisms of kaempferol against endometriosis based on network pharmacology and in vitro experiments. Zhao, et al., BMC complementary medicine and therapies doi: 10.1186/s12906-022-03729-4.

cytoHubba is available from the Cytoscape App Store.

[cytoscape-publications]

Interleukin-22 regulates neutrophil recruitment in ulcerative colitis and is associated with resistance to ustekinumab therapy. Pavlidis, et al., Nature communications doi: 10.1038/s41467-022-33331-8.

stringApp is available from the Cytoscape App Store.

Cytoscape cited!

[cytoscape-publications]

Translatome profiling in fatal familial insomnia implicates TOR signaling in somatostatin neurons. Bauer, et al., Life science alliance doi: 10.26508/lsa.202201530.

[cytoscape-publications]

Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes. Mach, et al., Communications biology doi: 10.1038/s42003-022-03977-7.

[cytoscape-publications]

Tissue-specific pathway activities: A retrospective analysis in COVID-19 patients. Pham, et al., Frontiers in immunology doi: 10.3389/fimmu.2022.963357.

Cytoscape cited!