Cytoscape announcements from core developers.
Joined October 2009
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Cytoscape retweeted
The NDEx IQuery paper is published in Bioinformatics!
Thanks to @xanderpico, @benjamingyori and the whole @NDExProject team for their hard work!
Read it now: bit.ly/3L63S0M
@WikiPathways @IndraSysBio @sigpathproject @signor_database @cbioportal @cytoscape #nciitcr
Cytoscape will again be participating in #GSOC 2023 as part of NRNB.org, with @cytoscapejs and others!
Calling all newcomers to open source to join us to work on #opensource #openscience #netbio projects: summerofcode.withgoogle.com/…
Cytoscape retweeted
Merry Christmas everyone! This weeks video is a small present from my group to you: a new version of @cytoscape stringApp featuring host–parasite interactions, improved support for heterogeneous networks, and group-wise enrichment analysis of clusters. youtu.be/pTJQzICz5Wc
📷 Semantic Annotation of Experimental Methods in Analytical Chemistry Palmblad et al., Anal Chem. doi: 10.1021/acs.analchem.2c03565. tmblr.co/ZhCnowcv-TVbee00
Cytoscape retweeted
Visualization of @cytoscape networks as interactive 3D multilayered graphs is now possible with the help of our #Arena3Dweb App.
apps.cytoscape.org/apps/aren…
📷 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! tmblr.co/ZhCnowcv1huJCq00
📷 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,... tmblr.co/ZhCnowcuOUGJ8a00
Cytoscape retweeted
#MyACSCover: @cytoscape visualization of 100 semantically annotated methods in @an_chem. pubs.acs.org/doi/10.1021/acs…
📷 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. tmblr.co/ZhCnowctlHT_ea00
Check out the latest version of RCy3 in this @Bioconductor release. Includes new image export functions and a handy selectEdgesAdjacentToNodes() function. #RStats #openscience
Package: bioconductor.org/packages/re…. Vignettes and workflows: cytoscape.org/cytoscape-auto….
Bioconductor 3.16 is Released. Thanks to all developers and community members for contributing to the project! Please see the full release announcement: bioconductor.org/news/bioc_3… #Rstats @Bioconductor
📷 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... tmblr.co/ZhCnowcsmdCw4q00
📷 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! tmblr.co/ZhCnowcs7QJM4i00
📷 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. tmblr.co/ZhCnowcs3KvYOy00
📷 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.... tmblr.co/ZhCnowcqWQf-0q00
Cytoscape retweeted
IQuery v1.4 is now released!
A new multi-method, pathway-based gene set interpretation tool integrated with @cytoscape and @NDExProject
Read the preprint: bit.ly/3TXZrpY
@WikiPathways @IndraSysBio @sigpathproject @signor_database @cbioportal @biorxiv_bioinfo #nciitcr
📷 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... tmblr.co/ZhCnowcptEiUmu00
📷 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... tmblr.co/ZhCnowcpE2nAea00
📷 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! tmblr.co/ZhCnowcoGESLSq00
Cytoscape retweeted
Next up for #ECRs:
A short interactive hands-on Multi-Omics #Data integration and visualisation workshop in early Nov.
Details in flyer :)
With @APBioNetorg #MABBI @bezmialem for #InSyB2022 over @cytoscape
@NIPGRsocial @SciComm_India @PhDsofIndia @unwomenasia @InSyBio – at Hillingdon, London
📷 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... tmblr.co/ZhCnowcnd1uQqm00