Developed @UCSanDiego, NDEx is an open source software infrastructure to store, share and publish biological network knowledge
La Jolla, CA
Joined September 2015
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The NDEx Project retweeted
Now online in @CD_AACR: Cancer Mutations Converge on a Collection of Protein Assemblies to Predict Resistance to Replication Stress - by @Xiaoyu_SysBio @aksinghal90 @TreyIdeker and colleagues doi.org/10.1158/2159-8290.CD… @UCSanDiego @UCSDCancer #MachineLearning
The NDEx Project retweeted
Looking for a new way to measure impact metrics for your database?
Introducing MBDBMetrics; an online tool designed to measure the impact of any biological data resource, freely accessible via Google Colab and GitHub.
Find out more and try MBDBMetrics👇
academic.oup.com/bioinformat…
ALT Title and authors of a journal article
The NDEx Project retweeted
In a world first, the UK medicines regulator has approved a therapy that uses CRISPR gene editing as a treatment for diseases go.nature.com/3QDtwuV
The NDEx Project retweeted
**We are moving platforms**
Bioconductor will cease posting on Twitter/X as of December 17, 2023. Instead we will be continuing to post on other social media platforms that better reflect our community’s code of conduct. Read more in our blog post: buff.ly/3RddEAV
ALT Moving Platforms Post for Bioconductor
The NDEx Project retweeted
Interested in programmatic access to the UniProt database using Python - protein entry searches, data filtering, batch downloads & further processing of downloaded target data? Sign up for our next free webinar ebi.ac.uk/training/events/pr…
16 Nov 2023, 15:30-16:30 (UK) @EBItraining
The NDEx Project retweeted
Our review+perspective paper on "Current and future directions in network biology" is online (arxiv.org/abs/2309.08478). This has been a Herculean effort by many co-authors, thank you all! Special thanks to @marinkazitnik, @_michellemli, @aydin_wells, and all section coordinators.
The NDEx Project retweeted
Improved the @NDExProject linking. Now linked via the @HGNC gene symbol, instead of the name.
The range of #protein path visualizations presented is truly impressive.
Link: conze.pt/explore/Calumenin?l…
Explore all the human protein encoding genes: tinyurl.com/52fzfwx3
The NDEx Project retweeted
Super excited to share with you the results of the CPTAC PanCancer Driver project, today officially out at @cellcellpress!
sciencedirect.com/science/ar…
Here’s a short tweetorial with the main findings where our lab mostly contributed
The NDEx Project retweeted
Top 50 most popular tools for pathway analysis.
1. Overrepresentation analysis (ORA) using a gene list
2. Functional class scoring (FCS) using expression data or some metrics.
Based on a survey by @mdziemann's group journals.plos.org/ploscompbi…
The NDEx Project retweeted
#DrugstOne: Turn your #Bioinformatics tool into a powerful, interactive #DrugRrepurposing 💊 webtool in <15mins with 3 lines of code. Check out drugst.one/call/ and join our initiative and publication (arxiv.org/abs/2305.15453). @janbaumbach @MichiHartung @MajoreAndi
The NDEx Project retweeted
The deadline was extended - so students, don’t wait!
The dkNET Summer of Data Student Program applications are due May 8, 2023! (dknet.org/about/Summer-Progr…)
#FAIRdata #OpenScience #reproducibility #rigor
The NDEx Project retweeted
Ever seen ads for #taltz on TV and wondered what its MOA is in resolving psoriasis? Wonder no more - collaborating with @EliLilly and @NDExProject we show how Taltz blocks an IL17A-MuvB pathway to inhibit keratinocyte proliferation in clinical #psoriasis bit.ly/3JVUKcU
The NDEx Project retweeted
We have released version 0.3.0 of the #OntologyAccessKit #oaklib github.com/INCATools/ontolog…. Includes preliminary compatibility with cytoscape CX format and @NDExProject, upgrade to the latest @bioregistry, and more support for working with the @OBOFoundry #RelationOntology!
The NDEx Project retweeted
Can't recommend this free 2-day #GeneOntology workshop enough!! If you can get to Rome the week after #biocuration2023, sign up now. Space is limited and yes the instructors are absolutely fantastic! @UCLgene @MINT_database
Join the Rome-UCL bioinformatics workshop in May @BiologiaUniRM2 with Ruth Lovering @UCLgene and Luana Licata @MINT_database
Registration free but essential: tinyurl.com/UCL-Rome-bioinfo…
The NDEx Project retweeted
I'm hiring for a position in the software development team at the Ideker Lab, UC San Diego. The position is closely integrated with the research in the lab and also the @cytoscape and @NDExProject projects. employment.ucsd.edu/research…
The NDEx Project retweeted
Would you like to use @HMSBioPlex data in your bioinformatics analyses? Now there's a package (or two) for that! For details, see our brand new tech note on BioPlexR and BioPlexPy to access our data in R and Python. buff.ly/3I6MoOx
The NDEx Project retweeted
SPP has been shortlisted for the @NIH and #FASEBdataworks prize, which recognizes data reuse in scientific discovery. With @NDExProject and @dkNET_Info we built a web resource for the role of circulating immune cells in #t1d. Vote for our entry here! bit.ly/3VmtM2o
The NDEx Project retweeted
Integration with the biochem project @NDExProject
"NDEx uses selected pathway and interactome networks in NDEx to power gene set analysis. The networks come from many different sources"
conze.pt/explore/RUNX2?l=en&…
Any recommend. for better presenting biochem are welcome! #biochem
The NDEx Project retweeted
The iQuery results include our curated pathways and 32k pathway figures that we extracted and OCR’d from the literature. Great tool for quickly searching our databases for enriched sets of genes.
The NDEx Project retweeted
Check out the new iQuery search tool on our front page. Enter your genes or proteins of interests and get enriched networks, pathways, figures and GO terms. Powered by @NDExProject. Then open the results in Cytoscape with a single click. cytoscape.org/