🔧 Ino de Bruijn 🧬
@inodb
building stuff for cancer genomics: @cbioportal @genomenexus
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Watch the excellent @cbioportal demo from Tali at #AACR2023! Helped me a lot to get a quick intro to the AACR GENIE BPC CRC dataset. Each video is only ~3 minutes, perfect for y'all busy people :)
Did you miss our presentations at #AACR2023? Now you can watch a series of videos from one of our talks which show how to use cBioPortal with data from the @AACR Project GENIE Biopharma Collaborative (BPC) colorectal cancer cohort youtube.com/watch?v=leDlA4…
youtube.com
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cBioPortal: Patient view using AACR GENIE - Biopharma Collaborative...
Learn about cBioPortal at #AACR25 next week! Visit us in the Exhibition Hall (Booth 3703) and come see our poster on Sunday afternoon presented by @inodb in the @AACR Project GENIE Use Cases Session (Section 48, Board 3).
YES! Excellent teamwork studying the development of fallopian tube precursors to high grade serous ovarian cancer. Very proud of the impressive effort by @TanjinaKader, @JiaRenLin, Clemens Hug, and team. A total joy to work with them and colleagues. And a delight to be able to…
This paper is the result of an incredibly fun collaboration with @SantagataMDPhD and Peter Sorger. Led by the fantastic @TanjinaKader with @JiaRenLin, we provide a pre-cancer atlas of Fallopian tube precursors to HGSOC. Don't miss our cbioportal entry of all the data!
Now in @CD_AACR: Multimodal Spatial Profiling Reveals Immune Suppression & Microenvironment Remodeling in Fallopian Tube Precursors to High-Grade Serous Ovarian Carcinoma - by @TanjinaKader, @JiaRenLin, Clemens Hug, @ronny_drapkin, @SantagataMDPhD, et al. doi.org/10.1158/2159-8…
Analysis & Visualization of Longitudinal Genomic & Clinical Data from the @AACR Project GENIE Biopharma Collaborative in cBioPortal—read this article featured in the AACR Journals Collection on AI and Data Science. bit.ly/3YrGjG4 @inodb @cbioportal #openaccess
On my way to the Festival of Genomics & Biodata in Boston! Will moderate a session on Data Sharing and present on Longitudinal Clinico-Genomic Data Analysis in cBioPortal leveraging #AACRProjectGENIEBPC data Registration is free, so check it out and come say hi!
1 day to go! ⏰ Tomorrow is the day! The Festival of Genomics & Biodata in Boston kicks off in less than 24 hours! Get ready for an amazing experience. Get your ticket now: hubs.la/Q02B1qjM0 #FOGBoston
@Inodb (Manager, Bioinformatics Software Engineering, @MSKCancerCenter) will be joining us at #FOGBoston to discuss big data sharing in cancer genomics. Want to hear more? Register now: hubs.la/Q02r2jHL0
If you want to learn more about AACR Project Genie while at #AACR24, read from @inodb on analyzing GENIE data in cBioPortal, and a pair of reviews discussing the use of big data in cancer research: bit.ly/4anrBDq bit.ly/3VKNSGN bit.ly/43Mg3ah @AACR
Stay up to date on the latest @cbioportal news!
Introducing the cBioPortal Newsletter! Stay updated with the latest developments, insights, and community highlights of cBioPortal. We'll be sharing valuable updates every few months. #cBioPortal #Newsletter linkedin.com/pulse/april-up…
Work with us on the open source @cbioportal for a summer!
Work on Open Source Software for a summer and support Cancer Research! Read more: github.com/cbioportal/gsoc
Single Cells as text? We developed Cell2Sentence, a method that allows training of Large Language Models on single-cell data! biorxiv.org/content/10.110… With @danielflevine @SyedARizvi5688 @sachalevy3 @rahuldhodapkar @YaleSEAS @YaleMed #AI #ML #NLP #genomics #CompBio #singlecell
An enormous thank you to @SamVolchenboum and his @PedsDataCommons team for hosting #ITCR2023 at @UChicago this year. It was an amazing three days with this #CancerInformatics community! itcr.cancer.gov
It's out y'all! A new @cbioportal paper! Super grateful for the opportunity to follow in the footsteps of @gaojj & @ecerami! The article highlights work from tons of people to improve joint longitudinal genomic & clinical data analysis in @cbioportal!
New cBioPortal paper by @inodb et al. in @CR_AACR Cancer Research: Analysis and visualization features for longitudinal genomic and clinical data from @AACR Project GENIE's Biopharma Collaborative (BPC). aacrjournals.org/cancerres/arti…
Excited to share Monopogen that performs SNV calling from single-cell DNA/RNA/ATAC-seq data, to enable cellular population genetics. nature.com/articles/s4158…. Thanks Rui Chen, @nicholas_navin, @shyam_lab, Li Ding, @czi @cziscience, #HTAN, @NatureBiotech collaborators/friends.
Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?ncbi.nlm.nih.gov/pmc/articles/P…
Check out the tools! Lmk if you'd like to add any or hate/love the UX :)
New cBioPortal paper by @inodb et al. in @CR_AACR Cancer Research: Analysis and visualization features for longitudinal genomic and clinical data from @AACR Project GENIE's Biopharma Collaborative (BPC). aacrjournals.org/cancerres/arti…
Work with the amazing @jmchan88!!
🎉Exciting News!🧬🔬 I’m starting a computational biology lab at Memorial Sloan Kettering Cancer Center in NYC! We're hiring at all levels to study how histological transformation and other forms of lineage plasticity drive progression across cancer types! joechanlab.org
These two incredible scientists, Dr. Sarah Suehnholz @OncoKB Senior Scientist & Ritika Kundra, Lead Software Liaison, showcasing @OncoKB w/ dedication & expertise. Meet them at booth 28161 or #ASCO23 poster #171 in Hall A poster 1pm. @gerlach_d we will connect later I’m sure!
Had a great discussion with @ritikakundra10 and @SPSuehnholz about @OncoKB at their booth 28161. Great resource and future visions shared for a deeper integration with cBioPortal. Missed @CDebyaniPhD unfortunately #ASCO23
Hope you caught our poster abt a new resource linked to @OncoKB & @cbioportal’s Genome Nexus called ReVUE = Repository of Variants w/ Unexpected Effects @ #AACR2023. Led by @inodb @nikolausschultz & me Funded by the ICI Go to cancerrevue.org & submit variants!
Come learn about cBioPortal at #AACR2023: Talks on Saturday by @NikolausSchultz at 8:30 AM in Room W224 (#NCIITCR session) as well as by Tali Mazor in Room W311 at 8:45 AM (@AACR Project GENIE session), a poster on Tuesday morning, and a booth in the exhibitor space (#1943).
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