building stuff for cancer genomics: @cbioportal @genomenexus

Brooklyn, NY
Joined March 2012
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=leDlA48N…
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🔧 Ino de Bruijn 🧬 retweeted
It was great to meet & chat with @inodb again! @AACR has been bringing friends and colleagues together for years. Thanks Ino for @cbioportal and HTAN- our #oncology network stays strong! #AACR26 @HarvardAlumni @MSKCancerCenter – at San Diego, CA
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🔧 Ino de Bruijn 🧬 retweeted
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).
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🔧 Ino de Bruijn 🧬 retweeted
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 lead this with the very best - @ronny_drapkin (@PennMedicine, Basser Center for BRCA) and @sorger_peter (@Harvard_Lab). The multiplex antibody imaging (CyCIF) data and GeoMx spatial transcriptomics can be explored in @cbioportal – the first such spatial dataset of its kind in cBioPortal. Many thanks to our friends at @MSKCancerCenter, especially @inodb and @nikolausschultz since our study does not include DNA sequencing … and we took liberty with the term “cancer genomics”! 😊) cbioportal.org/study/summary… This work would not be possible without the generosity of our funders and their belief in us including: grayfoundation.org/ (graybrcaatlas.org/) canaryfoundation.org/ ludwigcancerresearch.org/ The boldness to take this on was inspired by our time studying precancers in the @NCIHTAN Human Tumor Atlas Network, and supported by the technical know-how developed then. We hope that this data should provide a strong foundation for developing early detection and interception strategies for ovarian cancer. Great way to close 2024. But lots of work ahead after a brief rest. Coming right at you 2025! 🥳
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🔧 Ino de Bruijn 🧬 retweeted
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/10.1158/2159-8290.CD…
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🔧 Ino de Bruijn 🧬 retweeted
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
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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
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🔧 Ino de Bruijn 🧬 retweeted
Replying to @inodb
@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
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🔧 Ino de Bruijn 🧬 retweeted
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
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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-upd…
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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
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🔧 Ino de Bruijn 🧬 retweeted
Single Cells as text? We developed Cell2Sentence, a method that allows training of Large Language Models on single-cell data! biorxiv.org/content/10.1101/… With @danielflevine @SyedARizvi5688 @sachalevy3 @rahuldhodapkar @YaleSEAS @YaleMed #AI #ML #NLP #genomics #CompBio #singlecell
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🔧 Ino de Bruijn 🧬 retweeted
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
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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/a…
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🔧 Ino de Bruijn 🧬 retweeted
Excited to share Monopogen that performs SNV calling from single-cell DNA/RNA/ATAC-seq data, to enable cellular population genetics. nature.com/articles/s41587-0…. Thanks Rui Chen, @nicholas_navin, @shyam_lab, Li Ding, @czi @cziscience, #HTAN, @NatureBiotech collaborators/friends.
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🔧 Ino de Bruijn 🧬 retweeted
Evaluation of software impact designed for biomedical research: Are we measuring what's meaningful?ncbi.nlm.nih.gov/pmc/article…
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Check out the tools! Lmk if you'd like to add any or hate/love the UX :)
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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
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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
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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!
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