https://xitter.cf/t.co/aAS4gMRIMH | Cancer & Systems Biology | Spatial Technology | https://xitter.cf/t.co/upSMOQyqsp | Postdocs wanted! (https://xitter.cf/t.co/4ulDLFgrbS)
Boston
Joined August 2012
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Excited to see our new preprint out where we introduce dbverse! 🧬 It’s a big step toward making spatial omics analysis of massive datasets accessible to everyone.
biorxiv.org/content/10.64898…
We’ve already used dbverse to make Giotto Suite more scalable (GiottoDB) and extend it to genomic analysis (GiottoSeq).
github.com/giotto-suite
Check out the website dbverse-org.github.io/dbvers… and this thread from first author @Ed2uiz for a great summary! 👇 xitter.cf/Ed2uiz/status/20883758…
Can modern databases scale scientific analyses beyond RAM?
During my PhD, I explored whether matrix, spatial, and genomic operations could share a database execution layer without changing the APIs scientists rely on.
Today, I’m excited to finally share dbverse, a composable database framework built around that idea.
Across benchmarks, dbverse delivers up to 1,000× speedups and scales end-to-end spatial omics analyses to millions of cells on a 16 GB M4 Mac mini.
Paper: biorxiv.org/content/10.64898…
1/🧵
Ruben Dries retweeted
Got reviews back for a manuscript today, completely AI generated. 🫤
How should I respond?
Ruben Dries retweeted
🧵 Excited to share a study led by graduate student #JeannaQiu, now online @CCR_AACR 👉tinyurl.com/2anxps7x
We built a detailed single-cell atlas of pancreatic neuroendocrine tumors (PNETs) & found diverse cancer cell states and a glutamate signaling axis driving aggression.👇
Ruben Dries retweeted
Giotto Suite provides a comprehensive, flexible and scalable platform for technology-agnostic spatial omics analysis using R.
@GiottoSpatial @RnDries @gc_yuan @jiaji_g_chen @josschavezf1
nature.com/articles/s41592-0…
Very proud to finally publish Giotto Suite after many years of hard work. It's a big milestone for our lab and will be a massive stepping stone for our ongoing projects and ideas. Take a look at giottosuite.com and feel free to share feedback and ideas for improvement.
Thrilled to announce our new Nature Methods paper: Giotto Suite: an extensible, technology-agnostic ecosystem for spatial multiomics analysis.
Big thanks to co-first authors @jiaji_g_chen & @josschavezf1, and all Giotto devs in @RnDries & @gc_yuan labs! nature.com/articles/s41592-0…
Ruben Dries retweeted
Thrilled to announce our new Nature Methods paper: Giotto Suite: an extensible, technology-agnostic ecosystem for spatial multiomics analysis.
Big thanks to co-first authors @jiaji_g_chen & @josschavezf1, and all Giotto devs in @RnDries & @gc_yuan labs! nature.com/articles/s41592-0…
Ruben Dries retweeted
Thank you @ISEH for shining a light on our group! 🔦 It fills me with pride to introduce our amazing team @CReM_Boston @The_BMC @BUMedicine and we love being part of the wonderful experimental hematology research community! 🔬🩸
This week on #SimplyBlood🩸 we are spotlighting the Vanuytsel Lab (@kim_vanuytsel) and the work they are doing through the Center for Regenerative Medicine, Boston University. Read more about their lab on simplyblood.org/
Ruben Dries retweeted
This week Nick Eagles did a journal club presentation for my team on #GiottoSuite by @jiaji_g_chen @josschavezf1 et al from @gc_yuan @RnDries labs
Check the 📽️ below 👇🏽
📜 doi.org/10.1101/2023.11.26.5…
📽️ youtu.be/iG_HvBUSeoA
#SpatialTranscriptomics @Bioconductor #RStats
Ruben Dries retweeted
Earlier this week we carried out a preliminary analysis of our first @10xGenomics Xenium prime (5,000 gene) run. We had designed this experiment to get a sense of how the prime chemistry performed compared to the Xenium V1 chemistry.
Ruben Dries retweeted
Repo is at github.com/drieslab/dbverse
@RnDries
Ruben Dries retweeted
Ruben Dries @RnDries gave a great talk about #Giotto Suite which provides a great framework for analyzing spatial 🖼️ transcriptomics data
Preprint 🗞️
doi.org/10.1101/2023.11.26.5…
They are hosting a free workshop August 5-7, 2024. Sign up below 👇🏽
docs.google.com/forms/u/0/d/…
#FOGBoston
❤️ fASHtastic!
Happy Valentine's Day! 💕
We're showing our love to Dr. Kim Vanuytsel (@kim_vanuytsel) from @BUMedicine who is one of 36 recipients of the 2024 Scholar Awards from @ASH_hematology.
Congratulations! 🙌
Read more about Dr. Vanuytsel's work: bit.ly/49BiuOE
Ruben Dries retweeted
📢 It has been some time since #RStats {data.table} last major update in Feb 2021, but now it strikes back!
🚀 There are 41 new features in this release (v1.15).
👇 Below are the five features that I’m most excited about - the last one will blow your mind™!
🏃♂️ Lets’ go.
ALT A whimsical illustration featuring a large, yellow walrus with two long tusks, holding a lightsaber on a snowy landscape under a bright blue sky. The title “DATA TABLE STRIKES BACK” is displayed prominently at the top.
Wow!
Just posted a preprint on our new spatial genomic recording system, baseMEMOIR.
biorxiv.org/content/10.1101/…
Motivation: Cells divide, differentiate, and migrate to form exquisitely organized tissues. Reconstructing the dynamic histories of individual cells, including their lineage relationships and ancestral states, is essential for understanding how intrinsic and extrinsic signals generate tissues during development and in regenerative medicine.
Engineered genomic recording systems can reconstruct cell lineage histories from endpoint measurements. However, existing methods either require sequencing (disrupting spatial organization) or have been limited in memory size and scalability.
To address this need, @ChadlyDuncan, Kirsten Frieda, and others in the lab created a high memory capacity image-readable recording system termed baseMEMOIR.
Ruben Dries retweeted
🚨PREPRINT ALERT🚨
Systematic comparison of sequencing-based spatial transcriptomic methods🫶
#ST #benchmark #Visium #HDST #BMKMANUS1000 #SlideSeq #StereoSeq #PIXELSeq #DBiTseq
👉biorxiv.org/content/10.1101/…
Ruben Dries retweeted
Congrats Sami and team!
Systematic benchmarking of imaging spatial transcriptomics platforms in FFPE tissues biorxiv.org/content/10.1101/…
Ruben Dries retweeted
The most retweeted spatial omics preprint in our search this past week:
xitter.cf/GiottoSpatial/status/1…
Congrats @GiottoSpatial @RnDries @gc_yuan labs! 💪🙌🧵 3/5
Dear spatial afficionados, check out our latest contribution to the spatial data analysis landscape. In this work we present Giotto Suite, our completely new ecosystem designed to work with the most exciting and challenging spatial datasets. biorxiv.org/content/10.1101/…