Do science that is predictive and use it to improve lives.
Boston, MA
Joined March 2009
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Postdocs: Sander Lab, Systems Biology, Harvard Medical School. Data Science / AI / CompBio. Solve challenging biological problems. (1) Catch cancer early using AI #CancerRiskNet #ovariancancer hms.harvard.edu/news/ai-pred… - Apply to sander.research (gmail) Subj: postdoc application
End-to-end protein design for a broad scientific audience at evedesign.bio - try it !
Meet evedesign: a new open-source ML framework that makes protein design accessible and interoperable.
📢 See our post: deboramarkslab.substack.com/…
Protein design models are powerful, but combining them shouldn’t require custom glue code.
✅Combine models for multi-objective optimization
✅Integrate lab-in-the-loop experimental of data
✅100% secure: run on your own infra, no data sharing
Get started building therapeutics & industrial enzymes today 👇
📄Paper: biorxiv.org/content/10.64898…
💻Code: github.com/evedesignbio
🌐Webserver: evedesign.bio
Reach out to collaborate: [email protected]
Chris Sander aka cscbio retweeted
Announcing our new protein design server evedesign.bio:
• End-to-end protein design for everyone!
• Analyze your generated library interactively and on 3D structures
• Export codon-optimized DNA sequences for experimental testing.
Developed in collaboration between @deboramarks, @thomas_a_hopf, @SteineggerM, Simon d'Oelsnitz, Chris Sander, Artem Gazizov,@haysunny_hi, Milot Mirdita, Sergio Garcia Busto, Jake Reardon
Protein design with almost-AI -- evolution does it
"Simultaneous enhancement of multiple functional properties using evolution-informed protein design"
Novel b-lactamases designed w/ EVCouplings; "functional designs had large increases in thermostability and most had a broadening of available substrates"
biorxiv.org/content/10.1101/…
Things get better in science over time with good starting ideas and subsequent hard work. 2016 Evolutionary Couplings for RNA folding. 2025 Comprehensive RNA benchmark and tool comparison for everyone in the biomolecular AI field. Great team work with MarksLab!
RNA, RNA, RNA
biorxiv.org/content/10.1101/…
Been a long time goal of @deboramarks.bsky.social to help RNA sequence —> function mapping a million years ago we tried
sciencedirect.com/science/ar…
Now total refresh for our new world, led by Rohit Arora and Murphy Angelo for seeing this thru and Pascal Notin for pulling together!!!
Chris Sander aka cscbio retweeted
How can we use #GenerativeAI for #ProteinDesign? - check out work from our labs @deboramarks and @yaringal
nature.com/articles/s41587-0…
Chris Sander aka cscbio retweeted
The February issue, with a focus on protein engineering, is live nature.com/nbt/volumes/42/is…
Our cover shows the three data types key to machine learning for functional protein design: structure, sequence and labels, from a Review by Notin et al. go.nature.com/49EPi9x
A first step toward designing combo anticipatory vaccines !
Previous viral evolution can shed light on future immune evasion. EVEscape, now out in @Nature, is our first step in applying pre-pandemic data to forecast antibody escape through the course of a pandemic. nature.com/articles/s41586-0… 🧵1/6
Chris Sander aka cscbio retweeted
Looks like I was able to re-purpose ChatGPT's new function return support to enrich answers about human genes using the most up-to-date @genenames data.
This still has too much boilerplate stuff in it but here is the full notebook for the curious: gist.github.com/armish/45ffc…
Postdocs: Sander Lab, Systems Biology, Harvard Medical School. Data Science, AI, CompBio. Solve challenging biological problems. (2) Develop large-scale models of cell biology wellcomeleap.org/delta-tissu… https://bit/ly/CellBox
Apply: sander.research (gmail) Subj: postdoc application
More to come in international open collaboration #CancerRiskNet aka #BianQue << Solve Bo Yuan’s puzzle.
(1/6) Very excited to share our work on @NatureMedicine using #AI to predict #cancer with disease history only (no CT scan!). Glad to co-lead the work with @davplacido @jessicaxhu Chunlei Zheng @sandercbio @TheBrunakLab and many more great colleagues nature.com/articles/s41591-0… .
Chris Sander aka cscbio retweeted
AI Predicts Future Pancreatic Cancer hms.harvard.edu/news/ai-pred…
Risk of pancreatic cancer predicted using machine learning. International collaboration. @TheBrunakLab @DanaFarber_Hale @harvardmed @HMS_SysBio @GENES_PK @Nrfillmore @boyuan_data @davplacido @deboramarks @sandercbio nature.com/articles/s41591-0… hms.harvard.edu/news
Chris Sander aka cscbio retweeted
Ready to learn about protein design? Our beginner's guide breaks down this complex field into easy-to-understand concepts. Discover the potential of proteins to transform our world: ipd.uw.edu/2023/05/what-is-p…
ALT An artist’s depiction of a protein structure emerging from a computer chip.
Go cBioPortal ! Lots of new features for easy analytic access to cancer genomics, proteomics and more. Make your own discoveries on community-provided cancer data and analysis tools.
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).
Wish one could weigh in with NNF to reverse this decision. Very hard to understand. Our collaborations with CPR labs Mann and Brunak have been singularly successful. Great science & scientists.
Tremendously sad day for Danish science as Novo Nordisk Foundation is closing its flagship protein research institute, arguably the best in the world. @UCPH_CPR has been a beacon of science and progress for years. Let's cherish the remaining years & strive to continue the legacy.
Chris Sander aka cscbio retweeted
Very pleased to announce that our paper “Tranception: protein fitness prediction with autoregressive transformers and inference-time retrieval” was accepted at ICML!
Paper: arxiv.org/abs/2205.13760
Repo: github.com/OATML-Markslab/Tr…
(1/10)
Chris Sander aka cscbio retweeted
deboramarkslab.com is recruiting an Associate Lab Director! An outstanding opportunity for an ambitious computational biologist to manage projects at the cutting edge of machine learning and genomics. Send CV to [email protected]
Chris Sander aka cscbio retweeted
Harvard link sysbio.med.harvard.edu/caree…
deboramarkslab.com is recruiting an Associate Lab Director! An outstanding opportunity for an ambitious computational biologist to manage projects at the cutting edge of machine learning and genomics. Send CV to [email protected]