Scott Soderling
Neuroscientist-cell biologist, proteomics developer, deep learning collaborator, tackling brain disorders. PI @Duke. Chair of Cell Biology and Biochem. Founder, Triangle Protein Design.
http://soderlinglab.cellbio.duke.edu
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- Hope you get back soon!
- Our latest protein family-based GenAI collection of tools and datasets, ProFam, is out now. Everything -- from data, training and inference code, to a 215M llama-based ProFam-1 are fully open sourced. 🧵
- Congrats to the team!
- There is nothing sweeter than the first paper from your former postdoc’s own lab. Huge congratulations to Yudong and his lab! www.nature.com/articles/s41...
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- Congrats!! Well deserved.
- Sounds very exciting
- Congratulations to @swcanner.bsky.social for the successful defense of his thesis, “The Protein Sugar Interactome”! Leveraging deep learning and AI, he created tools and uncovered putative structural interactions underlying intercellular communication. He will receive his diploma in December.
- Deadline for applications- November 1st!
- Duke Cell Biology is hiring in AI/ML! @scottsoderling.bsky.social, @rohitsingh8080.bsky.social, and others are building a very active community around ML for discovery science, and Duke is a great place to be. academicjobsonline.org/ajo/jobs/30509
- Please repost!!: We are searching for new AI-Bio faculty at Duke to be part of a new Discovery AI center. Looking for faculty who focus on pushing boundaries in ML model development in a highly interactive environment. DEADLINE for applications- Nov 1st!! www.nature.com/naturecareer...
- Cool new work- DynamicsPLM adds prot conformational dynamics to LMs: fuses seq with per-residue structure-token distributions from an ensemble (no averaging) → state-aware embeddings. Gains: +4% HumanPPI, +11% on multi-state proteins. Firing this up in the lab soon! www.biorxiv.org/content/10.1...
- Man after my own heart
- Duke is recruiting a tenure-track Assistant Professor in AI/ML for Biology—joint Discovery AI Initiative × Cell Biology Search. Building models for protein design, single-cell/spatial omics, imaging, proteomics, genomics? Apply: academicjobsonline.org/ajo/jobs/30509 #hiring #AIforBio #CompBio
- Another milestone for the amazing Munjal lab!
- Great work from Huanghe Yang’s lab in Duke Biochemistry.
- New research from Duke could transform how complications related to the placenta during pregnancy are detected and prevented. This discovery may also lead to new insights into cancer, bone healing, and viral infections. 🔗 Read more: medschool.duke.edu/news/protein... #AcademicSky #MedSky
- I’m extremely honored to be recognized with the WICB Junior Research Award. ASCB and WICB have been key to my career development since I attended my first annual meeting in 2005. Congrats to the other awardees!
- Meet the 2025 ASCB Award Winners—trailblazing scientists honored for research, mentoring, education, and innovation. Celebrate excellence across all career stages in cell biology. Read more: www.ascb.org/society-news...
- Congrats!!!
- Congrats James! Loved hearing about this at an earlier CZI meeting!
- ⚡️Thrilled that #VirtualLab is published in @nature.com! www.nature.com/articles/s41... We created a team of AI agents to mirror my Stanford lab 🤖. Led by a PI agent, the AI scientists ran their own group meetings and discovered effective binders to new CoVID variants that we validated.
- I like o3 pro even better.
- o3, an AI model developed by the creators of ChatGPT, has been ranked the best AI tool for answering science questions in multiple fields go.nature.com/4lzaWlC
- Super excited to share that our new study is published @natneuro.nature.com today!! Here we show that intersectin and endophilin form condensates between the active zone and the reserve pool and maintain synaptic vesicles near the active zone for rapid replenishment. rdcu.be/evi5y
- Congrats!!
- Lab backpacking trip recently along the AT in NC. It's so nice to get away from it all, together.
- AI research in collaboration with cell biologists is transforming research at Duke. More discoveries coming soon!!
- The AI tool Raygun (named as an homage to “Honey, I Shrunk the Kids”) is just one of several tools that a team led by Duke's Rohit Singh, PhD, has built to help scientists work both faster and smarter. 🔗 Read more: medschool.duke.edu/stories/hone... #DukeB&B #DukeCellBiology #AcademicSky #MedSky
- Looking forward to reading this.
- With contributions from fantastic colleagues @martinsteinegger.bsky.social , @mikeinouye.bsky.social, @jlistgarten.bsky.social , @ideasbyjin.bsky.social, @michael-heinzinger.bsky.social, and many more, the first CSHL volume on ML for Protein Science and Engineering is out: lnkd.in/dQdgGPpp
- Glad to see our new paper finally out! We show how the GPR158 receptor controls synapse maturation and function by silencing an intrinsic inhibitory mechanism. authors.elsevier.com/a/1l7HS5Sx5g... Work from Ben Verpoort and colleagues, with special thanks to our collaborators.
- Congrats Joris!
- 🧠 New in Nature from the fabulous Silver Lab @ Duke: A human-specific enhancer, HARE5, boosts radial glia proliferation, expanding neocortical size and connectivity. Knock-in mice showed enlarged cortices and more neurons. This highlights how regulatory DNA changes shaped human brain evolution.
- Thrilled to share our latest study out in @natureportfolio.nature.com led by the fantastically talented Jing Liu. Our study provides insight into a long standing question in biology: What molecular features make us uniquely human and how do these function? www.nature.com/articles/s41...
- Introducing KolossuS to address a 50-year old problem: which kinases are active in your pathway of interest? As computational biologists, our work mostly involves post-hoc analysis algorithms. KolossuS is the rare case where a ML model enables entirely new capabilities. 1/
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View full threadThis was a wonderful collab with @scottsoderling.bsky.social , whose lab is situated next to ours. If you want to do cool collaborative work like this, join us! We're building a great ecosystem of AIxBio at Duke.
- Yes, we have lots of exciting collaborative projects at the interface of computation and biology. Deep expertise in many domains between our labs, so a wonderful and committed training environment!
- Just snagged some tickets for the upcoming Pearl Jam concert in Raleigh NC. SO EXCITED!
- Over 50 yrs since the discovery of protein kinases, 80% of human kinases still have ≤20 known substrates, and many are “dark.” I'm EXCITED to announce our new work towards solving this- combining (1) deep learning with (2) proximity proteomics in vivo! ➡️ www.biorxiv.org/content/10.1...
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View full threadWe find known and novel Sik3 substrates that shed new light on the molecular mechanisms of sleep by combining KolossuS and CRISPR-based BioID.
- The BEST part: This would not have been possible without the close (and SO FUN!) collaboration of my lab with @rohitsingh8080.bsky.social and the lab of Masashi Yanagisawa.
- (2) It is insufficient to simply predict kinase specificities in vitro; kinases must also meet their substrates in cellular contexts. We tag endogenous kinases with TurboID in mouse brain, capturing substrates within ~10 nm in living animals.
- This allows for the capture of nearby phosphorylated substrates for kinases in vivo. KolossuS accurately interprets this data. We validate our framework by capturing state-dependent substrates, focusing on Sik3 and its differential substrates in response to sleep deprivation in vivo. 😳 vs 😴
- (1) Our deep learning model, KolossuS, leverages large protein language models to learn the “grammar” of kinase–substrate recognition, achieving SOTA accuracy and performance across the mammalian kinomes. It is well-calibrated across kinase families, enabling real-world usage.
- Just had to share a proud dad moment—my son has published his first paper! 🎉 www.cureus.com/articles/354...
- Eye opening. Highly recommend. Research is intentional collateral damage in the service of a larger ideological goal.
- Required Listening www.nytimes.com/2025/04/11/p...
- This NIH policy was rescinded on Friday: grants.nih.gov/grants/guide...
- Key points gutted: It is the policy of NIH to: 1. Prohibit political interference or other inappropriate influence in the design, proposal, conduct, review, management, evaluation, communication of, and use of scientific activities and scientific information conducted by covered individuals.
- 3. Require that leadership and management ensure that covered individuals engaged in scientific activities can conduct their work objectively, free from political interference or other inappropriate influence, and free from retaliation.
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- So sorry to hear this Franck.
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- My understanding is that the cuts affect the innovation fund of the Cures act, and that this includes the BRAIN initiative. Hopefully my information is incorrect….
- Excited to share exciting new work from my former postdoc, Il Hwan Kim. His study reveals that SHANK3, an ASD-risk gene, is expressed in brain endothelial cells and plays a crucial role in maintaining tight junction integrity at the blood-brain barrier. www.nature.com/articles/s41...
- Two major life updates: - I'm moving to Senior Applied Research Scientist in Digital Biology at NVIDIA (Jan '25) - I'm starting a new lab at Duke as Visiting Assistant Prof (early '25) Both roles focus on tackling hard problems in biological machine learning through collaborative research. Long 🧵
- Excited to have you join the Departments of Cell Biology & Biostatistics- Bioinformatics at Duke!
- Amazing AI tool by Rohit Singh's lab at Duke. Shrink or Supersize your protein and retain functions- all based on protein language models.
- Congratulations to @youngsuko9.bsky.social on their top-10 placement in Adaptyv Bio's EGFR-binder competition! It's an elegant pipeline-- using our protein-design method Raygun to expand and modify the template (EGF), then filtering with ProTrek. foundry.adaptyvbio.com/competition 1/
- Been talking about exploring active learning for some projects. EVOLVEPro suggests we really should. www.science.org/doi/10.1126/...
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- Please add me
- 🚀 Big updates from our lab! We’re diving into deep learning for protein design and proteomics. For a glimpse of what’s ahead, check out our recent collab with Rohit Singh’s lab, which used AI to shrink proteins! 😱 Read more: www.biorxiv.org/content/10.1... @rohitsingh8080.bsky.social
- Bsky only: 🌟 Excited to share our latest research, now out in eLife! Using advanced mass spectrometry and genetic engineering, we demonstrate presynaptic Rac1's crucial role in working memory. 🧠 Dive into the details here: doi.org/10.7554/eLif... #Neuroscience
- 🚨 Exciting news from our lab! Our latest paper is out in Nature Communications ↪️We developed a scalable CRISPR-based method to map native protein-protein interactions in the brain, revealing new insights into the molecular networks underlying autism. Read more here: doi.org/10.1038/s414...
