Scott Soderling

Hope you get back soon!

You can use the model right now to freely generate families for single sequence inputs (i.e., diversification conditioned by intrinsic representations of evolution), or to engineer proteins based on family promts (diversification by conditioning on particular evoluationary trajectories).

Congrats to the team!

USHER: Guiding Foundation Model Representations through Distribution Shifts Foundation models pre-trained on certain biological data modalities exhibit systematic representational biases when encountering out-of-distribution (OOD) data from new assays. The embedding drift lar...

@rohitsingh8080.bsky.social USHER: Guiding Foundation Model Representations through Distribution Shifts
Aditya Pratapa, Purushothama Rao Tata, Rohit Singh
bioRxiv 2025.11.20.689462; doi: doi.org/10.1101/2025...

A distinct PP2A subunit regulates local protein phosphorylation at the axon initial segment - Nature Communications The existence of phosphatases specialized in regulating the axon initial segment (AIS) was unclear. Here, the authors show that a PP2A-B55 subunit is selectively enriched at the AIS and contributes to...

The existence of specialized phosphatases in regulating the AIS was unclear. In this initial report, we show that a PP2A subunit is enriched at the AIS and contributes to its local phosphoregulation. Fun collaboration with Dr. Matthew Rasband's lab, and thanks to all authors for their contribution!

A distinct PP2A subunit regulates local protein phosphorylation at the axon initial segment - Nature Communications The existence of phosphatases specialized in regulating the axon initial segment (AIS) was unclear. Here, the authors show that a PP2A-B55 subunit is selectively enriched at the AIS and contributes to...

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...

Congrats!! Well deserved.

Sounds very exciting

The published version of our study on the early-life transition from isolation USVs to adult-like USVs in juvenile mice is out in Animal Behaviour!

authors.elsevier.com/a/1m1YDmjMA4GP

bsky.app/profile/kati...

Deadline for applications- November 1st!

We are hiring!

Tenure-Track Assistant Professor Position –AI/ML for Cell Biology - Durham, North Carolina (US) job with Duke University School of Medicine | 12844591 Tenure-Track Assistant Professor Position –AI/ML for Cell Biology

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...

I am thrilled to share our latest story led by the incredibly talented Brooke D’Arcy and Camila Musso. We discover a rich world of local gene expression in radial glia, essential neural and glial precursors, and develop a new method for sub-cellular mRNA manipulation. www.biorxiv.org/content/10.1...

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 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

“Duke University School of Medicine” logo above a line with “Discovery AI” logo

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

Building a spine is no joke, but thankfully zebrafish have their own clocks to keep the pace. Excited to share our preprint on the role of biological oscillators in coordinating notochord development! (www.biorxiv.org/content/10.1...)
Additional thread below

Priyom's preprint is out on biorxiv. See below for a detailed thread. In a nutshell, she has discovered and characterized the oscillator that times notochord and spine segmentation in zebrafish. Turns out that there are uniform Erk oscillations across the entire tissue that act as timekeepers!

Duke researchers have uncovered a promising path to potentially treat a family of rare neurodegenerative disease called neurodegeneration with brain iron accumulation (NBIA).

🔗: https://mgm.duke.edu/news/fundamental-cell-molecule-could-help-fight-rare-brain-disorders

#AcademicSky #MedSky

Another milestone for the amazing Munjal lab!

Trump order gives political appointees vast powers over research grants Researchers are alarmed that the move might upend a long-standing tradition of peer-review for grants.

The order is the latest move by the Trump administration to assert control over US science

go.nature.com/3H6IxVr

Sharing our newest study led by the incredibly talented @federicamosti.bsky.social investigating new molecular mechanisms of human brain development. We discover a human-specific enhancer HAR1984 that influences chromatin looping to promote cortical size and folding! www.biorxiv.org/cgi/content/...

Great work from Huanghe Yang’s lab in Duke Biochemistry.

Congrats!!!

Congrats James! Loved hearing about this at an earlier CZI meeting!

I like o3 pro even better.

Steve Jobs was a vibe coder, he just prompted Steve Wozniak

Mini hearts, lungs and livers made in lab now grow their own blood vessels These sophisticated models will be used for human-development studies and drug testing.

Researchers are making ever more sophisticated mini organs in the lab — and now they can grow their own blood vessels

go.nature.com/4nNF3ri

A New Hub for Fighting Infectious Diseases with Smarter Models Duke University School of Medicine researchers will launch a new national Center of Excellence for Multiscale Immune Systems Modeling (MISM), funded by a U54 grant from the National Institutes of Heal...

The new Center of Excellence for Multiscale Immune Systems Modeling (MISM), launching soon by Duke University School of Medicine researchers, will transform how we understand and treat infectious and immune-related diseases.

#AcademicSky #MedSky