How do we interpret molecular mechanisms of protein allostery from deep mut scan experiments? We have built a generalized thermodynamic model to infer and predict how mutations impact inter-and-intradomain allostery. Great collab with Qiang Cui BU
eLife - the journal doi.org/10.7554/eLife.…

ACGT Research Fellows, and members of the ACGT Scientific Advisory Council, Carl June, MD (Penn), and Michel Sadelain, MD, PhD (@MSKCancerCenter), received the Breakthrough Prize for Life Sciences on Saturday!

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Really proud of this one! Used syn bio tools & genome editing to create inducible signaling receptors to remove cytokine dependence for RBC differentiation. Great collaborative work with Porteus Lab Stanford Pediatrics biorxiv.org/content/10.110…

Michael Baym Danielle Beckman Dava Jo Keavney 🏳️‍⚧️🩻👩‍🔬 Natalia Quinones-Olvera BioRender Hi Michael - as a BioRender cofounder, wanted to thank you for the feedback and clarify that BioRender does not claim copyright to figures you make, only to the icons/templates made by the BioRender team. We’ll work to fix the wording so it’s much clearer 🙏🏼

Very excited (& nervous) to share what we've been working on the past many years. Only took 3 first authors (Schreuder the experimentalist, Dr Dawn Lin the analyst, and stephen zhang the modeller) & co-senior Weber (computational, modeller, SynBio extraordinaire) biorxiv.org/content/10.110…

How to pick a problem. Today in Cell. 1/53
cell.com/cell/fulltext/…

Sequence-based ML methods (Enformer, ChromBPNet...) are invaluable in genomics but the ecosystem for their *use* after training is less developed.

Introducing, `tangermeme`: a PyTorch library for genomics discovery for everything-other-than-the-model. github.com/jmschrei/tange… 1.

Our immune system is amazing, but faces pandemics, cancer and aging. It's also wired to reject what we need to extend our healthspans & minds: organs, implants, new genes. It's time to radically augment it. We need to build an immune-computer interface (ICI). A manifesto🧵!

Identifying immune signatures of common exposures through co-occurrence of T-cell receptors in tens of thousands of donors biorxiv.org/content/10.110…

Our new study demonstrates extreme ruggedness and high epistasis in the evolutionary landscape of a TF family. Gain/loss function between adjacent nodes, rapid switches in specificity and spontaneous GoF at distinct clades. Colin Jackson Cell Systems
sciencedirect.com/science/articl…

Delivering and expressing a gene in cells is usually a messy (heterogeneous) process. The messiness interferes with research and applications such as gene therapy.
In two new papers, we introduce a toolbox of synthetic miRNA-based control circuits that enable more precise, gene

Why can RNA only be linear or circular? It can be branched! We made multi-tailed mRNA, and we had fun! Here is our story led by brilliant graduate student Hongyu Chen: rdcu.be/dB7ck and his cartoon illustration👇MIT Chemistry Broad Institute

LYTACs pioneered by Carolyn Bertozzi opened the door to degradation of cell surface and extracellular proteins through lysosomal targeting. Here, we introduce genetically-encoded LYTACs, or GELYTACs, which are (1) easier to produce by recombinant expression (LYTACs, antibody

To test this prediction, we performed experiments using a designed protein array made by @Arielbs100@UWproteindesign, to display pMHCs to T cells at defined spacing and copy number.  (9/n)

Our latest preprint, on T cell receptor (TCR) signaling by condensate nucleation!
This theory + experiment study was led by the brilliant Will White, with Jay Groves College of Chemistry and David Baker Institute for Protein Design and Ariel Ben-Sasson.  (1/n) biorxiv.org/content/10.110…

Ever wonder how microbes interact with the host at a molecular level? Check out our latest paper in @nature with Noah Palm and Curtis Huttenhower where we developed a host:microbe profiling technology, BASEHIT, to atlas interactions between commensal microbes and the human exoproteome.

Why do activated T/B cells wait to divide? Why is there heterogeneity in their daughter cell responses? How do we find peace in these troubled times? Check the Bailis Lab’s FIRST PAPER (🎉) for insight into 2 of these 3 questions! science.org/doi/10.1126/sc…

excited to share the first story from my postdoc today!! we profiled hundreds of transcription factor (TF) isoforms & found that two-thirds of alternative TF isos differ from their cognate reference iso in at least 1 key molecular activity

biorxiv.org/content/10.110…

For me: the effect from Trikafta was almost immediate. I was in the clinical trial and within 12 hours I knew I wasn’t on placebo. I went from pretty severe illness to almost no negative effects from CF basically over the course of a few days.

I was 27 years old and had never

Last year, the Make-a-Wish Foundation announced that kids with cystic fibrosis would no longer automatically qualify for a wish.

This was, actually, a good thing—a great thing even!