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I'm stoked to announce our new end-to-end framework for perturbation analysis! Our scverse advisory committee highlighted that a maintained and well-documented framework for perturbation analysis is missing. Pertpy is our attempt to satisfy this request biorxiv.org/content/10.110…

biorxiv.org/content/10.110… Nice benchmark of single cell "foundation models" (scGPT, scFoundation) and GEARS (a GNN model) further hyped as "virtual cell models" against linear baselines on perturbation prediction. Long-story short: they can't beat the linear baselines. 1/

Available now via bioRxiv is our preprint on live-cell transcriptomics with engineered virus-like particles Broad Institute biorxiv.org/content/10.110…

Our paper on continuous mutagenesis in living cells using HACE is now out in Science Magazine! We now demonstrate that HACE continuously generates mutations over a 10-day period and enables targeting using dCas9 without introducing DNA nicks. science.org/doi/10.1126/sc…

I ran 80,000 simulations… and the mean of the training data performed the best.

In collaboration with Reuben Saunders, Jonathan Weissman's Lab, and Xiaowei Zhuang, we are very excited to release Perturb-Multi: a platform for pooled multimodal genetic screens in intact mammalian tissue. Check it out! biorxiv.org/content/10.110…

What if you could design binders for specific peptide-MHC complexes instead of hoping for hits from a screen? Bingxu Liu and team show we can! 🤩

Excited to see the work from Matteo Gentili Becca J. Carlson and others from our collab with the Hacohen lab Broad Institute out now!

1/ Thrilled to share an advancement in gene therapy from my PhD in Nature Communications! We've developed a new approach to reduce immune responses while maintaining efficiency—paving the way for safer, more effective therapies. Big thanks to Feng Zhang & Mirco J. Friedrich! bit.ly/redicas9

The unique pharmacology of targeted degraders (eg PROTACs) leverages their sub-stoichiometric “catalytic” activity. Now ⁦Lycia Therapeutics⁩ reports catalytic (cata)LYTACs for potent, durable extracellular TPD, cleared IgE in NHPs, superior to omalizumab 👏 biorxiv.org/content/10.110…

Excited to share the 1st of several stories dissecting TEs + chromatin in normal/malignant hematopoiesis. We identified histone demethylases KDM4A/C as vulnerabilities in DLBCL + discovered novel KDM4 inhibitors. Preprint👇 Broad Institute Boston Children's biorxiv.org/content/10.110…

Out now in Cell Reports our collab w/ Biederer Lab on image-based pooled genetic screening to identify regulators of synapse formation cell.com/cell-reports/f…

Are you trying to build a so-called AI virtual cell? 🔬 Yet ... the mean still outperforms your perturbation-response prediction model. 😮‍💨 Our paper— just accepted to the 𝗚𝗲𝗻𝗕𝗶𝗼 𝗪𝗼𝗿𝗸𝘀𝗵𝗼𝗽 @ 𝗜𝗖𝗠𝗟 —dives into 𝘸𝘩𝘺 the mean excels and what you can do about it.

🎉Preprint alert! Our Ph.D. students Chujun He and Jiaqi Zhang , supervised by Eric and Wendy Schmidt Center Director Caroline Uhler and collaborator Munther Dahleh, have developed #MORPH, a MOdular framework for predicting Responses to Perturbational cHanges. Learn more ⬇️

Super cool work predicting perturbational responses at single-cell resolution!!! Congrats Chujun He Jiaqi Zhang and the team 🙌🥳🥂

We’re Blainey Lab sharing a major update to CROPseq-multi, our versatile system for CRISPR screens that is compatible with individual and combinatorial perturbations, diverse SpCas9-based technologies, and multiple high-content, single-cell readouts. biorxiv.org/content/10.110…

ID possible new drug targets for treating Ebola infection via CRISPR screen, including UQCRB as a post-entry regulator of viral replication & STRAP as host regulator of equilibrium between viral RNA-protein Becca J. Carlson Blainey Lab nature.com/articles/s4156…

Out Now! Single-cell image-based screens identify host regulators of Ebola virus infection dynamics bit.ly/46nKLtH #EbolaResearch #Microbiology #CRISPR

Our study on image-based genetic screens to identify novel host regulators of Ebola virus is now online Nature Microbiology! Thanks also to Broad Institute for writing a news story on our work: broad.io/Ebola-News-0724