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We are excited to introduce LoRNA-SH, a frontier RNA foundation model that leverages long-read transcriptomics and long-context inputs to learn and predict the transcriptome architecture with base-pair resolution: biorxiv.org/content/10.110…

Check out this amazing resource! High quality illustrations for free! bioart.niaid.nih.gov HT @LuciaScience

Our work describing molecular recording of sequential information by directing a chain of insertions with prime editor in mammalian cells is now published in Nature Chemical Biology here - nature.com/articles/s4158…. Congratulations to Theresa Loveless, Courtney Carlson, and the whole team!

Incredibly excited that our paper linking single molecule states of TF binding to gene expression using quantitative thermodynamic models is out in Nature today. An amazing collaboration with the Bintu Lab. Congrats to Ben, Michaela, and Julia! nature.com/articles/s4158…

A dream come true: in 2004 I started thinking about counting microstates to predict gene expression with Jane Kondev Rob Phillips Hernan Garcia. 20 years later we can measure them: nature.com/articles/s4158… Thank you William J. Greenleaf Benjamin Doughty Michaela Hinks Julia and all co-authors!

Check out our new review of molecular recording, exploring cutting-edge technologies and their transformative potential for biology. A collaborative effort across multiple labs—proud to have been part of this amazing team! 🌟

New Publication Alert! our perspective of "Aging on a chip" and "Spatial Omics" in aging single cells. Decoding senescence of aging single cells at the nexus of biomaterials, microfluidics, and spatial omics npj Aging10, 57 (2024) Link: lnkd.in/ef7-ad7Q Coulter BME | Emory & Georgia Tech

A month ago we Vevo Therapeutics announced that we have generated the largest single-cell perturbation atlas in history, Tahoe-100M. Today, we announce that we will fully open-source Tahoe-100M in Feb, as part of a collaboration with NVIDIA Healthcare to train cell state models.

It's published! rdcu.be/d6kVt

How does one (signaling) arm know what the other is doing in the cell? Through a network of bHLH transcription factors obviously! Our work showing how neural stem cells integrate signals to coordinate a fate response is now out: cell.com/cell-reports/f…

Nice article in Scientific American about our work on outer ear evolution and a complimentary study from the lab of Maksim Plikus on role of unique lipids in mammalian ear cartilage. Mathi Thiruppathy USC Stem Cell Keck School of Medicine of USC scientificamerican.com/article/our-ea…

So we beat on. Gene/cell therapies often use proteins that could be recognized/rejected as non-self by our immune system. We combine algorithms to build proteins that are therapeutically relevant and can masquerade as our own parts doi.org/10.1101/2025.0…

Spatial proteomics is here, but spatial functional proteomics? Here is our Nature BME paper on spatial protein interactomics (nature.com/articles/s4155…) illuminating how 47 proteins co-localize/ interact within 20 nm and their function in tissues. Nature Methods Rita Strack

Arjun Raj Adam MacLean Kai Hoa from Amjad Askary's lab Amjad Askary on recording signaling histories in single cells via INSCRIBE Check out their bioRxiv: biorxiv.org/content/10.110… #SysBioSC2025