Gerald Tiu

The hardest part of protein engineering isn't just finding good mutations – it’s deciphering which ones combine synergistically. Today in @ScienceMagazine, we present MULTI-evolve, a framework for rapid multi-mutant protein engineering, validated across three diverse proteins.

Viral DNA that is usually dismissed when sequencing the human genome could help to uncover useful information about complex diseases go.nature.com/4reVEoD

[Posted by Sandy Ho] For those who would like to make a contribution to continue the legacy of her work, Alice's GoFundMe gofundme.com/f/alice-wong-s…

We’re thrilled to share that our MERFISH+ preprint is now live on bioRxiv!👉biorxiv.org/content/10.110… In this work, the Bintu and Zhu labs (UCSD) developed MERFISH+, a next-generation spatial genomics platform that combines genome-wide RNA and epigenetic imaging over a large field of view. By introducing acrydite-modified probes covalently anchored to hydrogels, MERFISH+ achieves remarkable imaging stability and enables >1,800-gene, multi-modal, and multi-month experiments. With this platform, they, together with the Chi lab at UCSD, profiled a whole developing human heart at 12 post-conception week with merely two slides, resulting in a total of 53 slides, 3.1 million single cells and more than 30 cell types. Building upon our previous 3D reconstruction and modeling framework, Spateo (github.com/aristoteleo/sp…), we reconstruct the 3D human heart that nicely captures the anatomical structure of the heart, including the intricate vasculature network. Sophisticated analyses provide a holistic view of an entire organ and enable systematic characterization of 3D cellular neighborhoods and transcriptional gradients of substructures such as the descending arteries. Furthermore, using a generative integration framework for spatial multimodal data (Spateo-VI), we harmonized these MERFISH+ transcriptomic and chromatin data to reconstruct a 3D spatially-resolved multi-omics atlas of the developing human heart, shared at zhu.merfisheyes.com and viewer.spateo.aristoteleo.com. MERFISH+ thus sets a new standard for large-format, multi-omic spatial profiling, enabling holistic, 3D characterization of organs at subcellular resolution. Huge congratulations to first authors Colin Kern, @qingquanZhang2, @YifanLu2024 , and Jacqueline Eschbach, and to all collaborators from the Bintu, Zhu, Chi, and Qiu labs for this amazing team effort. Thanks for your diligence, creativity, and hard work on this project. We’re grateful for support from @arcinstitute and our generous donors. Our lab is expanding—if you’re excited about building the next generation of single-cell and spatial genomics techniques and predictive single cell and spatial foundation models, we’re hiring! If you are interested, please reach out to me via direct message or email at xiaojie@stanford.edu. We are excited for any potential collaborations along this line of research in Stanford, UCSF and Berkeley and other labs as well.

The ability to design antibodies against any protein of interest has major implications for medicine, biotech, and basic science. Today, we introduce Germinal, a pipeline for epitope-targeted de novo antibody design achieving  4–22% success rates with efficient experimental validation.

🚨 The first disease-modifying therapy for Huntington's disease was just announced this morning. 75% reduction in symptoms over 36 months. This isn't hype. It's field-changing. And it uses RNA. Here's what you need to know about $QURE AMT-130 🧵

🤯Three (!!!) new papers today in @ScienceMagazine on the application of generative AI for the de novo design of peptide/HLA binding molecules! Completely unique 3D structure and binding mode compared with natural TCRs and TCR mimics! Links to papers 👇

Excited to share our recent work, which addressed a mechanism by which the eukaryotic ribosomes increase the fidelity of mRNA translation than prokaryotic ribosomes through the eukaryote-specific tentacle-like ribosome structure. academic.oup.com/nar/article/53…

Excited to share our new story on drivers and communication networks in a lethal tumor in young children called ETMR. Fantastic collaboration with @hovestadt and team! @DanaFarber @BostonChildrens @DFBC_PedCare @broadinstitute #gograyinmay #endbraincancer 👇🏻👇🏻👇🏻

🧵1/N New study published in @JAMA_current on re-emergence of vaccine-eliminated infectious diseases under declining vaccination in the US. We model long-term risk and conditions for return to endemicity for measles, rubella, polio, & diphtheria. jamanetwork.com/journals/jama/…

David Liu receives Breakthrough Prize in Life Sciences. @davidrliu is honored for the development of base editing and prime editing, two gene editing technologies transforming medicine. @brkthroughprize broadinstitute.org/news/david-liu…

The NIH grant that supported 38 years of training the best pediatrician-scientists in the country (I’m a proud former recipient) was cancelled. It was just approved for a 5 year renewal. The @PSDP_AMSPDC is vital to our understanding of childhood diseases and making new therapies

Happy to share our new work with @haognguyen on targeting mRNA translation of oncogenes by RNA structure remodeling with a small molecule zotatifin. Congrats to ⁦@DuyguKuzuoglu⁩ an amazing postdoc and all the authors and collaborators! cell.com/cancer-cell/fu…

Last week, I was expelled from @Columbia for protesting the U.S.-backed genocide in Gaza. As president of @SW_Columbia , Columbia’s student workers union, I was also fired from my job. The Trump administration is pushing their narrative. Here’s the real story. 🧵

New review out today in Nature Biotech on nanopore-based protein sequencing. Feels... like... something... coming... soon... 👀

@mbarnalab @RobertoZoncu @adelefrancisxu @GarryPNolan Congratulations! So excited to read it!

Very proud of my graduate students ⁦@adelefrancisxu⁩ and Zijian Zhang & key members of our lab and collaborators ⁦⁦@GarryPNolan⁩ & Sharon Pitteri lfor the incredibly hard work to characterize subcellular ribosomes. science.org/doi/10.1126/sc…

UMAP was introduced to biology with the claim that it 'preserves the global structure of the data' better than t-SNE. This matters arising article shows that the claimed global structure preservation can be entirely attributed to different choices of initialization. 1/2

Molecular dynamics simulations in mixed reality! With @labriataphd and @lucien_krapp we’re scaling our multi-user WebXR platform to enable immersive molecular simulations, fully based on web technologies. Stay tuned, lots of cool stuff coming soon! @threejs #WebXR #Quest3