GGGenome: ultrafast DNA search gggenome.dbcls.jp/en/ gggenomes: A grammar of graphics for comparative genomics thackl.github.io/gggenomes/

What if we could use precision #microbiome editing in vivo to turn harmful gut microbes into allies against disease? We did it using #CRISPR Transposon & mobilome engineering. With Harris Wang and Tyler Perdue. In Nature Biomedical Engineering 👉 nature.com/articles/s4155… 👉 innovativegenomics.org/news/carlotta-…

CryoPhold: CryoEM meets AlphaFold and molecular simulation to reveal protein dynamics 1. CryoPhold introduces a groundbreaking modular workflow that integrates AlphaFold-based ensemble generation, Bayesian reweighting against experimental cryo-EM maps, molecular simulation, and

Omgsh!!, #posit:: conference.

#positconf2025

DynaFold: A Latent Diffusion Based Generative Framework for Protein Dynamic Trajectory 1. The article introduces DynaFold, a novel deep learning framework that uses latent diffusion models to predict protein dynamic trajectories with high accuracy and efficiency. This method

🥳Excited to share our latest collaborative work using whole-cell models and #AI to design genomes!🦠🧬 What a time to live! Project led by Ioana Gherman, with Claire G, Lucia Marucci + more #synbio authors.elsevier.com/sd/article/S24…

Two of the world’s deadliest mosquito vectors—Aedes aegypti and Anopheles funestus—have evolved, spread, and adapted in ways that complicate global disease control, two studies show in Science. 📄: scim.ag/46sCL8T 📄: scim.ag/46yoo33

I am thrilled to release ProteinDJ: a high-performance and modular protein design pipeline. Our open-source workflow incorporates #RFdiffusion, #ProteinMPNN, #FAMPNN, #AlphaFold2 and #Boltz-2. It is a fast, free, and fun way to design proteins (1/5) doi.org/10.1101/2025.0…

Thrilled to share our work on transcription initiation and termination being spatially coordinated out today in Science! science.org/doi/10.1126/sc…

Understanding P-Values is essential for improving regression models. In 2 minutes, I'll crush your confusion.

Our latest collaborative paper with David Baker's lab is now live in Cell Biomaterials (Cell Biomaterials, Cell Press)! Check out "Stimuli-triggered Formation of De Novo-designed Protein Biomaterials"! 🔓 : cell.com/cell-biomateri…

Today we are introducing the Key-Cutting Machine (KCM) for protein and peptide design. Like cutting a key to fit a lock, KCM sculpts sequences to match a target backbone—on a single GPU. No retraining. No clusters. 🧬🔑 Instead of black-box generation, KCM runs an optimization

Introducing Molview - the ipython/jupyter widget version of nano-protein-viewer🔍:

trying to make protein sequences viewable in Hugging Face datasets... seen cool stuff like this, but do people have a favorite protein viewer library? ideally lightweight so it renders fast x.com/stevenyuyy/sta…

🚀🚀David Baker paper from nature is here 👇 What if we could design antibodies from scratch to target any disease epitope with atomic precision?Institute for Protein Design "Atomically accurate de novo design of antibodies with RFdiffusion" • RFdiffusion was fine-tuned on antibody

Scientists built these tiny diamond crystals using a technique known as DNA origami, in which #DNA molecules fold themselves into elaborate shapes. Learn more in this 2024 #SciencePerspective on #OrigamiDay: scim.ag/4p5SdQk

Today in nature, in work led by Aditi Merchant, we report the ability to prompt Evo to generate functional de novo genes. You shall know a gene by the company it keeps! 1/n

We are looking for PhDs and Postdocs! So proud of my students on achieving so many amazing things during their "very first year". I have been asked many times how I like being faculty, especially with funding cuts. My answer is always "it is the prefect job for me"! Still

I will be attending NeurIPS Conference this year from Dec5-7. I am also actively recruiting PhD students and Postdocs in ML for scientific discovery, with a focus on biochemistry and lab-in-the-loop methodologies. Please reach out if you want to chat!