Hi 👋 I'm Alex and this is my blog, which is mostly about biology and computers.
I like to use ML to solve hard problems in biology—like designing new enzymes—by building cloud bioengineering platforms that scale.
I completed my PhD in using ML for protein design in 2017 📖 and spent the past 6 years at Ginkgo Bioworks 🌱, where I've scaled the use of machine learning for protein engineering to hundreds of different enzymes across dozens of functional classes ☕️.
🗓️ 2024. I'm currently looking for new opportunities where I can contribute to a team working on ML for protein design. Please get in touch by email!
🌳 2021–2023. As Sr. Engineer for protein ML at Ginkgo, I led dozens of protein ML projects, including benchmarking, scaling, and development of generative ML models for protein engineering and enzyme discovery. Some of my main responsibilities included implementing and onboarding new methods from the literature (diffusion models), scaling existing approaches (sequence and structure transformers), and detailed benchmarking of the strengths and weaknesses of existing methods for specific problems.
🌲 2017–2021. I joined Ginkgo Bioworks as a Protein Engineer focused on enzyme design and discovery using machine learning approaches. In addition to engineering hundreds of enzymes, some of my main achievements during this time were infrastructure: I created an enzyme engineering data platform that enabled both benchmarking and automated iterative design and has now been used across thousands of massively parallel design-build-test-learn cycles, as well as containerizing and deploying computational protein design workloads on cloud compute.
🌱 2013–2017. My PhD was focused on advancing the field of machine learning for protein design via leading a team to the construction of a large, high-quality benchmark dataset that enabled the improvement of ML protein design algorithms. My adviser was Justin Siegel at the University of California, Davis.
🍇 2010–2013. I made wine in Napa Valley (3 harvests) and decided to go to grad school
🧪 2006–2010. BA at Bard College in biology, for two years I was a teaching assistant for organic chemistry (which remains my favorite subject)
Papers, patents, and other publications:
- Writing on biology and computers, this site, where I write about biology and computers
- Google Scholar lists my scientific publications on ML for protein design, and Google Patents lists many of my inventions related to designed enzymes achieved over my career thus far with many brilliant coworkers
- I do lots of side projects for fun using ML, for example using AI to play card games, and since I am learning to develop apps for the iPad, I am building an AI-powered protein viewer called Rhodo