AI Agent -Driven Biochemical Optimization

When I started this space, I vowed not to become just a mouthpiece of my employer - but when my employer does something interesting, of course I'm not going to reflexively avoid writing about it.  On the autonomous labs front, there's an interesting preprint showing how an intelligent agent interacting with an autonomous laboratory system can generate new knowledge. I'd like to think I would have covered it anyways, but since it is the autonomous laboratory at my workplace, I'm especially eager to do so.  In a collaboration between Ginkgo and OpenAI, an agent was used to optimize a cell-free protein synthesis reaction using our autonomous laboratory based on Reconfigurable Automation Cart (RAC) technology.  This isn't the first time this has been done, but I think it has a number of interesting elements. Plus, optimizing complex biochemical reactions is a broadly interesting area to explore.  And, thinking up new services running on our autonomous laboratory is exactly my bailiwick, and I certainly reserve the right to use this space to be a mouthpiece of myself!

AGBT 2026 Preview

AGBT starts on Monday at the Signia by Hilton Bonnet Creek in Orlando on Monday, but the pre-conference flurry of announcements is already rolling out.  Here is a quick scan of what's already been telegraphed to be in store next week - and expect more announcements over the next few days.  I'm getting to Orlando on Friday - far before most people so perhaps I can actually focus on writing (though I also have a backlog of follow-ups from last week's SLAS lab automation conference).   I've supplied links for many of these items, though in some cases it isn't easy to find a single link to include

Pancreatic Adenocarcinoma Mutation Trajectories at Single Cell Resolution

Single cell RNA sequencing is nearly ubiquitous; single cell DNA sequencing has been much rarer.  I'm going to dive in a bit - but not a full review - of a recent paper which described single cell DNA sequencing of pancreatic ductal adenocarcinomas.  The paper applied the Mission Bio droplet-based PCR approach, which hasn't had quite the buzz of its close technological cousin 10X Genomics.  And there are some interesting implications of the findings in this paper to impending developments in oncology therapeutics - including one in which I have more than academic interest.

Non-coding DNA's Alpha Moment

I had been meaning to read the AlphaGenome paper on non-coding variant effect prediction from Google DeepMind which recently showed up in Nature, but had found excuses not to dive in.  Then DeciBio’s Stephane Budel posted on LinkedIn with some incisive comments and few things spur me to action better than my sense of competition! So here's a quick, incomplete & imperfect take on this giant paper.