Hi, I'm Ben
I work on genomic language models at Radical Numerics — plus quant finance, mountain biking, agentic coding, and lots more.
Previously, I worked on computational therapeutics at Pattern Biosciences — I truly believe it's one of the most exciting and impactful biology problems of our time. Before that, computational infrastructure and data tooling at Deep Origin, and I led the bioinformatics team at Loyal, an early-stage biotech dedicated to extending the lifespan and healthspan of dogs.
What seems like ages ago, I did my PhD in Dr. Ami Bhatt's lab at Stanford, where I used advanced genomic techniques to study the human microbiome. I'm proud to say I characterized the first examples of bacteria transmitted between the gut microbiome of adults, and of phages transmitted from the gut microbiome of a mother to that of her infant.
Latest writing
All posts →-
Reducing RNA-seq batch effects by re-aligning TCGA and GTEx
I want to be able to compare RNA-seq data between several public sources and internal datasets. I care a lot about the differential expression of certain…
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s3stasher simplifies using AWS S3 in python
Working with cloud files in python is a necessary pain at any biotech organization. While packages like pandas transparently handle S3 URIs, I still found…
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Fixing a Milli-q purifier for 99% off
We bought a used Milli-q 7005 ultrapure water purifier from an auction for a great price. It came with most of what we need, but was missing the external…
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Does AMD 3D V-Cache help in bioinformatics?
Introduction In our new office at Pattern, I have 42U of server rack space to play with, so I want to get an AMD EPYC server for some long-running…
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Tail risk hedging with VIX calls (Stanford MSE448 final)
A few years ago, while in the last year of my PhD at Stanford, I published this blog post on using VIX calls to hedge against severe market downturns. The…
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Cross-account AWS FSx for Lustre and S3 data repository associations
FSx for Lustre and S3 are two complementary methods of storing data in Amazon Web Services (AWS). FSx offers an extremely performant, reliable, true…