- #CLAUDE.md files that orient Claude to your project's structure, conventions, and domain quirks
- Reference materials (data dictionaries, trusted queries), so the model knows what's actually in your tables
- .claudeignore to prevent reading secrets, redundant files, or data you shouldn't share
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I wrote up my approach in a blog post: bennettwaxse.com/blog/bioinfo...
If you're a researcher curious about Claude Code, here's where I start.
If you have a different workflow, I'd love to hear about it.
Clearly a big fan of VZV vaccination as an ID doc, but I need to dig into this deeper before it makes its way into patient counseling for me. Curious what others took away from the sex-specific differences, and wonder if other types of analysis (e.g., TTE) might be better suited for this...
5/5
Bennett Waxse
Bennett Waxse
Bennett Waxse
Why bother? Because LLM context windows are big enough to hold an entire project—so use them. Don't hide how you derived a cohort when that derivation can inform what you're asking the model to do next.
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The 20% relative reduction in dementia risk is striking, and the regression discontinuity design is cool--particularly in the presence of no discontinuity among education (S15-S17) or in placebo temporal tests across other years (S12-S14). But, I was still left with more questions than answers.
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What I've been reading: a natural experiment to estimate the herpes #zoster vaccine's effect on dementia--did you know that the effect was predominantly observed in females?
pmc.ncbi.nlm.nih.gov/articles/PMC...
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Bennett Waxse
Bennett Waxse
Bennett Waxse
I've been using #ClaudeCode for #research #informatics—cohort building, debugging pipelines, genomics in #AllofUs. Before any of that was useful, I had to set things up right.
The setup isn't complicated, but it matters. Here's how I do it:
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First, this applies only to the live-attenuated vaccine, not Shingrix, which is now standard. Second (what's really nagging at me), the dementia protection really only appeared in women, even though the vaccine prevented shingles and post-herpetic neuralgia equally in both sexes (Table S3).
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Are we looking at detection bias? Do shingles episodes trigger cognitive screenings in women more readily? Is there a systematic difference in healthcare contacts between sexes? And we still don't know the mechanism: is it non-specific immunomodulation over VZV reactivation reduction?
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