Selective Th2
I'm a backend/infrastructure engineer at Uber with no wet-lab background.
Core trick
Reads only needed slices of a 16.8 GB S3 expression matrix, then has skeptic agents refute candidate suppressors against a permutation null.
Description
I'm a backend/infrastructure engineer at Uber with no wet-lab background. This week I used Claude Science and Claude Code to run a real analysis on the Zhu & Dann 2025 genome-scale CRISPRi Perturb-seq screen in primary human CD4+ T cells (Marson lab) — asking a question the original study's single Th2-minus-Th1 axis structurally can't answer: which gene knockdowns selectively suppress the Th2 (allergy) program without merely skewing cells toward Th1? That distinction is the whole target definition for asthma and allergy drugs.
I streamed the full 16.8 GB differential-expression matrix directly from public S3 — reading only what I needed, never downloading it — decomposed the Ota-2021 signature into independent Th2 and Th1 arms, and found an exciting signal: a clean selective quadrant, 420 candidate suppressors, and GATA3 on top.
Then I tried to destroy it. I built a multi-agent review layer in Claude Code — an investigator agent proposing mechanisms, a skeptic agent adversarially refuting them, and a 6-agent audit of my own methods. Under competitive scoring the headline arm-correlation collapsed (from +0.54 to +0.18, a scoring artifact); a permutation null put the empirical FDR near 1 (no better than random gene sets); and GATA3 re-scored as a Th1-skewer, exactly as canonical biology predicts.
The result is an honest, calibrated negative — plus a reproducible streaming pipeline and an agentic audit layer that caught the over-claim before it went out. It matters because most hits in high-dimensional screens are artifacts; the reusable contribution is the infrastructure for catching them, and a demonstration that a software engineer can do trustworthy computational biology precisely because the tools help you distrust your own results.
ShivenTripathi/claude-science-hackathon★ 00 forksHTMLMITCreated Jul 8, 2026 · last push Jul 14, 2026
README excerpt
# claude-science-hackathon Work from the **Built with Claude: Life Sciences** hackathon (Researcher track). 🎬 **2-minute demo video:** https://youtu.be/yL9Hp9oprlQ · local copy: [`media/demo.mp4`](./media/demo.mp4) · 🌐 **Live site:** https://shiventripathi.github.io/claude-science-hackathon/ > **Start with [`RECONCILIATION.md`](./RECONCILIATION.md)** — the single reconciled view across all > four tracks: what agrees, the one sharp correction (GATA3), the cross-pipeline convergence, and > what actually survives. Short version: the core scientific claim — single-gene *selective* Th2 > suppression — is a **calibrated negative**, reached independently by three tracks; a fourth track > reframes the phenotype to STAT6/GATA3 *collapse phenocopy* (the bar an oral STAT6 degrader clears), > which calibrates as a classifier and nominates a druggable off-axis map without rescuing the > selectivity negative. The durable deliverables are the reproducible streaming pipeline, the agentic > review infrastructure, the AD translational-filter layer, and the reusable collapse scorer. ## Projects ### [`th2-selective-suppressors/`](./th2-selective-suppressors) — Selective Th2 suppressor re-analysis A re-analysis of the **Zhu & Dann et al. 2025** genome-scale CRISPRi Perturb-seq screen in primary human CD4+ T cells, asking: *which gene knockdowns selectively suppress the Th2 program (GATA3 / IL4 / IL5 / IL13) without flipping cells toward Th1?* — the allergy-relevant d