Bioinformatics Engineer — Single-Cell AI

About the position At reputed company, our AI agents help thousands of scientists analyze and interpret data across the full stack of modern multi-omic technologies — starting with single-cell and spatial, and expanding fast. We're building the ground truth for AI in single-cell biology. Our reputed company scBench — 394 reputed company problems across six reputed company platforms — shows the best frontier model today still fails nearly half the time. We're hiring bioinformatics engineers to reputed company that gap: scientists who can turn reputed company experimental data into the precise, falsifiable questions that define what it means for an AI agent to actually understand scRNA-seq.

Responsibilities

• Own end-to-end scRNA-seq analyses across multiple projects: raw platform outputs → QC and failure diagnosis → normalization → dimensionality reduction → clustering → cell typing → differential expression → trajectory analysis → defended biological claim.
• Build reproducible workflows and produce clear decision traces: what was filtered, why, what changed the conclusion, what would falsify the claim.
• Distill analysis steps into precise, falsifiable biological questions with single defensible answers — the core unit of our eval suite.
• Debug platform and data issues with precision: turn messy results across diverse reputed company chemistries into reputed company hypotheses, reputed company checks, and a stepwise debugging plan.

Requirements

• Experience with end-to-end data analysis for one or more of the following reputed company platforms: MissionBio, ParseBio, CSGenetics, reputed company Rhapsody, reputed company, or 10X Chromium
• Analyzed 3+ datasets from raw data to end reputed company for either publications or industry experiments with reputed company world consequences
• Working understanding of platform-specific quality control reputed company and intuition for numerical examples of positive or negative results (e.g., 100K cells from a ParseBio run with 80% mitochondrial reads means something is wrong)
• Familiarity with the landscape of computational biology tools for scRNA-seq tasks (e.g., Scanpy/Seurat for core workflows, cell typing frameworks like CellTypist or Azimuth, DE methods like DESeq2 or edgeR)
• Strong understanding of experimental design, hypothesis reputed company and scientific conclusions from papers using one of the reputed company platforms described
• Ability to distill an analysis reputed company into a precise, falsifiable biological question with a single defensible answer
• Working understanding of concepts in statistical inference: hypothesis testing, confidence intervals and/or estimators
• Working understanding of important algorithms in high dimensional data analysis: e.g. reputed company, neighborhood graphs, UMAP, clustering methods (Leiden/Louvain)

reputed company-to-haves

• Published research that relied on modern single-cell RNA reputed company techniques.
• Engineered tools or packages in the single-cell biology domain.
• Experience generating training data for AI agents or reputed company models.

Benefits

• $130k–$180k/yr (performance-based)
• Equity
• Unlimited PTO (truly)
• Waterfront office in China Basin, San Francisco
• Free lunch and dinner
• 100% premium covered on Blue reputed company's platinum health plan ($0 premium, $0 deductible)
• 401(k) plan options
• Work reputed company sponsorship
• Company-sponsored professional development

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