Senior Bioinformatics Engineer — Spatial AI

LatchBio • San Francisco, CA

49d • $160,000 - $200,000 • Onsite

About The Position

At LatchBio, we're building AI agents that help 4,000+ scientists analyze and interpret data from the next generation of spatial and multi-omic tools in biotech.
We are seeking a senior bioinformatics engineer with hybrid computational and experimental expertise in spatial biology to help pioneer a new category of agentic analysis tools.

In this role, you'll both do the work yourself and set the quality standard for others: reviewing analyses, catching errors, and ensuring every deliverable is defensible.

Requirements

• Experience with end-to-end data analysis for one or more of the following spatial technologies: Seeker or Trekker (Slide-seq), MERFISH, DBiT-seq, Xenium, Visium, Stereo-seq, GeoMx, CosMx, or other similar assays
• Analyzed 3+ datasets from raw data to end insight for either publications or industry experiments with real world consequences
• Working understanding of kit specific quality control thresholds and intuition for numerical examples of positive or negative results (eg. 100K cells from 10X Chromium means something is wrong)
• Familiarity with the landscape of computational biology tools for spatial specific tasks (eg. cell segmentation, cell typing, ligand-receptor analysis)
• Strong understanding of experimental design, hypothesis generation and scientific conclusions from papers using one of the spatial technologies described
• Working understanding of concepts in statistical inference: hypothesis testing, confidence intervals and/or estimators.
• Working understanding of important algorithms in high dimensional data analysis: eg. PCA, neighborhood, UMAP

Nice To Haves

• Published research that relied on modern spatial biology techniques.
• Engineered tools or packages in the spatial biology domain.
• Experience generating training data for AI agents or foundation models.

Responsibilities

• Own end-to-end spatial transcriptomics analyses across multiple projects: raw platform outputs → QC and failure diagnosis → cell segmentation and assignment → cell typing → DE/enrichment → spatial inference → defended biological claim.
• QC and review the work of other spatial bioinformatics engineers: catch analytical errors, validate conclusions, and ensure every notebook and decision log meets gold-standard quality.
• Build reproducible workflows and produce clear decision traces: what was filtered, why, what changed the conclusion, what would falsify the claim.
• Perform spatial reasoning beyond standard clustering: neighborhood and adjacency enrichment, spatial gradients and niches, spatial DE, and spatial autocorrelation-aware analyses.

Benefits

• Significant Equity (stock)
• Unlimited PTO
• Waterfront office in China Basin (five days per week in person in San Francisco)
• Free lunch and dinner
• 100% premium covered on Blue Shield’s platinum health plan ($0 premium, $0 deductible)
• 401(k) plan options
• Company-sponsored professional development
• Work visa sponsorship
• Team-wide science reading groups

What This Job Offers

• Job Type: Full-time
• Career Level: Mid Level
• Education Level: No Education Listed