Job Description

Company Description

Yale University, located in New Haven, Connecticut, has been at the forefront of education and research for over 300 years, fostering global impact through connection, creativity, and innovation. As a premier research university, Yale emphasizes interdisciplinary collaboration and provides a dynamic environment for discovery and growth.

Role Description

The Ishizuka Lab is recruiting a post-graduate dry lab Research Associate to work at the intersection of AI, protein design, single cell genomics and cancer immunotherapy. 

This role sits within a broader effort to design next-generation biologics (e.g., nanobodies, immune modulators) using reinforcement learning, diffusion/generative models, and structure-based evaluation (e.g., AlphaFold3), integrated with single-cell and functional genomics data from tumor immune systems. 

You will also be involved in building computational frameworks to learn from tumor immune single-cell data, helping to improve our models of cellular state and response.

You will work closely with computational and experimental collaborators to build closed-loop design systems: models propose sequences, experimental systems evaluate function, results feed back into model improvement. 

We are looking for someone highly technical, ambitious, and independent, who is excited to push toward AI-native biologics discovery.

Commitment: We strongly prefer candidates who can commit to two consecutive one-year renewable terms (2 years total)

What you’ll do:

Core AI / protein design work 

• Develop and implement reinforcement learning pipelines for protein design
• Work with protein language models (e.g., ESM) and generative approaches (diffusion / masked modeling) to generate novel sequences 
• Contribute to nanobody and biologics design workflows targeting cancer-relevant proteins

Single Cell + data workflows

• Lead scRNA-seq and multi-modal analysis (QC, integration, clustering, annotation, differential expression, trajectory/perturbation analysis) across patient tumor immune samples
• Build and maintain reproducible analysis pipelines (clean code structure, documentation, version control, experiment tracking)

Communication + collaboration 

• Generate publication quality figures and analyses 
• Clear writing and story telling skills 
• Present results internally and contribute to manuscripts

You might be a fit if you’re

• Deeply interested in AI for biology and therapeutic design
• Strong in Python and modern ML frameworks (PyTorch / JAX)
• Experienced with or excited to learn:
• Reinforcement learning (e.g., policy optimization, offline RL)
• Generative models (diffusion, masked language models)
• Protein modeling or structural biology (e.g., AlphaFold, sequence models)
• Comfortable working in fast-moving, research-driven environments
• Rigorous, organized, and able to own projects end-to-end
• Able to communicate complex technical ideas clearly across disciplines

Education

Bachelor’s degree (or higher) in biology, computer science, math, engineering, or a related field.

How to apply

Email CV + brief cover letter + 3 references to jeffishizukalab@gmail.com.

Encouraged: include GitHub/portfolio, prior ML projects, or 1–2 example figures/analyses you’ve produced.

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