Scientific AI Engineer

Harvard Medical School; Boston (MA); On-site; USD 130,000 - 170,000; Full time

Benefits offered by this job

Parental leave

Medical, dental, and vision coverage

Retirement plans with universitycon-

Wellbeing resources

Support for families and caregivers

Tuition assistance and reimbursement

Commuter benefits

Job summary

Harvard Medical School's ImmGen program seeks a Scientific AI Engineer to design an AI-powered data agent that leverages ImmGen data with external resources to answer scientists’ questions in natural language. You will wrap and orchestrate existing tools, define use cases, and ensure robust, reproducible results.

The role emphasizes safe, cost-conscious AI workflows, collaboration with immunology researchers, and developing interfaces to connect data resources to an AI agent.

Qualifications

• Minimum of five years’ post-secondary education or relevant work experience.
• Advanced degree or equivalent professional experience in computational biology, bioinformatics, genomics, or a related field.
• Strong Python programming skills and experience with scientific computing libraries such as pandas, NumPy, SciPy, scikit-learn, Scanpy, Bioconductor, or equivalent tools.
• Strong software-engineering skills, including experience with APIs, data schemas, testing, version control, logging, documentation, and reproducible workflows.
• Experience integrating software with existing scientific data platforms, analytical pipelines, web services, or computational tools.
• Hands-on experience with LLM applications, including tool/function calling, retrieval-augmented generation, structured outputs, agent orchestration, or natural-language-to-SQL/code systems.

Responsibilities

• Work closely with ImmGen scientists to understand datasets, metadata, tools, APIs, and access mechanisms.
• Wrap existing ImmGen data so they can be invoked by an LLM-based agent.
• Collaborate to define use cases, formats, and scientific language and graphics.
• Map questions to ImmGen resources and workflows.
• Develop interfaces, schemas, guardrails and orchestration logic to connect the agent to ImmGen infrastructure.
• Implement safeguards against hallucinations, invalid interpretations and unsupported claims.
• Ensure that expensive computes are not triggered automatically.
• Be a team player in rewriting scientific data propagation.

Skills

Python

LLM applications

Education

Advanced degree in computational biology

Tools

APIs

Data schemas

Testing

Version control

Logging

Documentation

Reproducible workflows

Job description

Company Description

By working at Harvard University, you join a vibrant community that advances Harvard's world-changing mission in meaningful ways, inspires innovation and collaboration, and builds skills and expertise. We are dedicated to creating a diverse and welcoming environment where everyone can thrive.

Company Description

By working at Harvard University, you join a vibrant community that advances Harvard's world-changing mission in meaningful ways, inspires innovation and collaboration, and builds skills and expertise. We are dedicated to creating a diverse and welcoming environment where everyone can thrive.

Why join Harvard Medical School?

Harvard Medical School's mission is to nurture a diverse, inclusive community dedicated to alleviating suffering and improving health and well-being for all through excellence in teaching and learning, discovery and scholarship, and service and leadership.

You’ll be at the heart of biomedical discovery, education, and innovation, working alongside world-renowned faculty and a community dedicated to improving human health. This is more than a job - it’s an opportunity to shape the future of medicine.

About the Department of Immunology:

Position open for a Scientific AI Engineer, to work in the context of the ImmGen consortium at Harvard Medical School. ImmGen is an NIH-funded consortium of Immunology and Computational biology labs who pool expertise to decipher gene expression and it regulation in the immune system, whose data have become a valuable resource for the Immunology research community worldwide. The group wishes to develop a data analysis AI agent that will harness ImmGen data together with external databases to answer user questions formulated by scientists in natural language and return data-grounded visualizations and contextualization.

Job Description

We are seeking an autonomous Scientific AI Engineer who will work closely with the existing ImmGen computational team and immunologists to design and implement this agent. They will integrate ImmGen’s existing data resources and analytical capabilities with the AI-powered interface. They will not be expected to acquire or manage ImmGen data, nor rebuild analytical tools. Instead, they will determine how to expose, adapt, orchestrate, and extend those tools so they can be reliably accessed through natural-language interaction, using MCP strategies that can be exploited by AI agents.

The position will:

• Work closely with ImmGen scientists and data analysts to understand existing datasets, metadata, documentation, tools, APIs, and access mechanisms, adapt and wrap existing ImmGen data so they can be invoked reliably by LLM-based agent that calls on public analytical and visualization tools.
• Collaborate with ImmGen scientists to define supported use cases, desired answer formats, and appropriate scientific language and graphics.
• Map existing and potential researcher questions to the appropriate existing ImmGen resources and analytical workflows.
• Develop the software interfaces, APIs, schemas, computational guardrails and orchestration logic required to connect the agent to ImmGen’s existing infrastructure.
• Implement safeguards against hallucinated results, invalid comparisons, inappropriate statistical interpretations, and unsupported biological claims.
• Ensure that the agent does not automatically initiate unduly expensive computes.
• We are looking for a team player eager to participate in the exciting re-writing of scientific data propagation.

Qualifications

Basic Qualifications:

• Minimum of five years’ post-secondary education or relevant work experience.

Additional Qualifications and Skills:

• Advanced degree or equivalent professional experience in computational biology, bioinformatics, genomics, or a related field.
• Strong Python programming skills and experience with scientific computing libraries such as pandas, NumPy, SciPy, scikit-learn, Scanpy, Bioconductor, or equivalent tools.
• Strong software-engineering skills, including experience with APIs, data schemas, testing, version control, logging, documentation, and reproducible workflows.
• Experience integrating software with existing scientific data platforms, analytical pipelines, web services, or computational tools.
• Hands‑on experience with LLM applications, including tool/function calling, retrieval‑augmented generation, structured outputs, agent orchestration, or natural‑language‑to‑SQL/code systems.

Additional Information

• Term: This is a 2-year term position from the date of hire, with the possibility of extension, contingent upon work performance and continued funding to support the position.
• Standard Hours/Schedule: 35 hours per week.
• Visa Sponsorship Information: Harvard University is unable to provide visa sponsorship for this position.
• Pre-Employment Screening: Identity.
• Interview Format: The interview process will include both virtual and in-person components (e.g., initial virtual screening followed by on‑campus final interviews).
• Staying Informed About Your Application: Due to the high volume of applications, we may not always be able to reach out right away, but you can track your status anytime through the Careers@Harvard portal.

Work Format Details

This position has been determined by school or unit leaders that all duties and responsibilities must be performed at a Harvard or Harvard-designated location. Certain visa types may limit work location. Individuals must meet work location sponsorship requirements prior to employment.

Salary Grade and Ranges

This position is salary grade level 057. Please visit Harvard's Salary Ranges to view the corresponding salary range and related information.

Benefits

Harvard offers a comprehensive benefits package that is designed to support a healthy work-life balance and your physical, mental and financial wellbeing. Because here, you are what matters. Our benefits include, but are not limited to:

• Generous paid time off including parental leave
• Medical, dental, and vision health insurance coverage starting on day one
• Retirement plans with university contributions
• Wellbeing and mental health resources
• Support for families and caregivers
• Professional development opportunities including tuition assistance and reimbursement
• Commuter benefits, discounts and campus perks

Learn more about these and additional benefits on our Benefits & Wellbeing Page.

EEO/Non-Discrimination Commitment Statement

Harvard University is committed to equal opportunity and non-discrimination. We seek talent from all parts of society and the world, and we strive to ensure everyone at Harvard thrives. Our differences help our community advance Harvard's academic purposes.

Harvard has an equal employment opportunity policy that outlines our commitment to prohibiting discrimination on the basis of race, ethnicity, color, national origin, sex, sexual orientation, gender identity, veteran status, religion, disability, or any other characteristic protected by law or identified in the university's non-discrimination policy. Harvard's equal employment opportunity policy and non-discrimination policy help all community members participate fully in work and campus life free from harassment and discrimination.