Director, Research AI

Alnylam Pharmaceuticals, Inc.; Cambridge, Northern (MA, KY); Hybrid; USD 210,000 - 260,000; Full time

Job summary

Alnylam Pharmaceuticals, Inc. is seeking a highly technical Director of Artificial Intelligence to expand AI capabilities across the Research organization.

You will design and deploy agentic workflows that integrate into scientific research and siRNA discovery, leading a small but focused team of data scientists and engineers. This hands-on leadership role blends computational biology, AI engineering, and platform design, partnering with Research and IT to deliver durable, enterprise-grade AI

Qualifications

• PhD (or MS with equivalent experience) in Computational Biology, Computer Science, AI/ML, or related field.
• 10+ years of computational biology experience applying AI/ML in industry, preferably within drug discovery.
• Proven experience leading technical teams and delivering AI-driven products or platforms in complex environments.

Responsibilities

• Embed AI into day-to-day scientific workflows in partnership with Research teams.
• Develop and deploy multi-agent AI workflows to automate core research activities.
• Lead AI strategy and scientific enablement to align with data & AI strategy.
• Build and lead a 3–5 person interdisciplinary team of data scientists and software engineers.
• Integrate AI workflows with enterprise data platforms and IT environments.
• Deliver production-grade systems with robust pipelines and MLOps practices.

Skills

Agentic AI systems

AWS Bedrock

GCP environments

LLM ecosystems

Leadership

Computational Biology

Education

PhD or MS in Computational Biology/CS/AI/ML

Tools

AWS Bedrock

GCP

LLM platforms

Job description

Alnylam Pharmaceuticals is seeking a highly technical and strategic Director of Artificial Intelligence to lead the expansion of AI capabilities across the Research organization. This role will establish and lead a focused team to design and deploy next-generation agentic workflows that integrate directly into scientific research and the discovery of novel siRNA therapeutics.

The Director will play a central role in partnering with Research teams to embed AI into daily scientific workflows, enabling faster, more scalable, and more reproducible discovery processes. This is a hands-on leadership role combining computational biology, AI engineering, and platform design, with strong partnership across Research and IT to deliver durable, enterprise-aligned solutions.

You will join a growing Data & AI organization (20+ scientists and engineers) focused on transforming Alnylam into an AI-enabled research enterprise.

Responsibilities

Embed AI into Scientific Workflows (Primary Focus)

• Partner deeply with Research teams to embed AI-driven solutions into day-to-day scientific workflows


• Identify high-value opportunities to augment target and ligand discovery, and where appropriate, experimental design, data analysis, and decision-making


• Drive adoption and measurable impact through close collaboration with assay teams and scientific leadership

Develop and Deploy Agentic AI Workflows

• Architect and deploy multi-agent systems that automate and orchestrate core research activities, including:
  
  
  
  • Target Discovery that encompasses human genetics datasets
  
  
  • Ligand Discovery for the delivery of siRNAs to novel tissues and cell types
  
  
  • Competitive intelligence (landscape monitoring, literature synthesis, target scouting)
  
  
  • Experimental design and hypothesis generation
  
  
  • Data analysis and interpretation
  
  
  • Knowledge synthesis from public and in-house data
  
  
  
  


• Integrate coding agents, research agents, and evaluation frameworks into scientific pipelines


• Ensure systems are scientifically grounded, validated, and continuously improved via lab feedback loops

Lead AI Strategy & Scientific Enablement

• Define and execute the AI roadmap for Research aligned to Alnylam’s broader Data & AI strategy


• Drive adoption of AI to improve speed, quality, and scalability of research workflows


• Identify and prioritize AI use cases with clear scientific and operational impact

Build and Lead an AI Engineering & Science Team

• Recruit, lead, and develop a 3–5 person interdisciplinary team of data scientists and software engineers


• Establish a high-performance culture blending scientific rigor with agentic software engineering discipline


• Provide hands-on technical leadership in AI/ML, agent development, and production deployment

Integrate with Enterprise Data & IT Platforms

• Partner with IT to integrate AI workflows into the enterprise data platform and lakehouse environment


• Contribute to secure, scalable, and compliant AI systems across AWS and GCP environments


• Ensure alignment with data governance, security, and regulatory standards

Deliver Production-Grade Systems

• Oversee development of robust pipelines, model deployment frameworks, and evaluation systems


• Drive best practices in MLOps, reproducibility, and model validation


• Ensure AI solutions are reliable, scalable, and operationalized within Research

Support Computational Enablement of Design Efforts

• Provide computational and infrastructure support for ligand and antibody design efforts


• Work with the Alnylam Human Genetics (AHG) team to bring best-in-class AI workflows to human genetics analyses


• Partner with domain experts to ensure alignment with ongoing design strategies and scientific leadership

Qualifications

Education & Experience

• PhD (or MS with equivalent experience) in Computational Biology, Computer Science, AI/ML, or related field


• 10+ years of computational biology experience applying AI/ML in industry, preferably within drug discovery


• Proven experience leading technical teams and delivering AI-driven products or platforms in complex environments

Technical Expertise

• Demonstrated experience building agentic or multi-agent AI systems and workflow automation


• Experience with AWS (including Bedrock) and/or GCP environments


• Experience with modern LLM ecosystems and data integration at scale

Domain Knowledge

• Experience in biopharma research or drug discovery environments


• Understanding of experimental workflows and scientific data generation


• Familiarity with nucleic acid-based therapeutics is preferred

Preferred Qualifications

• Experience building AI systems integrated with lab-in-the-loop workflows


• Familiarity with enterprise data platforms and regulated environments


• Track record of deploying AI solutions in cross-functional organizations

Why Join Alnylam

• Build agentic AI systems that directly impact scientific workflows and lend further speed to our already speedy rationale-design siRNA discovery pipeline.


• Work at the interface of computational science, engineering, and drug discovery


• Shape how AI is operationalized across a leading RNAi therapeutics organization


• Deliver life-altering medicines to patients in need of novel therapies

About Alnylam

We are the leader in RNAi therapeutics– a revolutionaryapproach with the potential to transform the lives of people with rare and common diseases. Built on Nobel Prize-winning science, Alnylam has delivered the breakthroughs that made RNAi therapeutics possibleand are just at the beginning of what’s possible. Our deep pipeline, late-stage programs, and bold vision reflect our core values: fierce innovation, passion for excellence, purposeful urgency, open culture and commitment to people. We're proud to be a globally recognized top employer, wherean authentic, inclusive culture and breakthrough thinkingfuel one another.

At Alnylam, we commit to an inclusive recruitment process and equal employment opportunity. Qualified applicants will receive consideration for employment without regard to their sex, gender or gender identity, sexual orientation, race, color, ethnicity, national origin, ancestry, citizenship, religion, creed, physical or mental disability, pregnancy status or related conditions, genetic information, veteran or military status, marital or familial status, political affiliation, age, or any other factor protected by federal, state, or local law. Alnylam is an E-Verify Employer.

Before applying, please review Alnylam's Candidate Privacy Notice regarding how Alnylam handles Personal Data you provide with your application for employment.

The pay range below reflects the full-time base salary range we expect to pay for this role at the time of posting. Base pay will be determined based on a number of factors including, but not limited to, relevant experience, skills, and education. This role is eligible for an annual short-term incentive award (e.g., bonus or sales incentive) and an annual long-term incentive award (e.g., equity).

Alnylam’s robust Total Rewards package is designed to support your overall health and well-being. We offer comprehensive benefits including medical, dental, and vision coverage, life and disability insurance, a lifestyle reimbursement program, flexible spending and health savings accounts and a 401(k)with a generous company match. Eligible employees enjoy paid time off, wellness days, holidays, and two company-wide recharge breaks. We also offer generous family resources and leave. Our commitment to your well-being reflects our belief that caring for our people fuels the impact we create together.