Machine Learning Data Engineer (AIM2)
- United States - Massachusetts - Cambridge
We are seeking an experienced Machine Learning Data Engineer to develop, operationalize, and continuously improve production bioinformatics pipelines and data products that support AI-driven discovery within the Internal Medicine Research Unit (IMRU).
The successful candidate will integrate and curate complex biological and clinical datasets for machine learning model development and deployment, while building scalable cloud-based data pipelines that enable insight generation across IMRU's proprietary and external data resources.
This role will partner closely with the Integrative Biology organization and the AI for Internal Medicine (AIM2) Discovery Group to deliver scientifically robust, trusted, and reusable data capabilities that accelerate evidence generation and improve the speed and quality of research across the portfolio.
ROLE RESPOSIBILITIES
- Developing, deploying, and operating production‑grade Nextflow pipelines on cloud infrastructure, ensuring scalable and reproducible execution.
- Owning pipeline lifecycle management, including upgrades, troubleshooting, performance tuning, and reliability improvements for reusable workflows.
- Implementing DevOps best practices for pipelines and platform services (e.g., CI/CD, automation, and engineering tooling).
- Partnering with wet‑lab and research scientists to translate data analysis requirements into robust, production‑ready pipeline and platform solutions.
- Processing, organizing, harmonizing and integrating relevant data types (e.g.single-cell omics, bulk transcriptomics, ATACseq, proteomics, functional genetics, and genetics) as inputs for ML model training or inference.
- Developing and evolving an omics data platform that enables efficient, scalable processing and delivery of *omics datasets as reliable data products.
- Driving collaborations with external partners and vendors to strengthen pipeline quality, sustainability, and adoption of best practices.
BASIC QUALIFICATIONS
- PhD in Computational Biology, Biology, Physics, Statistics, or a related technical discipline
- Masters in Computational Biology, Biology, Physics, Statistics, or a related technical discipline and a minimum of two years of experience developing data products and data integration solutions in a research or industry environment
- Single‑cell/NGS, functional genomics, genetics, or proteomics data analysis experience
- Hands‑on experience developing Nextflow pipelines for processing NGS data
- Strong full‑stack programming skills with a focus on Python
- Experience solving complex analyses/problems in a timely fashion
- Excellent communication and collaboration skills with experience working effectively in cross-functional teams
PREFERRED QUALIFICATIONS
- Background or demonstrated interest in life sciences, pharmaceutical research, drug discovery, or bioinformatics.
- Proven expertise in software engineering best practices, including python package development, DevOps, cloud architectures, CI/CD, and engineering tooling
- Hands-on experience handling, processing, integrating, and analyzing large heterogenous data sets data in a drug discovery research environment
- Experience with Claude Code or equivalent
- Strong publication record with demonstrated contributions to the field
ORGANIZATIONAL RELATIONSHIPS
Director of AIM2; AIM2 Innovation Fellows; Head of IMRU Integrative Biology; Integrative Biology Scientists; IMRU biology line teams; Integrative Biology and Digital ecosystem partners; AI/ML practitioners, computational biologists, translational scientists.
External:
May interact, as appropriate, with external technology partners, vendors, or academic / industry collaborators relevant to AI capability evaluation, development, and adoption.
Candidate demonstrates a breadth of diverse leadership experiences and capabilities including: the ability to influence and collaborate with peers, develop and coach others, oversee and guide the work of other colleagues to achieve meaningful outcomes and create business impact.
This is a site based hybrid role.
#LI-PFE

The annual base salary for this position ranges from $106,000.00 to $176,600.00. In addition, this position is eligible for participation in Pfizer’s Global Performance Plan with a bonus target of 15.0% of the base salary and eligibility to participate in our share based long term incentive program. We offer comprehensive and generous benefits and programs to help our colleagues lead healthy lives and to support each of life’s moments. Benefits offered include a 401(k) plan with Pfizer Matching Contributions and an additional Pfizer Retirement Savings Contribution, paid vacation, holiday and personal days, paid caregiver/parental and medical leave, and health benefits to include medical, prescription drug, dental and vision coverage. Learn more at Pfizer Candidate Site – U.S. Benefits | (uscandidates.mypfizerbenefits.com). Pfizer compensation structures and benefit packages are aligned based on the location of hire. The United States salary range provided does not apply to Tampa, FL or any location outside of the United States.



Relocation assistance may be available based on business needs and/or eligibility.

Candidates must be authorized to be employed in the U.S. by any employer.
U.S. work visa sponsorship (such as TN, O-1, H-1B, etc.) is not available for this role now or in the future.

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Research and Development
Breakthroughs that change patients’ lives
Research confirms what intuition tells us: that purpose-driven companies perform better, are more innovative, attract and retain the best people, and know how to unleash the power of those people. Pfizer’s purpose—Breakthroughs that change patients' lives—fuels everything we do and reflects our passion for building on our legacy as one of the greatest contributors of good to the world.
Each word in our purpose has meaning and reflects the value we strive to bring to patients and society:
“Breakthroughs” - These are the innovations, scientific and commercial, that we seek to deliver every day. All colleagues, regardless of role, level or location, strive for breakthroughs every day.
“Change” - We want to do more than simply improve patients’ medical conditions; we want to dramatically change their lives for the better.
“Patients’ lives” - We consider not only patients, but everyone they touch—including their families, caregivers, and friends—and everything they love to do. It’s an intentionally holistic view.
Our purpose ensures that patients remain at the center of all we do. We live our purpose by sourcing the best science in the world; partnering with others in the healthcare system to improve access to our medicines; using digital technologies to enhance our drug discovery and development, as well as patient outcomes; and leading the conversation to advocate for pro-innovation/pro-patient policies.
Every decision we make and every action we take is done with the patient in mind—and to nurture an environment where breakthroughs can thrive.
Our Values
To fully realize Pfizer’s purpose, we have established a clear set of expectations regarding “what” we need to achieve for patients and “how” we will go about achieving those goals.
The “how” is represented by four simple, powerful values—courage, excellence, equity, and joy—that define our company and our culture.
Courage: Breakthroughs start by challenging convention, especially in the face of uncertainty or adversity. This happens when we think big, speak up, and are decisive.
Excellence: We can only change patients’ lives when we perform at our best together. This happens when we focus on what matters, agree who does what, and measure our outcomes.
Equity: We believe that every person deserves to be seen, heard, and cared for. This happens when we are inclusive, act with integrity, and reduce healthcare disparities.
Joy: We give ourselves to our work, but it also gives to us. We find joy when we take pride, recognize one another, and have fun.
Pfizer Research & Development
Pfizer Research & Development serves as the beating heart of Pfizer's trailblazing product pipeline, the essence of our mission to bring life-changing medicines to the world.
With an unwavering commitment to innovation, we use a multidisciplinary approach that blends scientific expertise, cutting-edge technologies, and strategic collaborations, igniting a powerful engine that propels groundbreaking discoveries into life-saving treatments for patients in need.
Through our relentless pursuit of progress, we envision a future where cutting-edge medicines pave the way to healthier, happier lives worldwide.
Benefits at Pfizer
Pfizer offers competitive compensation and benefits programs designed to meet the diverse needs of our colleagues. Our Pay for Performance Philosophy and Practices reward colleagues based on the contributions they make to our business.
Our Competitive Benefits Programs help our colleagues by:
- Promoting Health and Wellness to help colleagues maintain and improve their physical and mental wellbeing. Pfizer offerings include health and disability insurance, preventative health programs, medical screenings, free or reduced-cost vaccinations, discounts on Pfizer products, mental health support, nutrition and fitness counseling and more.
- Strengthening Colleagues’ Financial Security by providing company contributions to retirement plans, life insurance and financial planning education to help colleagues achieve their financial goals.
- Providing Benefits and Time off for the Moments that Matter to ensure Pfizer colleagues have the time away from the office to recharge, recover and return to work as the best version of themselves. Vacation, Holiday time and Sick time are just the beginning, with a 12 week parental leave policy for both parents of a new born, 10 day of caregiver leave for those times when your family needs you whether it’s a child, spouse or parent, bereavement leave, and additional country-specific programs.
- And so much more, depending on your country and site, Pfizer offers childcare facilities or discount programs, on-site health and/or fitness centers, movement and mindfulness solutions, “Log in for your Day” work flexibility and so much more.
For U.S. based jobs, view an overview of Pfizer’s U.S. benefits program (opens in a new window)