Machine Learning Data Engineer (AIM2)

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 RESPOSIBILITIESDeveloping, 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 QUALIFICATIONSPhD in Computational Biology, Biology, Physics, Statistics, or a related technical disciplineMasters 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 environmentSingle‑cell/NGS, functional genomics, genetics, or proteomics data analysis experienceHands‑on experience developing Nextflow pipelines for processing NGS dataStrong full‑stack programming skills with a focus on PythonExperience solving complex analyses/problems in a timely fashionExcellent communication and collaboration skills with experience working effectively in cross-functional teamsPREFERRED QUALIFICATIONSBackground 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 toolingHands-on experience handling, processing, integrating, and analyzing large heterogenous data sets data in a drug discovery research environmentExperience with Claude Code or equivalentStrong publication record with demonstrated contributions to the fieldORGANIZATIONAL RELATIONSHIPSDirector 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. Sunshine ActPfizer reports payments and other transfers of value to health care providers as required by federal and state transparency laws and implementing regulations. These laws and regulations require Pfizer to provide government agencies with information such as a health care provider’s name, address and the type of payments or other value received, generally for public disclosure. Subject to further legal review and statutory or regulatory clarification, which Pfizer intends to pursue, reimbursement of recruiting expenses for licensed physicians may constitute a reportable transfer of value under the federal transparency law commonly known as the Sunshine Act. Therefore, if you are a licensed physician who incurs recruiting expenses as a result of interviewing with Pfizer that we pay or reimburse, your name, address and the amount of payments made currently will be reported to the government. If you have questions regarding this matter, please do not hesitate to contact your Talent Acquisition representative. EEO & Employment EligibilityPfizer is committed to equal opportunity in the terms and conditions of employment for all employees and job applicants without regard to race, color, religion, sex, sexual orientation, age, gender identity or gender expression, national origin, disability or veteran status. Pfizer also complies with all applicable national, state and local laws governing nondiscrimination in employment as well as work authorization and employment eligibility verification requirements of the Immigration and Nationality Act and IRCA. Pfizer is an E-Verify employer. This position requires permanent work authorization in the United States. Pfizer endeavors to make accessible to all users. If you would like to contact us regarding the accessibility of our website or need assistance completing the application process and/or interviewing, please email View email address on click.appcast.io. This is to be used solely for accommodation requests with respect to the accessibility of our website, online application process and/or interviewing. Requests for any other reason will not be returned. To learn more about acceptable and prohibited uses of AI during the recruitment process, please review our candidate AI-use guidelines available on Pfizer Careers. Research and Development SummaryLocation: United States - Massachusetts - CambridgeType: Full time