Company Summary:

Ampersand Biomedicines is an innovative, privately held biotechnology company leading the way in developing multi-specific medicines that direct a wide range of therapeutic molecules to specific cells and biological contexts (  Ampersand was founded in Flagship Pioneering’s venture creation engine, where companies such as Moderna Therapeutics (NASDAQ: MRNA) and Seres Therapeutics (NASDAQ: MCRB) were conceived and created.  With a strong emphasis on innovation, Ampersand cultivates a highly dynamic and entrepreneurial environment. 

Position Summary:

Ampersand Biomedicines, Inc is looking for an enthusiastic and self-driven AI/ML Engineer with deep expertise in development of AI/Machine Learning/Deep Learning to join our team in developing a cutting-edge platform to identify and design new multi-specific medicines across a spectrum of therapeutic areas. This is a unique opportunity to help drive the growth of a rapidly growing early-stage science and technology company within a well-resourced environment. S/he will enjoy working in a pioneering, fast-paced, and collaborative start-up environment.


  • Develop and maintain novel AI/ML predictive models.
  • Lead the engineering efforts in creating and implementing methodologies and workflows for ML/Generative AI model development, LLM advancements.
  • Use publicly available and proprietary data to build AI pipelines and models for a variety of use-cases including prediction of drug targets and generation of target-binding antibodies.
  • Actively participate in designing experimental approaches to generate relevant data as well as to validate computational insights.
  • Develop computational frameworks to systematically characterize results from machine learning models from a biological perspective and provide feedback on improving the models.
  • Contribute new ideas, strategies, and approaches that further the company's goals.
  • Create concise data visualizations and communicate complex results to an interdisciplinary audience.

Key Qualifications:

  • PhD. or M.S in computational sciences (e.g. computer science, physics, mathematics, computational biology) preferably with applications in biology. Industry experience (2+ for Ph.D. and 5+ for M.S preferred).
  • Experience in applying ML techniques and/or deep learning to one or more of the following: omics data analysis, binder design, building knowledge bases etc. Expertise in at least one deep learning library - PyTorch, Tensorflow, JAX, keras required.
  • Coding experience (Python, Rust, C++, R or other languages) Experience with cloud computing (AWS), MLOps, next-generation-sequencing (NGS), single-cell genomics is a plus.
    • Must have a positive "can do" attitude, be a team player, show excellent judgment as well as work well independently.
    • Strong organizational, analytical, and problem-solving skills.
    • Ability to thrive in a fast-paced, multidisciplinary, and rapidly growing biotech environment.
    • Instinctive team player with excellent communication skills and precise attention to detail.

What We Will Offer you:

  • Comprehensive, competitive healthcare and dental coverage through Blue Cross Blue Shield, vision coverage through VSP, family leave, paid time off, 401k retirement plan, disability and life insurance, and fully covered parking/commuter benefits.
  • A dynamic early-stage work environment and highly interdisciplinary, talented, and collaborative team.
  • Participation in an unprecedented opportunity to significantly impact the quality of life of patients by developing a targeted approach to delivering therapeutic molecules.
  • Professional growth opportunities through mentoring, training, immersion in cross-functional projects, and opportunities to learn and try new things.

About Flagship

Flagship Pioneering is a bioplatform innovation company that invents and builds platform companies, each with the potential for multiple products that transform human health or sustainability. Since its launch in 2000, Flagship has originated and fostered more than 100 scientific ventures, resulting in more than $90 billion in aggregate value. Many of the companies Flagship has founded have addressed humanity’s most urgent challenges: vaccinating billions of people against COVID-19, curing intractable diseases, improving human health, preempting illness, and feeding the world by improving the resiliency and sustainability of agriculture. Flagship has been recognized twice on FORTUNE’s “Change the World” list, an annual ranking of companies that have made a positive social and environmental impact through activities that are part of their core business strategies and has been twice named to Fast Company’s annual list of the World’s Most Innovative Companies. Learn more about Flagship at

Flagship Pioneering is committed to equal employment opportunity regardless of race, color, ancestry, religion, sex, national origin, sexual orientation, age, citizenship, marital status, disability, gender identity or Veteran status.

At Flagship, we recognize there is no perfect candidate. If you have some of the experience listed above but not all, please apply anyway. Experience comes in many forms, skills are transferable, and passion goes a long way. We are dedicated to building diverse and inclusive teams and look forward to learning more about your unique background.

Recruitment & Staffing Agencies: Flagship Pioneering and its affiliated Flagship Lab companies (collectively, “FSP”) do not accept unsolicited resumes from any source other than candidates. The submission of unsolicited resumes by recruitment or staffing agencies to FSP or its employees is strictly prohibited unless contacted directly by Flagship Pioneering’s internal Talent Acquisition team. Any resume submitted by an agency in the absence of a signed agreement will automatically become the property of FSP, and FSP will not owe any referral or other fees with respect thereto.




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