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. 

Ampersand Biomedicines‘ Pilsen Team, formerly Abcheck and now a Flagship Pioneering Company, discovers and optimizes human therapeutic antibodies with one of the industry’s most versatile technology platforms. Tailored to specific needs and desired Target Product Profiles, the experienced team leverages both cutting-edge (e.g., microfluidics, rabbit mass humanization) and state-of-the-art (e.g., phage display libraries) technologies to provide high quality leads against a range of diverse targets.

Position Overview:

As Bioinformatician you will be responsible for various tasks across the antibody discovery workflow – starting with antibody sequence analysis, clustering, liability screening and storing data in databases, to in silico humanization and structure modelling. Your role will be to support antibody discovery for internal campaigns and external customers. You will work in tight collaboration with Antibody discovery team to organize data and provide feedback to experimental teams. The successful candidate will have relevant experience with various bioinformatics tools (e.g., programming in R, Python or other, experience with database data storage, sequence analysis) gained at academia or industry and ability to learn and develop novel algorithms and pipelines. Individual tasks will be executed in cooperation with both teams at AbCheck in Pilsen and at Ampersand in Boston.

This role will be based in Plzen, Czech Republic, with partial home-office possibility.


  • Analyse antibody sequences (liability screening, clustering, etc.) from Sanger and Next Generation sequencing platforms.
  • Develop and implement computational pipelines and algorithms for analysing antibody sequences.
  • Organize data storage in accessible formats for other team members.
  • Prepare data summaries, overviews, and visualizations.
  • Participation on in silico design of humanized antibodies.
  • Integration of Electronic Lab Notebook system in the laboratory.
  • Cooperation with Computational biology team at Ampersand Boston.

Minimum Qualifications:

  • Master's or Ph.D. degree in Bioinformatics, Computational Biology, or a related field.
  • Strong background in protein bioinformatics with a focus on sequence analysis. 
    • Knowledge of next-generation sequencing (NGS) data analysis and genomics databases.
  • Proficiency in programming languages commonly used in bioinformatics such as Python or R.
  • Familiarity with statistical methods and machine learning techniques applied to biological sequence data.
  • Excellent problem-solving skills and ability to troubleshoot complex experimental setups.
  • Ability to work across multiple teams and support various technology development.
  • Proficiency in English.

Preferred Qualifications:

  • Familiarity with Electronic Lab Notebook environment.
  • Experience with programming environments for instrument operation (e.g., LabView) is beneficial.
  • Experience working in a Cloud environment (AWS)
  • Experience with dynamic visualization tools (Tableau, Shiny)

What We Will Offer you:

  • 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 biotechnology 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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