Scientist – Cellular Immunology and Inflammation

Company Summary

Prologue Medicines is creating powerful new medicines by unlocking the therapeutic potential of viral proteins. Viral proteins have evolved with humans for millions of years and have been optimized to modulate human biology. Powered by the largest known database of viral protein structures, Prologue’s DELVE™ machine learning platform systematically identifies the proteins that precisely regulate human biology, uncovers new therapeutic targets and programs transformative features into novel therapeutics. Prologue was founded by Flagship Pioneering in 2021.

Position Summary

Prologue Medicines is seeking a highly motivated, focused, and creative Scientist, Cellular Immunology and Inflammation to join our Research and Discovery team. You will advance therapeutic discovery programs by designing, developing and running cellular immunology and inflammation studies that support target validation, biological characterization and mechanism-of-action investigations.

This is a team-based, collaborative role in a matrixed environment. You will work closely with colleagues across disciplines and programs, share ownership of program outcomes, and succeed through partnership as much as individual contribution.

The ideal candidate brings deep expertise in cellular immunology, innate and adaptive immune cell biology, human primary immune cell systems, multiparameter flow cytometry and functional assay development. This is a highly hands-on laboratory role that calls for strong experimental design, analytical thinking and the ability to troubleshoot complex biological assays independently.

In a fast-paced discovery environment, you will generate and interpret high-quality data and contribute to scientific strategy to advance novel therapeutic programs.

Key Responsibilities

• Independently design, execute and analyze in vitro and ex vivo cellular immunology and inflammation experiments that support target validation, therapeutic discovery and mechanistic investigations.
• Develop, optimize and implement robust cell-based assays to evaluate immune cell activation, differentiation, proliferation, signaling, inflammatory responses and functional outputs.
• Apply multiparameter flow cytometry expertise, including panel design, staining optimization, data acquisition, analysis and cell sorting, to characterize immune cell populations and biological responses.
• Isolate, culture and manipulate primary human and/or animal immune cells, including innate (e.g., monocytes, macrophages, dendritic cells, neutrophils, NK cells) and adaptive (e.g., T and B cells) populations, using established techniques such as MACS and FACS.
• Design and execute phenotypic and mechanism-of-action studies to investigate immune and inflammatory pathways, validate therapeutic targets and test biological hypotheses.
• Apply complementary readouts to characterize cellular responses and assess therapeutic activity, including transcriptomic profiling and biomarker and cytokine assays.
• Critically analyze experimental data, troubleshoot assay performance and recommend follow-up experiments to inform discovery program decisions.
• Collaborate with cross-functional research teams to integrate cellular immunology findings into broader discovery and translational research strategies.
• Develop and maintain experimental protocols, assay documentation and laboratory best practices that ensure scientific rigor, reproducibility and data integrity.
• Present experimental findings, scientific interpretations and recommendations to cross-functional teams and leadership through presentations, technical discussions and written reports.
• Stay current with emerging scientific literature, technologies and methodologies in cellular immunology, inflammation and therapeutic discovery.

Required Qualifications

• PhD in Immunology, Cell Biology, Molecular Biology or a related biological discipline, or an M.Sc. with 6+ years of directly relevant experience in cellular immunology (or equivalent combination of education and experience).
• Demonstrated hands-on expertise with patient-derived tissues and primary immune cells, including isolation, culture, stimulation, differentiation and functional characterization.
• Strong proficiency in multiparameter flow cytometry, including panel design, staining protocol optimization, data acquisition and analysis.
• Proven experience developing, optimizing and troubleshooting cell-based functional and mechanistic assays.
• Strong understanding of immune cell biology, immune and inflammatory signaling pathways, and the mechanisms underlying innate and adaptive immune responses.
• Experience with immunological and biomarker readouts performed in singleplex and multiplex formats, such as MSD, Luminex, ELISA, ELISpot, AlphaLISA and TR-FRET.
• Demonstrated ability to design experiments independently, critically evaluate results and translate scientific findings into actionable recommendations.
• Proficiency in quantitative data analysis and statistical interpretation, with experience using relevant scientific analysis tools (e.g., FlowJo, GraphPad Prism, R or Python).
• Excellent organizational, problem-solving, communication and presentation skills.
• Ability to work independently and collaborate effectively as part of team-based, matrixed, multidisciplinary research teams in a dynamic laboratory environment.

Preferred Qualifications

• Experience in biotechnology or pharmaceutical research supporting early-stage therapeutic discovery, target identification, validation and mechanism-of-action studies.
• Experience with bulk RNA-seq and, ideally, single-cell approaches (e.g., scRNA-seq, CITE-seq), plus qPCR and targeted expression panels.
• Familiarity with genomic analysis and bioinformatics (e.g., differential expression, pathway analysis), or the ability to partner effectively with computational biologists.
• Experience with mammalian cell transfection and genetic perturbation (e.g., CRISPR knockout or CRISPRi, siRNA, lentiviral or electroporation in primary cells) to study cellular mechanisms.
• Familiarity with plate-based assay formats (96- and 384-well), assay miniaturization and robustness metrics, and laboratory automation such as liquid handling and high-throughput workflows.
• Experience developing new experimental workflows, establishing assay platforms or implementing innovative immunological technologies.
• Experience designing or contributing to in vivo immunology studies and integrating findings with in vitro and ex vivo results.
• Demonstrated scientific leadership, including mentoring junior scientists or research associates and contributing to research strategy.

What Will Make You Successful

You are deeply curious about how immune and inflammatory biology works and how to turn it into medicines. You enjoy connecting data across modalities, from flow and functional assays to transcriptomic and biomarker readouts. You hold yourself to a high standard of scientific rigor and positive behaviors and enjoy solving problems together with colleagues.

About Flagship Pioneering

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, and has been twice named to Fast Company's annual list of the World's Most Innovative Companies. Learn more about Flagship at www.flagshippioneering.com.

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.

The salary range for this role is $100,000 - $143,000. Compensation for the role will depend on a number of factors, including a candidate’s qualifications, skills, competencies, and experience. Prologue Medicines, Inc. currently offers healthcare coverage, annual incentive program, retirement benefits and a broad range of other benefits. Compensation and benefits information is based on Prologue Medicines, Inc.'s good faith estimate as of the date of publication and may be modified in the future.

Pay Range: 100000.0 - 143000.0 USD