Immunology Senior Research Scientist - Flow Cytometry

Job Description Job Description At Vertex, we invest in scientific innovation to create transformative medicines for people with serious diseases. Our growing Molecular Profiling team is seeking a Senior Scientist, Flow Cytometry to provide deep technical expertise in flow cytometry and cellular profiling to support discovery, translational, and development programs. This role will lead and drive the generation of high-dimensional insights into cell phenotype, function, and biology that help inform mechanism of action, biomarker strategies, patient stratification, and program decision-making. The successful candidate will independently own cytometry workstreams across multiple programs and contribute to the scientific direction of molecular profiling efforts. The ideal candidate is a highly motivated scientist with strong experience in multiparameter and high-dimensional flow cytometry (spectral flow), cell sorting, and immunophenotyping and a proven ability to thrive in a collaborative, fast-paced research environment. Key Duties and Responsibilities Design, develop, optimize, and execute flow cytometry-based assays to support research and translational objectives across discovery and development programs Lead multicolor immunophenotyping panel design, including marker selection, fluorochrome strategy, controls, and advanced gating and data analysis approaches Apply flow cytometry in conjunction with molecular profiling data to enable deeper characterization of cell states, pathway activity, target engagement, and disease-relevant biology Partner with cross-functional teams to integrate cellular and molecular datasets, including transcriptomic, proteomic, and biomarker data, to support hypothesis generation and program strategy Analyze and interpret complex flow cytometry data to support actionable biological insights, mechanism of action studies, and translational hypotheses Establish and apply best practices for sample preparation, staining, acquisition, compensation, quality control, and data analysis Troubleshoot technical issues and drive continuous improvement in assay robustness, reproducibility, and efficiency Contribute to experimental design, study planning, and strategic program discussions and decision-making Prepare technical documentation, protocols, study summaries, and presentations Evaluate and implement emerging cytometry and profiling technologies, reagents, and workflows where appropriate Mentor junior team members and serve as a scientific resource within the broader organization Independently lead cytometry workstreams across multiple programs, ensuring alignment with program goals and timelines Influence program decisions through data-driven insights and clear communication of complex biological findings Knowledge and Skills Deep expertise in flow cytometry principles, instrumentation, and assay development Strong understanding of immune profiling, cellular phenotyping, and molecular profiling strategies Experience connecting cell-based phenotypic data with broader molecular signatures and translational biomarkers Experience designing and optimizing high-parameter or multicolor flow cytometry panels, including intracellular and phospho-flow analysis Proficiency in flow cytometry analysis software such as FlowJo, Dotmatics or equivalent Working knowledge of data analysis approaches and familiarity with R or Python-based workflows (preferred) Strong scientific reasoning, data interpretation, and problem-solving skills Ability to communicate complex technical findings clearly to technical and cross-functional stakeholders Strong organizational skills and the ability to manage multiple priorities in a matrixed environment Demonstrated ability to operate with a high degree of independence while contributing to team-based goals Education and Experience PhD in Immunology, Cell Biology, Molecular Biology, Biology, Biomedical Sciences, or related discipline with 2+ years of relevant experience; or Master’s degree with 6+ years of relevant experience; or Bachelor’s degree with 8+ years of relevant experience Preferred Qualifications Experience with primary human samples, including blood- or tissue-derived specimens Familiarity with spectral flow cytometry and cell sorting (BD, Cytek, Sony platforms) Experience working in environments where molecular profiling and cell-based assays are jointly used to answer translational questions Experience in immunology and inflammation disease areas Experience supporting translational research, biomarker strategies, or clinical development Experience integrating cytometry data with single-cell genomics, spatial transcriptomics, or proteomics datasets Pay Range: $124,200 - $186,400 Disclosure Statement: The range provided is based on what we believe is a reasonable estimate for the base salary pay range for this job at the time of posting. This role is eligible for an annual bonus and annual equity awards. Some roles may also be eligible for overtime pay, in accordance with federal and state requirements. Actual base salary pay will be based on a number of factors, including skills, competencies, experience, and other job-related factors permitted by law. At Vertex, our Total Rewards offerings also include inclusive market-leading benefits to meet our employees wherever they are in their career, financial, family and wellbeing journey while providing flexibility and resources to support their growth and aspirations.  From medical, dental and vision benefits to generous paid time off (including a week-long company shutdown in the Summer and the Winter), educational assistance programs including student loan repayment, a generous commuting subsidy, matching charitable donations, 401(k) and so much more. Flex Designation: On-Site Designated Flex Eligibility Status: In this On-Site designated role, you will work five days per week on-site with ad hoc flexibility.   Note: The F