Immunology Senior Research Scientist - Spatial Transcriptomics

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, Spatial Transcriptomics to provide scientific and deep technical expertise in spatial biology to support discovery, translational, and development programs. This role will be instrumental in driving mechanistic insights into disease biology, tissue microenvironments, and therapeutic response through spatial profiling of gene expression in tissue context. The ideal candidate will bring deep expertise in spatial transcriptomics, tissue-based molecular profiling, experimental design, and data interpretation, along with strong cross-functional collaboration skills and a passion for technical innovation. Key Duties and Responsibilities: Lead the design, execution, and optimization of spatial transcriptomics studies to address key biological questions in disease-relevant tissues and model systems Lead efforts to characterize tissue architecture, cellular microenvironments, cell-cell interactions, and spatial organization of biological processes Generate and interpret high-quality spatial data to derive biological insights that support disease biology, target biology, mechanism of action, and biomarker strategies Integrate spatial transcriptomics data with complementary datasets, including single-cell RNA-seq, proteomics, imaging, histology, and other molecular profiling approaches to enable multi-modal biological insights Develop, validate, and implement robust workflows for sample preparation, assay execution, quality control, and data review Evaluate and apply emerging spatial biology technologies to expand research capabilities and enable innovative scientific applications Drive adoption of best practices and contribute to establishing robust spatial biology workflows and standards across the team Partner closely with cross-functional teams across disease biology, pharmacology, translational medicine, biomarker sciences, bioinformatics, and clinical development to inform study design, data interpretation, and program strategy Contribute to internal scientific strategy through clear communication of results, technical recommendations, and experimental insights Prepare technical documentation, protocols, study summaries, and presentations Mentor junior scientists and help build a collaborative, high-performing team environment Knowledge and Skills: Deep expertise in spatial transcriptomics and tissue-based molecular profiling Strong understanding of transcriptomics, RNA biology, tissue architecture, and cellular heterogeneity Experience with fresh frozen and FFPE tissue processing, tissue quality assessment, and assay optimization Familiarity with one or more spatial biology platforms, including sequencing-based and imaging-based technologies Experience integrating spatial data with single-cell, proteomic, imaging, and histologic datasets Working knowledge of computational approaches for spatial data analysis, visualization, and interpretation, including proficiency in R and/or Python and familiarity with relevant analysis tools and workflows Strong experimental rigor, problem-solving ability, and attention to data quality and reproducibility Excellent communication skills and ability to work effectively in a matrixed, multidisciplinary environment 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: Hands-on experience with one or more spatial transcriptomics platforms (e.g., sequencing-based or imaging-based such as 10x Genomics Visium, Nanostring CosMx or similar technologies) Experience with histology, immunofluorescence, image analysis, and multiplexed tissue profiling Experience supporting drug discovery, translational research, or clinical biomarker development, ideally in immunology or inflammation Familiarity with single-cell RNA-seq analysis and integration of multi-omics datasets Experience in immunology and inflammation disease areas Knowledge of spatial proteomics or broader tissue-based profiling approaches 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 Flex status for this position is subject to Vertex’s Policy on Flex @ Vertex Program and may be changed at any time. #LI-Onsite Company Information Vertex is a global biotechnology company that invests in scientific innovation. Vertex is committed to equal employment opportunity and non-discrimination for all employees and qualified applicants without regard to a person's race, color, sex, gender identity or expression, age, religion, national origin, ancestry, ethnicity, disability, veteran status, genetic information, sexual orientation, marital status, or any characteristic protected under applicable law. Vertex is an E-Verify Employer in the United States. Vertex will make reasonable accommodations for qualified individuals with known disabilities, in accordance with applicable law. Any applicant requiring an accommodation in connection with the hiring process and/or to perform the essential functions of the position for which the applicant has applied should make a request to the recruiter or hiring manager, or contact Talent Acquisition at View email address on click.appcast.io Help Us Achieve Our Mission Vertex is a global biotechnology company that invests in scientific innovation to create transformative medicines for people with serious diseases. The company has approved medicines that treat the underlying causes of multiple chronic, life-shortening genetic diseases — cystic fibrosis, sickle cell disease and transfusion-dependent beta thalassemia — and continues to advance clinical and research programs in these diseases. Vertex also has a robust clinical pipeline of investigational therapies across a range of modalities in other serious diseases where it has deep insight into causal human biology, including APOL1-mediated kidney disease, acute and neuropathic pain, type 1 diabetes, myotonic dystrophy type 1 and alpha-1 antitrypsin deficiency . Founded in 1989 in Cambridge, Mass., Vertex's global headquarters is now located in Boston's Innovation District and its international headquarters is in London. Additionally, the company has research and development sites and commercial offices in North America, Europe, Australia, Latin America and the Middle East. Vertex is consistently recognized as one of the industry's top places to work, including 14 consecutive years on Science magazine's Top Employers list and one of Fortune’s 100 Best Companies to Work For. For company updates and to learn more about Vertex's history of innovation, visit or follow us on Facebook, Twitter/X , LinkedIn, YouTube and Instagram. The diversity and authenticity of our people is part of what makes Vertex unique, and we recognize that each employee brings diverse perspectives and strengths. By embracing those strengths and celebrating differences, we are fostering an inclusive culture where each of us can bring our authentic selves to work, inspire innovation together, and change people’s lives. Our vision is clear: to be the place where an authentic, diverse mix of talent want to come, to stay, and do their best work.