Immunology Senior Research Scientist - Spatial Transcriptomics

Vertex Pharmaceuticals Incorporated; Seattle (WA); On-site; USD 124,200 - 186,400; Full time

Benefits offered by this job

Annual bonus

Equity awards

Comprehensive benefits

Paid time off

Job summary

Vertex Pharmaceuticals Incorporated is seeking a Senior Scientist, Spatial Transcriptomics in Seattle to provide expert leadership in spatial biology. You will drive studies that reveal tissue architecture and cellular microenvironments, integrating spatial data with single-cell, proteomic, and imaging datasets to inform disease biology and biomarker strategies.

The role requires PhD or equivalent experience with 2+ years in relevant work, strong experimental design, and collaboration across

Qualifications

• Deep expertise in spatial transcriptomics and tissue-based molecular profiling.
• Experience with fresh frozen and FFPE tissue processing and assay optimization.
• Strong cross-functional collaboration skills and data interpretation ability.

Responsibilities

• Lead design, execution, and optimization of spatial transcriptomics studies.
• Characterize tissue architecture and cellular microenvironments.
• Integrate spatial data with multi-omic datasets to derive biological insights.
• Develop robust workflows for sample prep, assay execution, QC, and data review.
• Mentor junior scientists and contribute to a high-performing team.

Skills

Spatial transcriptomics

Tissue profiling

RNA biology

Single-cell RNA-seq

Data interpretation

Experimental design

Cross-functional collaboration

Python

R

Education

PhD in Immunology/Cell Biology/Molecular Biology or related

Master's degree with 6+ years of relevant experience

Bachelor's degree with 8+ years of relevant experience

Tools

R and Python

Bioinformatics workflows

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, 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 [e-mail].