Immunology Senior Research Scientist - Spatial Transcriptomics

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

Job summary

Vertex Pharmaceuticals is seeking a Senior Research Scientist in Spatial Transcriptomics to drive design and execution of tissue-based spatial profiling studies. This role focuses on understanding tissue architecture and cell interactions to inform disease biology and biomarker strategies.

You'll integrate spatial data with single-cell and proteomics datasets, optimize workflows, and mentor junior scientists in a collaborative, cross-functional team.

Qualifications

• Deep expertise in spatial transcriptomics and tissue-based profiling.
• Strong background in RNA biology and tissue architecture.
• Experience with FFPE and fresh-frozen tissue workflows.
• Experience integrating spatial data with other omics datasets.

Responsibilities

• Lead design, execution, and optimization of spatial transcriptomics studies.
• Characterize tissue architecture and cellular microenvironments.
• Integrate spatial data with scRNA-seq, proteomics, and imaging datasets.
• Develop robust workflows for sample prep, QC, and data review.
• Mentor junior scientists and collaborate cross-functionally.

Skills

Spatial transcriptomics

Tissue-based profiling

RNA biology

Experimental design

Data interpretation

Cross-functional collaboration

R

Python

Communication skills

Education

PhD in Immunology (or related)

MS in related field

BS in related field

Tools

10x Genomics Visium

Nanostring CosMx

Histology imaging

Single-cell RNA-seq

R

Python

Job description

## Immunology Senior Research Scientist - Spatial TranscriptomicsApplylocations: Seattle, WAtime type: Full timeposted on: Posted Todayjob requisition id: REQ-29498**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