Computational Genomics Research Scientist

Vertex Pharmaceuticals Inc (US); United States; Hybrid; USD 112,000 - 168,000; Full time

Benefits offered by this job

Medical benefits

Dental & Vision benefits

Paid time off

Educational assistance

Commuting subsidy

401(k)

Job summary

Vertex Pharmaceuticals Inc (US) seeks a Computational Genomics Research Scientist in Boston. The hybrid role focuses on designing and executing genomic analyses, including bulk RNA-seq, single-cell profiling, and spatial transcriptomics, to generate biological insights for cell and gene therapies.

You will work across stem cell biology, immunology, and pre-clinical development, partnering with software teams to improve workflows and reproducibility, and communicating findings to

Qualifications

• PhD in computational biology, bioinformatics, genomics, systems biology, biomedical engineering, statistics, CS or related field with 0–3 years postdoc/industry or Master's with 3+ years industry
• Demonstrated expertise in design, analysis, visualization and interpretation of single-cell genomics and spatial transcriptomics experiments
• Proficiency in Python and/or R for scientific computing and data analysis
• Experience in Linux-based HPC and/or cloud computing environments
• Strong foundation in statistics, experimental design and reproducible computational research
• Proven ability to translate complex findings into actionable recommendations for research teams

Responsibilities

• Collaborate with cross-functional teams to identify key scientific questions addressed via genomics and bioinformatics
• Lead spatial transcriptomics methods and develop best practices across teams
• Analyze and integrate bulk RNA-seq, single-cell, spatial transcriptomics and multiomics datasets to generate insights
• Perform sophisticated computational analyses with statistics and data visualizations
• Distill results into take-home messages and next-step recommendations for a broad audience
• Improve analytical workflows and reproducibility with software teams

Skills

Genomic data analysis

Spatial transcriptomics

Single-cell sequencing

Bioinformatics

Statistics

Education

PhD in computational biology / genomics

MS in related field with 3+ years industry experience

Tools

Python

R

Linux HPC

Cloud computing

Job description

Job Description We are seeking a Computational Genomics Research Scientist to support the development of transformative cell and gene therapies across Vertex's research portfolio. This Boston-based position is part of the global Data and Computational Sciences organization and will collaborate closely with research teams spanning stem cell biology, immunology, gene editing, and pre-clinical development to design studies, execute and analyze complex genomic analyses, and ultimately generate biological insights that drive early research across multiple disease programs. As an embedded computational scientist, you will be responsible for performing bulk and single-cell sequencing analyses, spatial transcriptomics, and multiomic profiling to help uncover the molecular programs that govern therapeutic cell identity, differentiation, function, and safety to accelerate the development of next‑generation cell and gene therapies. This is a Boston based, hybrid position requiring 3 days/week onsite.

Key Responsibilities

• Collaborate closely with cross-functional research teams to identify key scientific questions that can be addressed through genomics, sequencing, and bioinformatics approaches.
• Lead the application and advancement of spatial transcriptomics methods, collaborating across teams and sites to develop, implement, and share analytical best practices.
• Analyze and integrate diverse genomic datasets, including bulk RNA‑seq, single‑cell profiling, spatial transcriptomics, and other multiomic datasets to generate actionable insights.
• Perform sophisticated computational analyses of sequencing and other biological data through deep critical thinking, incorporation of published findings and best practices from the field, strong statistical rigor, and data science visualizations
• Distill complex analyses and scientific results into key take‑home messages and recommendations for next steps to a broad audience.
• Partner with computational and software teams to improve analytical workflows, reproducibility, usability, and robustness.
• Practice reproducible research and maintain well‑documented, version‑controlled analytical workflows.
• Author study reports and technical documentation to support research and regulatory activities.
• Evaluate emerging genomics technologies and computational methods and incorporate new approaches where appropriate.

Knowledge and Skills

• A proven track record in the analysis, visualization, and interpretation of genomic and next‑generation sequencing (NGS) data
• Solid scientific understanding of gene editing, the role of genetic variation in human disease, molecular biology, and cellular biology
• Expertise with applying computational methods and bioinformatics tools to large‑scale data
• Solid understanding of statistics

Education and Experience

Ph.D. in computational biology, bioinformatics, genomics, systems biology, biomedical engineering, statistics, computer science, or a related quantitative discipline, with 0-3 years of relevant postdoctoral or industry experience; or a Master's degree in a related field with 3+ years of relevant industry experience. Demonstrated expertise in the design, analysis, visualization, and interpretation of single‑cell genomics and spatial transcriptomics experiments. Proficiency in Python and/or R for scientific computing and data analysis. Experience working in Linux‑based high‑performance computing (HPC) and/or cloud computing environments. Strong foundation in statistics, experimental design, and reproducible computational research. Proven ability to derive biological insight from complex datasets and translate findings into actionable recommendations for research teams. Excellent communication and presentation skills, with the ability to effectively convey complex scientific findings to multidisciplinary audiences. Demonstrated ability to work collaboratively within cross‑functional teams and contribute to a positive, team‑oriented environment.

Pay Range

Pay Range: $112,000 - $168,000 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.

• medical, dental and vision benefits
• generous paid time off (including a week‑long company shutdown in the Summer and the Winter)
• educational assistance programs including student loan repayment
• generous commuting subsidy
• matching charitable donations
• 401(k)
• and so much more

Flex Designation

Hybrid‑Eligible Or On‑Site Eligible Flex Eligibility Status: In this Hybrid‑Eligible role, you can choose to be designated as: 1. Hybrid: work remotely up to two days per week; or select 2. On‑Site: 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.

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].

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 www.vrtx.com 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.