Research Scientist, Analytical Development – Functional Genomics & Multi-omics

Vertex Pharmaceuticals • Boston, MA

4d • Onsite

About The Position

Vertex is seeking a highly motivated Research Scientist to develop, optimize, qualify, and implement sequencing-based analytical methods supporting pluripotent stem cell (PSC) bank characterization, process development, and biomarker translation. The role combines wet-laboratory work in nucleic acid preparation, stem cell culture, and sequencing library construction with bioinformatics analysis and integration of transcriptomic and epigenomic datasets. The scientist will establish fit-for-purpose multi-omic workflows and translate sequencing findings into practical targeted assays, including RT-qPCR and ChIP-qPCR, for in-process monitoring, comparability, and release strategies. The role works closely with analytical development, process development, bioinformatics, and stem cell biology teams to develop rigorous, reproducible, scalable methods ready for implementation.

The scientist will also design and conduct complex analytical experiments, assess method performance, apply relevant regulatory guidance, and prepare and present study conclusions. The position calls for sound judgment in prioritizing studies, effective collaboration, and the ability to move multiple projects forward. Vertex encourages continuous learning and thoughtful adoption of advances in AI, technology, automation, and industry trends to improve decision-making, innovation, efficiency, and patient outcomes.

This is an on-site-designated role requiring work on-site five days per week, with ad hoc flexibility. Flex status is subject to Vertex policy and may change. The position offers a base salary range of $102,800–$154,200 and is eligible for an annual bonus and annual equity awards. Some roles may also be eligible for overtime pay in accordance with applicable requirements. Vertex states that its Total Rewards offerings include medical, dental, and vision benefits; paid time off, including a week-long summer and winter company shutdown; educational assistance programs including student loan repayment; a commuting subsidy; matching charitable donations; and a 401(k).

Requirements

• Ph.D. or equivalent degree.
• 0–3 years of relevant postdoctoral employment experience.
• Experience with PSC culture, maintenance, characterization, and passaging across multiple passages.
• Experience with single-cell transcriptomic or epigenomic analysis, including cell QC, filtering, integration, clustering, annotation, differential expression, trajectory analysis, or fate-probability estimation.
• Experience with epigenomic data analysis, including differential chromatin accessibility, accessible-region analysis, chromatin-gene linkage, transcription-factor motif analysis, or footprinting.
• Experience developing and managing reproducible bioinformatics pipelines, including containerization with Singularity or equivalent tools and local program installation and configuration.
• Familiarity with high-performance computing environments, including institutional or enterprise research-computing platforms, and foundational AWS concepts.
• Experience translating discovery-stage multi-omic biomarkers into targeted RT-qPCR, ChIP-qPCR, or other scalable analytical assays.
• Experience designing and/or performing assay qualification, including authoring and/or reviewing relevant documentation.
• Knowledge of relevant biological systems and ability to develop methods while considering therapeutic-area and manufacturing constraints and limitations.
• Understanding of relevant regulatory guidance and assay qualification, transfer, and validation components.
• Technical expertise across a range of platforms and ability to design and execute complex, challenging experiments.
• Ability to multitask and move multiple projects forward in parallel.
• Skill in routine statistical analysis and in describing method performance.

Nice To Haves

• Experience with automated cell annotation or representation-learning tools such as CellTypist, scVI, scGPT, or related methods.

Responsibilities

• Develop, optimize, troubleshoot, and apply omics- and sequencing-based analytical methods, including bulk and single-cell RNA-seq, ATAC-seq, and ChIP-seq.
• Develop workflows for deep transcriptomic and epigenomic characterization of PSC banks, including assessment of cell-state heterogeneity, lineage priming, chromatin accessibility, and gene-regulatory programs.
• Design and execute experiments to characterize method performance, including data quality, reproducibility, precision, robustness, sample-input requirements, and fit-for-purpose acceptance criteria.
• Translate sequencing-derived biomarker findings into targeted assays, including RT-qPCR, ChIP-qPCR, or other practical methods for in-process control, comparability, or release-supporting applications.
• Analyze and interpret bulk, single-cell, and multi-omic sequencing datasets in partnership with computational biology and analytical-development colleagues.
• Perform transcriptomic analyses, including sample and cell quality control, filtering, normalization, dataset integration, dimension reduction, clustering, cell-type or cell-state annotation, and differential-expression analysis.
• Apply trajectory reconstruction and fate-probability approaches, where appropriate, to assess PSC state transitions, differentiation trajectories, and cell-state heterogeneity.
• Perform epigenomic analyses, including accessible-loci compilation, differential chromatin-accessibility analysis, principal-component analysis, chromatin-to-gene linkage analysis, and transcription-factor or nucleosome footprinting.
• Use R, Python, and shell scripting for data analysis, workflow automation, and visualization.
• Use high-performance computing environments and foundational cloud-computing concepts to execute, manage, and scale sequencing-data workflows.
• Design and conduct complex analytical experiments consistently, using appropriate controls.
• Apply regulatory guidance in the development and qualification of analytical methods.
• Perform complex analytical procedures to understand and describe assay performance.
• Prioritize studies based on feasibility, timelines, and project impact.
• Prepare study presentations independently and present experimental conclusions at internal team meetings.
• Collaborate across functions and within the team to achieve program goals.
• Write method documents, analytical-development protocols, and reports.

Benefits

• Annual bonus eligibility
• Annual equity awards
• Medical benefits
• Dental benefits
• Vision benefits
• Paid time off, including a week-long company shutdown in the summer and winter
• Educational assistance programs, including student loan repayment
• Commuting subsidy
• Matching charitable donations
• 401(k)
• Some roles may be eligible for overtime pay in accordance with federal and state requirements

What This Job Offers

• Job Type: Full-time
• Career Level: Entry Level
• Education Level: Ph.D. or professional degree