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

Vertex Inc. • Boston, MA

6d • $102,800 - $154,200 • 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 expertise in nucleic acid preparation, stem cell culture, and sequencing library construction with bioinformatics capabilities to analyze and integrate transcriptomic and epigenomic datasets.

The Research Scientist will establish fit-for-purpose workflows for transcriptomic and epigenomic multi-omic analysis and translate high-dimensional sequencing findings into robust targeted assays, including RT-qPCR and ChIP-qPCR, for in-process monitoring, comparability, and release-supporting applications. The role collaborates with analytical development, process development, bioinformatics, and stem cell biology teams to ensure methods are scientifically rigorous, reproducible, scalable, and ready for implementation.

The position also requires applying relevant regulatory guidance, understanding assay qualification, transfer, and validation, preparing method documents and analytical development protocols and reports, and presenting experimental conclusions at internal team meetings. Vertex encourages continuous learning and thoughtful adoption of advances in AI, technology, automation, and industry trends.

Requirements

• Ph.D. or equivalent degree.
• 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 with automated cell annotation or representation-learning tools, such as CellTypist, scVI, scGPT, or related methods.
• Experience translating discovery-stage multiomic 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 with an understanding of therapeutic-area constraints and manufacturing capabilities.
• Understanding of relevant regulatory guidance and the components of assay qualification, transfer, and validation.
• 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 writing method documents, analytical development protocols, and reports.
• Ability to analyze method performance, including knowledge of routine statistical analysis.

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 evaluation 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 multiomic 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 to support 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, employing 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 using sound judgment and consideration of feasibility, timelines, and project impact.
• Prepare study presentations and present experimental conclusions at internal team meetings.
• Work collaboratively across functions and within the team to achieve program goals.

Benefits

• Annual bonus and annual equity awards; some roles may also be eligible for overtime pay.
• 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.
• Commuting subsidy.
• Matching charitable donations.
• 401(k).
• Additional inclusive benefits and resources supporting employees’ career, financial, family, and wellbeing needs.

What This Job Offers

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