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

Location: Boston, MA; on-site five days per week with ad hoc flexibility.

Base salary: $102,800–$154,200 per year, plus eligibility for an annual bonus and annual equity awards.

Company

Vertex is a global biotechnology company focused on scientific innovation and developing better outcomes for patients.

What you will do

• Develop, optimize, troubleshoot, qualify, and implement sequencing-based analytical methods for pluripotent stem cell bank characterization, process development, and biomarker translation.
• Build transcriptomic and epigenomic workflows using bulk and single-cell RNA-seq, ATAC-seq, and ChIP-seq to evaluate cell-state heterogeneity, lineage priming, chromatin accessibility, and gene-regulatory programs.
• Design and execute complex experiments to assess data quality, reproducibility, precision, robustness, sample-input requirements, and fit-for-purpose acceptance criteria.
• Translate sequencing-derived biomarkers into targeted RT-qPCR, ChIP-qPCR, and other scalable assays for in-process control, comparability, and release-supporting applications.
• Analyze transcriptomic, epigenomic, and multiomic datasets, including quality control, filtering, normalization, integration, dimension reduction, clustering, annotation, differential-expression analysis, trajectory reconstruction, fate-probability estimation, chromatin-accessibility analysis, chromatin-to-gene linkage, and transcription-factor or nucleosome footprinting.
• Collaborate with analytical development, process development, bioinformatics, computational biology, and stem cell biology teams; prepare study presentations and communicate experimental conclusions.

Requirements

• Ph.D. or equivalent degree and 0–3 years of relevant post-doctoral employment experience.
• Experience with PSC culture, maintenance, characterization, and passaging across multiple passages.
• Experience with single-cell transcriptomic or epigenomic analysis, including cell quality control, 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 or performing assay qualification, including authoring or reviewing relevant documentation. Knowledge of regulatory guidance, assay qualification, transfer and validation, routine statistical analysis, method documents, analytical-development protocols, and reports is required.
• Ability to design and execute complex experiments with appropriate controls, manage multiple projects in parallel, prioritize studies based on feasibility, timelines, and impact, and work collaboratively across functions.
• Programming skills in R, Python, and shell scripting for data analysis, workflow automation, and visualization.

Nice to have

• No separate optional qualifications were specified.

Culture & Benefits

• On-site work five days per week with ad hoc flexibility under the Flex @ Vertex Program.
• Medical, dental, and vision benefits, generous paid time off, and summer and winter company shutdown weeks.
• Educational assistance programs, including student loan repayment support.
• Commuting subsidy, matching charitable donations, 401(k), and other total rewards benefits.
• Culture emphasizes continuous learning, curiosity, external perspectives, sound judgment, and thoughtful adoption of AI, technology, and automation.