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

Job Description General Summary: We are seeking a highly motivated Research Scientist, Analytical Development – Functional Genomics & Multi-omics to develop, optimize, qualify, and implement sequencing-based analytical methods supporting pluripotent stem cell (PSC) bank characterization, process development, and biomarker translation. This role will combine strong wet-laboratory expertise in nucleic acid preparation, stem cell culture, and sequencing library construction with bioinformatics capabilities for analysis and integration of transcriptomic and epigenomic datasets. The Research Scientist will establish fit-for-purpose workflows spanning transcriptomic and epigenomic methods for multi-omic analysis. A central responsibility will be translating high-dimensional sequencing findings into robust, practical targeted assays—including RT-qPCR and ChIP-qPCR methods—that can support in-process monitoring, comparability, and release strategies. The successful candidate will work closely with analytical development, process development, bioinformatics, and stem cell biology teams to ensure methods are scientifically rigorous, reproducible, scalable, and ready for implementation. Key Duties and Responsibilities: Develop, optimize, troubleshoot, and apply omics- and sequencing-based analytical methods, including but not limited to 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 suitable 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 foot printing. Apply programming skills in 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. Designs and conducts complex analytical experiments with consistency employing appropriate controls Applies regulatory guidance in the development and qualification of analytical methods Understands and performs complex analytical procedures to understand and describe assay performance Exercises solid judgment to prioritize studies, considering feasibility, timelines and project impact Independently prepares study presentations and presents experimental conclusions at internal Team meetings Works collaboratively cross-functionally and within the team to achieve program goals Knowledge and Skills: Designs and executes complex, challenging experiments Demonstrates knowledge of relevant biological systems and the ability to develop methods understanding the constraints and limitations of the therapeutic area and manufacturing capabilities. Demonstrates understanding of relevant regulatory guidance Demonstrates technical expertise in a range of platforms Understands the components of assay qualification, transfer and validation Able to multi-task in order to move multiple projects forward in parallel Must be skilled in writing method documents and analytical development protocols and reports Demonstrated abilities in analysis methods to describe method performance including knowledge of routine statistical analysis Education and Experience: 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 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/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 At Vertex, we embrace continuous learning and encourage employees to stay informed on advances in AI, technology, automation, and industry trends. We seek talent who bring an external perspective, demonstrate curiosity and sound judgment, and thoughtfully adopt new capabilities that improve decision-making, drive innovation, increase efficiency, and help deliver better outcomes for patients. Pay Range: $102,800 - $154,200 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 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 ApplicationAssistance@vrtx.com 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 and conditions. The company has approved therapies for cystic fibrosis, sickle cell disease, transfusion-dependent beta thalassemia, acute pain and acromegaly, and it continues to advance clinical and research programs in these areas. 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 IgA nephropathy, neuropathic pain, APOL1-mediated kidney disease, primary membranous nephropathy, congenital adrenal hyperplasia, ACTH-dependent Cushing's syndrome, autosomal dominant polycystic kidney disease, type 1 diabetes, generalized myasthenia gravis, and myotonic dystrophy type 1. Vertex was founded in 1989 and has its global headquarters in Boston, with international headquarters 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 16 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 LinkedIn, Facebook, Instagram, YouTube, and X We believe our culture is one of Vertex’s greatest strengths and a key enabler of our ability to deliver transformative medicines for patients who need them. Rooted in innovation, purpose and collaboration, our culture empowers people to take smart risks, challenge conventional thinking and do their best work. The diversity of our people is central to that culture. By bringing together individuals with different backgrounds, experiences and perspectives, we foster an environment where new ideas thrive, better decisions are made and breakthrough innovation is possible. We are committed to creating a workplace where everyone feels valued, included and connected to our shared mission, because we know that our unique culture and the collective strength of our people are what set Vertex apart.