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

Job DescriptionGeneral 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 controlsApplies regulatory guidance in the development and qualification of analytical methodsUnderstands and performs complex analytical procedures to understand and describe assay performanceExercises solid judgment to prioritize studies, considering feasibility, timelines and project impactIndependently prepares study presentations and presents experimental conclusions at internal Team meetingsWorks collaboratively cross-functionally and within the team to achieve program goalsKnowledge and Skills:Designs and executes complex, challenging experimentsDemonstrates 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 guidanceDemonstrates technical expertise in a range of platformsUnderstands the components of assay qualification, transfer and validationAble to multi-task in order to move multiple projects forward in parallelMust be skilled in writing method documents and analytical development protocols and reportsDemonstrated abilities in analysis methods to describe method performance including knowledge of routine statistical analysisEducation and Experience:Ph.D. (or equivalent degree) and 0-3 years of relevant post-doctoral employment experienceExperience 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 documentationAt 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 - $154,200Disclosure 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 DesignatedFlex 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-OnsiteCompany InformationVertex 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 : Boston, MAType: Full time