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 assaysincluding RT-qPCR and ChIP-qPCR methodsthat 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:

Disclosure Statement:

Flex Designation:

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 Vertexs 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 persons 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