Principal Scientist, Bioinformatics

About the position

Nkarta is seeking a highly motivated, collaborative, detail-oriented Principal Scientist to join our Translational Medicine team. This is a high-impact, hands-on leadership role for a senior bioinformatics scientist. The successful candidate will have deep expertise in single-cell and spatial omics technologies, along with experience in functional genomics and leading computational biology and/or bioinformatics programs in a biotech or pharmaceutical setting.
This individual will work collaboratively within Translational Medicine and cross-functionally to advance, support, and execute biomarker discovery, mechanism-of-action (MOA) investigations, and translational data analysis from clinical samples. A central focus of this role is to drive and execute on Nkarta’s strategy for single-cell and spatial transcriptomics, leveraging scRNA-seq, spatial, and functional genomics approaches to drive translational insights, biomarker development, and clinical decision-making in early development.

Responsibilities
• Lead and actively participate in the design and execution of computational strategies and hands-on analysis of clinical and biological datasets to support go/no-go decisions
• Hands-on development and application of computational methods for single-cell and spatial transcriptomics to generate actionable translational insights from clinical samples
• Establish scalable pipelines for multi-modal data integration across programs
• Integrate and analyze functional genomics datasets (e.g., bulk RNA-seq) to generate mechanistic insights that inform translational and clinical strategies
• Provide high-impact analyses with direct influence on clinical decision-making and visibility to senior leadership
• Collaborate with senior leadership to define priorities, allocate resouces, and establish timelines aligned with company objectives
• Partner with experimental scientists to design studies leveraging advanced omics approaches and interpret results
• Ensure reproducibility, scalability, and data quality across bioinformatics pipelines
• Communicate complex findings effectively to scientific and non-scientific stakeholders, including senior leadership

Requirements
• Deep expertise in single-cell and spatial transcriptomics analysis, including scRNA-seq and related high-dimensional omics datasets
• Strong experience analyzing functional genomics and transcriptomic data (e.g., bulk RNA-seq, WES) to derive biological and translational insights
• Strong foundation in biological sciences, with experience or interest in immunology and disease biology
• Deep understanding of modern statistical and computational methods for high-dimensional data analysis
• Proficiency in Python and/or R, with experience using relevant bioinformatics frameworks
• Experience developing and maintaining scalable data analysis pipelines and working with cloud-based infrastructure (e.g., AWS)
• Excellent communication and presentation skills, with the ability to influence cross-functional stakeholders and translate complex data into clear, actionable insights
• Demonstrated experience managing external CROs and bioinformatics vendors
• Proven leadership experience, including mentoring and developing scientific teams
• Strong cross-functional collaboration skills and ability to translate computational insights into biological and clinical impact
• Ability to work both independently and collaboratively in a fast-paced environment, with strong organizational skills and attention to detail

Benefits
• annual discretionary bonus
• equity grant(s)
• medical, dental, vision and life insurance coverage
• 401K plan
• flexible spending account
• ESPP
• employee assistance program
• paid vacation, holiday and personal days
• paid parental, pregnancy, and bereavement leave

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