Principal Scientist, Bioinformatics

Nkarta, Inc.; South San Francisco (CA); On-site; USD 180,000 - 215,000; Full time

Benefits offered by this job

Annual discretionary bonus

Equity grant(s)

Medical, dental, vision and life insurance

401K plan

Flexible spending account

Employee assistance program

Paid vacation and personal days

Paid parental and bereavement leave

Job summary

Nkarta, Inc. in South San Francisco is seeking a Principal Scientist for its Translational Medicine team. This pivotal role demands leadership in bioinformatics, focusing on single-cell and spatial omics technologies. You will collaborate cross-functionally to drive biomarker discovery and data analysis in clinical settings.

The ideal candidate holds a PhD and has significant experience in functional genomics, data integration, and statistical methods. Benefits include an annual bonus, equity grants, and comprehensive insurance coverage.

Qualifications

• Experience in single-cell and spatial transcriptomics analysis.
• Strong foundation in biological sciences, preferably in immunology.
• Excellent communication and presentation skills.

Responsibilities

• Lead design and execution of computational strategies.
• Develop computational methods for actionable insights.
• Establish scalable pipelines for multi-modal data integration.

Skills

Single-cell and spatial transcriptomics analysis

Functional genomics analysis

Statistical and computational methods

Python and/or R proficiency

Leadership and team mentoring

Cross-functional collaboration

Education

PhD in Biological Sciences or related field

Tools

AWS

Job description

Overview

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

Qualifications

• 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

Education / Background

PhD in Biological Sciences, Computational Biology, Biostatistics, Bioinformatics, Genomics, or a closely related discipline with 5 years of industry experience.

Pay Range

$180,000 -- $215,000 USD

Location

This role is based in the South San Francisco office, with hybrid work arrangements possible.

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