Senior Scientist, Computational Biology

Denali Therapeutics Inc; South San Francisco (CA); On-site; USD 147,000 - 191,000; Full time

Benefits offered by this job

401k

Healthcare coverage

ESPP

Job summary

Denali Therapeutics Inc is seeking an experienced computational biologist to define and guide computational biology efforts across Discovery. You will work with scientists to advance projects from early target validation through IND-enabling studies, leveraging analysis of high-dimensional data and external partners as needed.

The role combines hands-on analysis with strategic oversight, shaping analytical approaches, developing tools, and contributing to regulatory filings and publications.

Qualifications

• PhD in a relevant field such as Computational Biology, Epidemiology, Neuroscience, Statistics, or similar, with 3+ years of industry experience.
• Proven track record analyzing single-cell/single-nucleus RNA-seq data with publications and solid statistical methods.
• Experience with high-dimensional data types (proteomics, mass spectrometry, human genetics) is a plus.
• Strong experience in R or Python for analysis of high-dimensional biological data.
• Knowledge of version control (Git) and report-generation tools (R Markdown, Quarto).
• Experience building dashboards (Shiny) is a plus.

Responsibilities

• Serve as SME for analysis of high-dimensional data, including bulk and single-cell/nucleus transcriptomics.
• Collaborate with Discovery scientists to design, analyze, and interpret in vitro and in vivo experiments.
• Perform rigorous, reproducible analyses across transcriptomic and genomic datasets.
• Develop and extend internal computational tools and oversee external analysis efforts.
• Independently define analytical approaches and validate results with minimal oversight.
• Incorporate AI-assisted analysis while evaluating outputs for accuracy and rigor.
• Apply best practices for code and data management, including workflows and version control.
• Communicate results to cross-functional teams and contribute to filings and publications.

Job description

We invite you to consider an opportunity with Denali to help achieve our goal of delivering meaningful therapeutics to patients. This role helps define the direction of computational biology efforts across Discovery and continues to adapt this strategy as needs evolve. This is a highly cross-functional role, collaborating with scientists to enable project advancement from early target validation through IND-enabling studies. This position develops tailored analytical approaches for a variety of data types and manages external partners as needed to achieve our goals. Through a combination of hands-on analysis and strategic oversight, this role has the opportunity to directly contribute to the advancement of Denali's early-stage portfolio.

Key Accountabilities / Core Job Responsibilities

• Serves as the subject matter expert for the analysis of high-dimensional data, including bulk and single-cell/-nucleus transcriptomics data
• Effectively collaborates with scientists across Discovery to design, analyze, and interpret in vitro and in vivo experiments to support projects across the portfolio
• Performs rigorous, reproducible analysis across transcriptomic, genomic, and other high-dimensional datasets, adapting methods to fit the specific scientific question as needed
• Develops and extends internal computational tools and workflows, as well as overseeing external analysis efforts as needed
• Operates as a highly-independent contributor, defining analytical approaches, building solutions where none exist, and validating results with minimal oversight
• Able to build and adapt analysis workflows using AI-assisted approaches while critically evaluating outputs for accuracy and scientific rigor
• Applies best practices to code- and data-management, including workflow orchestration and version control; identifies opportunities for improvement where appropriate
• Effectively communicates results to cross-functional teams and contributes to regulatory filings, patents, and publications

Qualifications/Skills

PhD in a relevant field such as Computational Biology, Epidemiology, Neuroscience, Statistics, or similar with 3+ years relevant work experience in industry. Proven track record of analyzing single-cell/single-nucleus RNA-seq data, as evidenced by relevant publications, a deep understanding of relevant statistical methods, and experience using common software tools for analysis (e.g. Cell Ranger, CellBender, Seurat, scanpy, etc) Additional experience with other high-dimensional data types (e.g., proteomics, mass spectrometry, human genetics) is a plus Extensive experience in R or Python for analysis of high-dimensional biological data Knowledge of version control (e.g., Git) and methods to generate analysis reports (e.g., R Markdown, Quarto). Experience building dashboards (e.g., with Shiny) is a plus Track record of impactful research, including publications in peer-reviewed journals Strong analytical and problem-solving skills, excellent oral and written communication skills

Salary Range: $147,000.00 to $191,000.00 . Compensation for the role will depend on a number of factors, including a candidate's qualifications, skills, competencies, and experience. Denali offers a competitive total rewards package, which includes a 401k, healthcare coverage, ESPP and a broad range of other benefits. Learn more at https://www.denalitherapeutics.com/careers This compensation and benefits information is based on Denali's good faith estimate as of the date of publication and may be modified in the future.

Denali is committed to its core company value of unity by creating a diverse and inclusive environment. We are proud to be an equal opportunity employer and do not discriminate against any employee or applicant for employment because of race, color, sex, age, national origin, religion, sexual orientation, gender identity and/or expression, status as a veteran, basis of disability, or any other federal, state, or local protected class.

"Life at Denali" is a living reflection of our values: trust, unity, grit and growth. These are not just words we share - they shape how we show up, collaborate and push boundaries together. From the lab to the community, across functions and milestones, our culture thrives on shared purpose and relentless pursuit.