Senior Scientist, Computational Biology

Denali Therapeutics; 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 seeks a highly skilled computational biologist to lead analysis across bulk and single-cell transcriptomics, collaborating with Discovery scientists to advance early-stage programs.

The role emphasizes development of analytical tools, robust methods, and the ability to communicate results for publications and potential regulatory submissions. A PhD with 3+ years in industry is preferred, with expertise in scRNA-seq and Python/R.

Qualifications

• PhD in Computational Biology, Epidemiology, Neuroscience, Statistics, or similar with 3+ years relevant industry experience.
• Proven track record of analyzing single-cell/single-nucleus RNA-seq data with publications and sound statistical methods.
• Experience with other high-dimensional data types (proteomics, mass spectrometry, human genetics) is a plus.
• Extensive experience in R or Python for high-dimensional data analysis.
• Knowledge of Git and reporting tools (R Markdown, Quarto); dashboard-building (Shiny) is a plus.
• Track record of impactful research and peer-reviewed publications.
• Strong analytical and problem-solving skills with excellent communication.

Responsibilities

• Acts as subject matter expert for high-dimensional data analysis, including bulk and single-cell transcriptomics.
• Collaborates with Discovery scientists to design, analyze, and interpret in vitro and in vivo experiments.
• Performs rigorous, reproducible analyses across transcriptomic and genomic datasets.
• Develops and extends internal tools and oversees external analyses as needed.
• Acts as an independent contributor, defining analytical approaches and building solutions.
• Adapts analysis workflows with AI-assisted approaches while ensuring accuracy.
• Applies best practices in code and data management with version control; improves workflows.
• Communicates results to cross-functional teams and supports regulatory filings and publications.

Skills

scRNA-seq analysis

Python

R

Git

Shiny dashboards

Analytical thinking

Education

PhD in Computational Biology/related field

Tools

Cell Ranger

CellBender

Seurat

Scanpy

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.