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Director/Senior Director - Computational Biology

Eli Lilly and Company
Boston, Massachusetts
Start date
Feb 9, 2024

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Science/R&D, Biology
Required Education
Position Type
Full time
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Job Details

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. We’re looking for people who are determined to make life better for people around the world.

Director/Senior Director - Computational Biology

Akouos is seeking a talented and highly motivated Director/Senior Director of Computational Biology. The candidate will be responsible for leading the computational biology efforts of Akouos and will work in close collaboration with members of the Research team within Akouos as well as throughout other divisions of Eli Lilly. The candidate will be responsible for experimental design, analysis, and interpretation of large data sets including bulk RNA-seq, single-cell/single-nucleus RNA seq, single-cell ATAC seq, single-cell barcoding strategies, spatial transcriptomic data, and imaging analysis. The job requires innovative problem solving in all parts of the process from sequencing, estimating gene and transcript expression, applying statistical methods for dimensionality reduction, differential analyses and clustering, to biological interpretation and multimodal data integration. Reporting to the Chief Scientific Officer, this individual will apply these assays in service of developing novel gene therapies for hearing loss and disorders of the ear. 

As the Head of Computational Biology, you will develop and apply cutting edge machine learning and bioinformatic methods to integrate and analyze diverse data in order to enable deep characterization of cellular states in data sets generated from human disease and physiology, in animal models, and in response to candidate therapeutics.

  • Develop and deploy barcoding strategies to enable the collection of robust and reproducible data from highly multiplexed in-vivo experiments.
  • Develop and deploy both classical data science and cutting-edge ML methods to analyze data from diverse ‘omic modalities, including transcriptomic and imaging data, addressing challenges such as distribution shift, experimental artifacts, data sparsity, and more
  • Work with lab colleagues to design experiments that generate datasets that are fit for purpose for machine learning, including ones generated explicitly for training ML models
  • Lead yearly and quarterly planning, set impactful goals, generate team budget and forecast, and align with cross-functional stakeholders
  • Engineer robust, reusable platform components in partnership with the Information Technology team.

Basic Qualifications:
  • Ph.D. in computational biology, genetics, computer science, bioinformatics or a related discipline.
  • Minimum of 5 years' experience in a relevant field, post-PhD.

Additional Skills & Preferences:
  • 10+ years practical experience using and developing cutting-edge methods for analyzing biological data sets, including extensive experience with genomic and/or transcriptomic data sets with single-cell RNA-seq experience strongly preferred.
  • 5+ years working in industry, including experience with managing projects and deliverables.
  • Experience working with multiplexed barcoding strategies coupled with viral delivery strongly preferred.
  • Experience and demonstrated ability to work closely with diverse teams including IT professionals, engineers and scientists,
  • Demonstrated ability to architect and build reusable code infrastructure and work with engineering teams
  • Strong fundamentals in applied multivariate statistics Expertise in machine learning algorithms
  • Strong programming skills in Python and R Ability to communicate effectively and collaborate with people of diverse backgrounds and job functions in a fast-paced environment
  • Passion for making a difference in the world
  • Some understanding of virology, human physiology or disease biology
  • Strong publication record in machine learning, computer vision, or life sciences Familiarity with cloud computing services (e.g., AWS or GCP)

Eli Lilly and Company, Lilly USA, LLC and our wholly owned subsidiaries (collectively “Lilly”) are committed to help individuals with disabilities to participate in the workforce and ensure equal opportunity to compete for jobs. If you require an accommodation to submit a resume for positions at Lilly, please email Lilly Human Resources ( ) for further assistance. Please note This email address is intended for use only to request an accommodation as part of the application process. Any other correspondence will not receive a response.

Lilly is an EEO/Affirmative Action Employer and does not discriminate on the basis of age, race, color, religion, gender, sexual orientation, gender identity, gender expression, national origin, protected veteran status, disability or any other legally protected status.

Our employee resource groups (ERGs) offer strong support networks for their members and help our company develop talented individuals for future leadership roles. Our current groups include: Africa, Middle East, Central Asia Network, African American Network, Chinese Culture Network, Early Career Professionals, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinos at Lilly, PRIDE (LGBTQ + Allies), Veterans Leadership Network, Women’s Network, Working and Living with Disabilities. Learn more about all of our groups.



Science has been our calling from the beginning. Colonel Eli Lilly founded the company in 1876 and charged employees to “take what you find here and make it better and better.” More than 147 years later, we remain committed to his vision through every aspect of our business and the people we serve, starting with discovering the best treatments for those who take our medicines and extending to health care professionals, employees and the communities in which we live. Moreover, you can also count on the team at Lilly to be incredibly civic-minded, supporting our communities through philanthropy, volunteerism, and a creative and innovative can-do spirit. 

Company info
893 S Delaware St
United States

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