Research Advisor - Computational Genomics

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.

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 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 are looking for people who are determined to make life better for people around the world.

We are seeking a highly motivated computational genomics scientist to join our team and contribute to high-visibility research on RNA therapeutics. The Lilly Genetic Medicine (LGM) team is an innovation-focused group working to identify, develop, and apply cutting-edge technologies to deliver maximum benefit to our patients. Our Data Science and AI/ML team collaborates with experimental scientists from diverse backgrounds, contributing to study design, scalable genomics infrastructure, and data-driven discovery that accelerates the RNA therapeutic pipeline.

Responsibilities:

In this role, you will build, scale and maintain the production genomics infrastructure that powers RNA drug discovery at scale - from raw sequencer output through QC to the DataLake - while also contributing to ML models that link sequence design to pharmacology outcomes. You will work closely with global experimental and computational scientists, statisticians, data scientists, and IT professionals to develop study design, analyze data, and present results.

Key responsibilities include:

• Build and maintain production NGS analysis pipelines scaled for high-throughput RNA drug discovery including bulk RNA-seq, smRNA-seq, SHAPE-seq, and eCLIP-seq assays

• Own the full data path from sequencer output through QC to DataLake ingestion, ensuring data integrity, reproducibility, and accessibility for downstream analysis and ML ready data

• Design and execute analytical strategies for spatial transcriptomics and single-cell sequencing to resolve cellular heterogeneity and tissue-level biology relevant to RNA therapeutics

• Support and contribute to ML model development connecting RNA sequence design and chemistry to pharmacology outcomes, including potency and off-target liability prediction

• Partner with enterprise AI, Statistics, and Tech@Lilly teams to translate platform-level AI/ML capabilities into RNA-specific tooling and reusable analytical assets

• Contribute to reusable data assets and standardized analysis frameworks that support downstream machine learning and cross-program integration

• Generate visualizations and reports to communicate results to stakeholders; participate in scientific discussions and present findings to the team

Basic Requirements:

• PhD degree in bioinformatics, computational biology, computational genomics, integrated biomedical sciences, or a related field

Additional Skills/Preferences:

• Demonstrated expertise with standard bioinformatics tools, pipelines, and databases for genomic analysis

• Strong programming skills in Python, R, or similar languages

• Experience with high-throughput, high-dimensional NGS data analysis and interpretation

• Excellent written and oral communication skills with ability to present complex data to diverse audiences

• Demonstrated ability to work collaboratively in cross-functional team environments

• Self-directed and highly motivated individual with strong learning agility

• Extensive experience developing scientific solutions using Python, R, or similar languages

• Experience working with High-Performance Computing and/or cloud environments

• Experience with workflow orchestration platforms such as Seqera Platform (Nextflow Tower) and community-maintained pipelines (e.g., nf-core/rnaseq) for scalable, reproducible analysis

• Hands-on experience with RNA-seq analysis tools for alignment, gene expression quantification and pathway analyses

• Hands-on experience with spatial transcriptomics (e.g., Visium, Xenium) and single-cell RNA-seq analysis (e.g., Seurat, Scanpy)

• Exposure to AI/ML methods applied to biological sequence data or drug discovery (e.g., regression, deep learning, generative models for sequences)

• Deep understanding of nucleic acid, cellular, and molecular biology; familiarity with RNA therapeutics biology is a strong plus

• Demonstrated knowledge of genetics and molecular biology, particularly as they relate to RNA

• Track record of peer-reviewed publications in bioinformatics, computational biology, or a closely related field

• Experience in algorithm development, statistics, data management, data mining, data visualization, and/or analytics

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form (https://careers.lilly.com/us/en/workplace-accommodation) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.

Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, 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 are open to all employees. Our current groups include: Africa, Middle East, Central Asia Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ+ Allies), Veterans Leadership Network (VLN), Women’s Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups.

Actual compensation will depend on a candidate’s education, experience, skills, and geographic location.  The anticipated wage for this position is

Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lilly’s compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.

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