Research Advisor - Bioinformatics

Overview

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

We are seeking a highly motivated bioinformatics 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 and contributes to study design and protocol development that accelerates discovery.

In this role, you will support projects, build new capabilities, and analyze high‑throughput NGS sequencing data (e.g. RNA‑seq, smRNA‑seq, SHAPE‑seq, CLIP‑seq) to extract biological insights. 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.

• Collaborate effectively with scientists across RNA therapeutics, LRL and IT organizations to contribute to drug discovery efforts.
• Design and execute analytical strategies for high‑throughput sequencing data to extract biological insights.
• Partner with others in the group to develop new analysis tools, pipelines, and methodologies.
• Contribute to reusable data assets and standardized analysis frameworks that support downstream machine learning and cross‑program integration.
• Develop and execute quality control analysis and troubleshoot any issues.
• Design and perform differential expression analysis, pathway analysis, gene set enrichment analysis to identify biological processes and pathways affected by RNA therapeutics.
• Generate visualizations and reports to communicate results to stakeholders.
• Participate in scientific discussions and present results to the team.

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

• Demonstrated expertise with standard bioinformatics tools, pipelines, and databases for genomic analysis.
• Expertise in systems biology, bioinformatics and genomics.
• Strong programming skills in Python, R, or similar languages.
• 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 who wants to learn new techniques.
• Proficient in data analysis and reporting.
• Strong problem‑solving skills and ability to troubleshoot issues.
• Extensive experience in solving scientific problems using at least one language relevant to data analysis such as Python or R.
• Experience working with High‑Performance Computing and/or Cloud environments.
• Experience with next‑generation sequencing data analysis.
• Experience with workflow orchestration platforms such as Seqera Platform (Nextflow Tower) and community‑maintained pipelines (e.g., nf‑core, including nf‑core/rnaseq) for scalable and reproducible RNA‑seq analysis.
• Experience with RNA‑seq analysis tools such as STAR, HISAT2, DESeq2, edge
  
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• Experienced with gene expression data analysis / transcriptomics.
• Track record of peer‑reviewed publications in high‑impact journals demonstrating expertise in bioinformatics and/or computational biology.
• Deep understanding of nucleic acid, cellular and/or molecular biology.
• Understanding of the biological principles underlying RNA therapeutics.
• Demonstrated knowledge of genetics and molecular biology, particularly relating to RNA.
• Experience in algorithm development, statistics, data management,…