Advisor Engineer - Data, Molecule Discovery

Company: Eli Lilly and Company
Location: Indianapolis
Posted on: July 2, 2025

Job Description:

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. The Discovery Data Team at Lilly is focused on accelerating molecule discovery using advanced data, lab automation and machine learning technologies. We build the next generation of discovery workflows, integrating laboratory data, computational results, and biological insights at scale. We are seeking a highly skilled and versatile Data Engineer to design and implement robust data pipelines that support molecule discovery and experimental workflows. This individual will be responsible for architecting scalable data systems, integrating electronic lab notebooks (ELNs) like Benchling and Signals, working across AWS-based infrastructure and modern data tooling, and collaborating with the lab automation engineers to build robust data infrastructure for the automated labs. This position will be responsible for building automated pipelines to support our efforts in drug discovery across all modalities (small molecule, large molecule and genetic medicines). The role involves working closely with scientists and other engineers who are developing new software tools and applying AI/ML to the life sciences domain. We are seeking individuals with experience using data engineering techniques such as ETL (Extract Transform Load) and relational database design. Knowledge of bioinformatics concepts and tools would be advantageous but not essential. The successful candidate should have excellent communication skills and enjoy working collaboratively within multidisciplinary teams. They should also demonstrate initiative by identifying opportunities to streamline processes and implement best practices wherever possible. Key Responsibilities: Architect and implement scalable, fault-tolerant data pipelines for ingesting and transforming scientific data, including large datasets from ELNs such as Benchling and Signals. Collaborate with Tech@Lilly, data scientists, bio and cheminformaticians, and laboratory scientists to understand data needs and translate them into robust data models and workflows. Build and manage workflows using Airflow, Spark clusters, and PostgreSQL, with performance-aware use of columnar databases. Develop APIs and microservices using FastAPI to serve processed data to downstream applications and teams. Leverage AWS services (Lambda, Batch, S3, EC2, etc.) to build scalable, cloud-native pipelines and data infrastructure. Design and implement data models that capture scientific concepts and experimental data for analytics and ML workflows. Collaborate with the lab automation engineers to build robust data infrastructure for the automated labs Serve as a technical leader and data architect within the Discovery Data Team in Molecule Discovery Develop novel methods and approaches for solving complex problems related to the storage, analysis, and integration of diverse types of structured and unstructured data sets. Apply data science principles and practices to develop innovative solutions for extracting valuable insights from large datasets. Contribute to the development of standards and guidelines for data management and sharing within the organization. Collaborate with cross-functional teams to ensure seamless integration between different components of the data pipeline. Stay up-to-date with emerging trends and advancements in data engineering, machine learning, and artificial intelligence. Actively participate in code reviews and provide constructive feedback to peers. Maintain data quality, integrity, lineage, and security across systems and ensure compliance with relevant regulations and security protocols when handling sensitive biological data. Basic Qualifications: Bachelor's degree or higher level degree (i.e. PhD, Masters, etc.) in engineering, computer science or related sciences fields 5 years of experience in data engineering or architecture roles, preferably in biotech, pharma, or scientific domains. Additional Skills/Preferences: Deep expertise in data pipeline development using tools like Apache Airflow, Apache Spark, and PostgreSQL. Proficient in Python and familiar with FastAPI for building data-centric APIs. Experience integrating ELNs (e.g., Benchling, Signals) or other scientific data systems. Strong data modeling skills, especially in structuring complex experimental and chemical/biological data. Experience with columnar databases (e.g., Parquet, Redshift, or ClickHouse). Excellent communication skills with the ability to interface with both scientific and technical stakeholders. Excellent problem-solving skills and ability to troubleshoot complex issues Experienced in developing solutions using agile methodology (e.g. Scrum) and tools (e.g. JIRA) Experience working with AWS technologies: Lambda, Batch, S3, EC2, IAM, CloudFormation/Terraform (preferred). Background in life sciences, chemistry, or a related field is a strong plus. Familiarity with cheminformatics or bioinformatics data formats and concepts. Experience supporting machine learning pipelines or analytics platforms in a scientific context. Experience working with lab instrumentation data extraction and integration into cloud data stores. Why Join Us? Work on real-world challenges at the intersection of science and data. Join a collaborative, mission-driven, and cutting-edge molecule discovery team accelerating discovery through technology. Competitive compensation, equity options, and comprehensive benefits. 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 $135,000 - $213,400 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. WeAreLilly

Keywords: Eli Lilly and Company, Terre Haute , Advisor Engineer - Data, Molecule Discovery, Science, Research & Development , Indianapolis, Indiana