Applied Bioinformatics Engineer, Pipelines – AI

Eli Lilly and Company

Bioinformatics Pipeline Engineer at Lilly enhancing analytical pipelines across multiple omics workflows. Collaborating with scientists and engineers to build reliable computational biology tools for research applications.

Posted 5/8/2026full-timeBoston • Massachusetts • 🇺🇸 United StatesSeniorLead💰 $166,500 - $266,200 per yearWebsite

Tech Stack

Tools & technologies

AWSAzureCloudDockerGoogle Cloud PlatformLinuxPython

About the role

Key responsibilities & impact

Support for computational biology workflows, including single cell, spatial, and other multi-omics analysis workflows for clinical and preclinical applications
Use modern workflow managers (e.g. Nextflow, Snakemake, or similar) and containerization (Docker, Singularity) to make pipelines portable, testable, and reusable across projects and teams
Help build and maintain reproducible analytical pipelines for statistical genetics and bioinformatics workflows
Wrap and harden ad-hoc analytical scripts written by scientists into production-quality tools that can be re-run reliably by others
Write tests, documentation, and clear examples so the pipelines you build are usable by colleagues with a range of technical backgrounds
Prototype agentic workflows that automate established and routine analytical tasks — for example, pulling target evidence across data sources, generating standardized due-diligence reports, or letting scientists interrogate complex datasets in natural language
Build and maintain MCP connectors that expose internal data, public resources, and analytical pipelines to LLM-based agents and tools like Claude
Identify and develop use cases where LLMs and agentic AI workflows can improve the speed, quality, consistency, or accessibility of work across therapeutic areas, focusing on end-to-end capabilities rather than isolated task completion
Contribute to a shared library of reusable AI tooling, prompt patterns, and integration code that the team can build on.
Define technical standards for evaluation, documentation, guardrails, and workflow quality so that AI-based solutions are trusted, reproducible, and suitable for repeated use across teams and projects
Know the latest with the AI tooling landscape and bring back ideas the team can put to work.

Requirements

What you’ll need

B.S. in computer science, computational biology, bioinformatics, biological sciences, statistics, or a related field, with 10+ years relevant work experience, OR M.S. in computer science, computational biology, bioinformatics, biological sciences, statistics, or a related field, with 7+ years relevant work experience OR Ph.D. in computer science, computational biology, bioinformatics, biological sciences, statistics, or a related field, with 1+ years relevant work experience.
Strong programming skills in Python and/or R including comfort with version control (Git), code review, testing, and writing maintainable code
Demonstrated experience building data analysis pipelines, ideally using a workflow manager such as Nextflow, Snakemake, or WDL
Working familiarity with bioinformatics file formats (VCF, BED, GTF, BAM, etc.) and standard tools (PLINK, samtools, bcftools, or similar)
Familiarity with typical data types in high-throughput biology, including NGS data
Hands-on experience or strong demonstrated interest in modern AI tooling — using LLMs through APIs, building MCP servers/connectors, prompt engineering, or wiring up agentic workflows
Demonstrated ability to build stable and practical, reusable workflows and not just code for one-off analyses, with strong implementation skills in Python and modern AI/ML tooling
A collaborative, low-ego mentality; you enjoy building tools that other people use and you take feedback well
Comfort with cloud computing environments (AWS, GCP, or Azure) and Linux/command-line work
Ability to work successfully in a matrixed environment

Benefits

Comp & perks

Comprehensive benefit program to eligible employees
Eligibility to participate in a company-sponsored 401(k)
Pension benefits
Vacation benefits
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
Well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities)

ATS Keywords

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Applicant Tracking System Keywords

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Hard Skills & Tools

PythonRGitNextflowSnakemakeWDLbioinformatics file formatsPLINKsamtoolsbcftools

Soft Skills

collaborative mentalitylow-ego mentalityability to take feedbackstrong implementation skills