Senior Automation Engineer• Molecular Tool Development We are searching for an Automation Engineer, Senior to lead the automation group in the Molecular Tool Development team within Shared Resources. The mission of the Molecular Tool Development team is to pioneer, develop, and deploy advanced molecular tools and cutting-edge liquid handling automation across the Allen Institute. By serving as a centralized engine of innovation, the team partners directly with accelerators and high-throughput standardized services to seamlessly translate novel workflows into robust, scalable pipelines. This role sets the team's automation strategy and partners with scientists and technical teams across the Allen Institute to translate emerging molecular methods and complex laboratory workflows into reliable, scalable automation solutions. The Automation Engineer, Senior leads automation initiatives through requirements definition, design, integration, validation, deployment, and ongoing improvement; establishes team technical standards and best practices; and guides the adoption of automation across diverse scientific programs. The position also manages and develops the automation group in the Molecular Tool Development team, aligns staff and financial resources with Institute priorities, and ensures the team delivers reproducible, high-throughput workflows that expand scientific capabilities across the Institute.
Essential Functions - Partner with scientists and technical stakeholders early in project lifecycles to identify automation opportunities, define technical requirements, translate scientific concepts into scalable engineering plans, and develop automation roadmaps that accelerate scientific and operational outcomes.
- Build, lead and manage the automation group in the Molecular Tool Development team, including recruiting, coaching, performance management, resource allocation, and workforce planning to meet Institute-wide automation needs. This includes tracking financial spend and cost recovery models
- Develop and maintain strategic vendor partnerships and provide technical leadership for equipment evaluation, procurement, implementation, and ongoing support
- Drive the full lifecycle of automation development including requirements gathering, custom scripting, system validation, release, and ongoing operational support
- Design and integrate automation platforms across complex workflows, including lab-in-the-loop systems, proteomics, functional cell assays, and NGS assays enabling scalable, high-throughput research and scientific discovery
- Demonstrate impact through increased scientific discovery, presentations and publications
- Establish Institute-wide technical standards, scripting guidelines, and validation protocols to ensure high-throughput platform reliability, reproducibility, and operational excellence across scientific programs
- Evaluate emerging automation technologies and approaches and recommend adoption strategies that advance scientific capabilities, scalability, and operational effectiveness across the Institute
- Lead cross-functional collaboration with staff scientists, computational biologists, engineers, and operational teams to align automation solutions with scientific priorities and Institute objectives
- Develop training materials, provide instruction on validated workflows, and foster team growth through mentoring, hiring, employee development, and performance management processes
Required Education and Experience - Bachelor's degree in life sciences, engineering or biotech related field (or combination of degree and experience) and 5 years of relevant experience
- 5 years of experience in laboratory automation, liquid handling, and high-throughput molecular assay development, with demonstrated progression into technical roles
- Deep expertise in method development for liquid handling robots (e.g. Tecan, Hamilton, Integra, etc.) and associated scripting software
- Demonstrated proficiency translating complex manual workflows into scalable, validated automated liquid handling solutions
- Experience with LIMS integration and barcode-based sample tracking in high-throughput environments
Preferred Education and Experience - Bachelor's degree in life sciences, engineering or biotech related field (or combination of degree and experience) and 5 -7 years of relevant experience
- Proven ability to lead cross-functional projects with significant organizational impact, managing complex dependencies and delivering results with minimal supervision
- Experience authoring verification protocols, SOPs, and validation documentation to industry or regulatory standards
- Excellent communication and stakeholder management skills, with demonstrated ability to influence technical direction across teams
- Experience with NGS library preparation workflows and automating these protocols, at scale
- Background in functional cell assays
- Publication record or technical contributions to open-access datasets or scientific resources
- Working knowledge of scripting or data analysis tools (e.g., R, Python) for QC and pipeline reporting
Physical Demands - Occasional lifting to 30 pounds
- Fine motor movements in fingers/hands to operate computers and other office equipment
- Working at a computer and using a mouse for extended periods of time
Expected Hours of Work - Occasional evening and weekend hours required
- This role is currently able to work both remotely and onsite in a hybrid work environment. We are a Washington State employer, and the primary work location for all Allen Institute employees is 615 Westlake Ave N.; any remote work must be performed in Washington State.
Additional Comments - **Please note, this opportunity does sponsor work visas
- **Please note, this opportunity does offerrelocation assistance
Annualized Salary Range * Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable.
Benefits - Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institute's Benefits Guide. These benefits include medical, dental, vision, and basic life insurance. Employees are also eligible to enroll in the Allen Institute's 401k plan. Paid time off is also available as outlined in the Allen Institutes Benefits Guide. Details on the Allen Institute's benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits .
