Senior Automation Engineer– Molecular Tool Development

alleninstitute; Seattle (WA); Hybrid; USD 137,000 - 171,000; Full time

Benefits offered by this job

Visa sponsorship

Relocation assistance

Job summary

The Allen Institute seeks a Senior Automation Engineer to lead the Molecular Tool Development automation group, translating complex biological workflows into scalable automation solutions. The role partners with scientists, engineers, and operations to enable reproducible, high-throughput pipelines.

Responsibilities include defining automation strategy, managing resources, and driving cross-functional projects across proteomics, NGS, and cell assays, with a focus on scalable, reliable platforms.

Qualifications

• 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

Responsibilities

• Identify automation opportunities and define technical requirements, translate concepts into scalable engineering plans and develop automation roadmaps
• Lead the automation group in staffing, coaching, performance management, and resource planning
• Develop and maintain strategic vendor partnerships for equipment evaluation and support
• Drive full lifecycle of automation development from requirements to deployment and ongoing support
• Design and integrate automation platforms across complex workflows enabling high-throughput research
• Demonstrate impact through publications and presentations
• Establish technical standards, scripting guidelines, and validation protocols
• Lead cross-functional collaboration to align automation with scientific priorities
• Develop training materials and mentor team members

Skills

Leadership

Liquid handling robots

Scripting (Python/R)

LIMS integration

High-throughput automation

Education

Bachelor’s degree in life sciences/engineering/biotech

5 years in lab automation

Experience with automation platforms (Tecan, Hamilton, Integra)

Tools

Tecan

Hamilton

Integra

Job description

Senior Automation Engineer– Molecular Tool Development

The Allen Institute accelerates science for a healthier world through large-scale research designed to answer some of the most complex questions in biology. Our multi-disciplinary teams generate foundational knowledge, tools, and data to understand how our brain, cells, and immune system work. We share our work openly so others can build on it, move faster, and ask bigger questions. We drive discovery forward and create new possibilities for improving human health.

The mission of Scientific Shared Resources and Technologies is to enable biological insight through technology innovation, development and application in partnership with the Accelerators at the Allen Institute. This includes generation of world leading datasets.

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.

At the Allen Institute, we believe that science is for everyone – and should be open to everyone. We are dedicated to combating biases and reducing barriers to STEM careers more broadly.

We also believe that science is better when it includes different perspectives and voices. We strive to make the Allen Institute a place where everyone feels like they belong and are empowered to do their best work in a supportive environment.

We are an equal-opportunity employer and strongly encourage people from all backgrounds to apply for our open positions.

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

• $137,050 - $171,250*

* 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.

It is the policy of the Allen Institute to provide equal employment opportunity (EEO) to all persons regardless of age, color, national origin, citizenship status, physical or mental disability, race, religion, creed, gender, sex, sexual orientation, gender identity and/or expression, genetic information, marital status, status with regard to public assistance, veteran status, or any other characteristic protected by federal, state or local law. In addition, the Allen Institute will provide reasonable accommodations for qualified individuals with disabilities