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Senior Automation Engineer, Molecular Tool Development

allen institute • United States
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Lead the automation group within Molecular Tool Development, setting automation strategy and translating molecular methods into scalable automation solutions. This role requires deep expertise in laboratory automation, liquid handling, and high-throughput assay development. Responsibilities include managing the team, developing automation roadmaps, and ensuring reproducible, high-throughput workflows.

Key Highlights
Lead automation strategy and initiatives for molecular tool development.
Develop and deploy advanced molecular tools and cutting-edge liquid handling automation.
Manage and develop the automation group, ensuring reproducible, high-throughput workflows.
Key Responsibilities
Partner with scientists and technical stakeholders to identify automation opportunities and define technical requirements.
Translate scientific concepts into scalable engineering plans and develop automation roadmaps.
Build, lead, and manage the automation group, including recruiting, coaching, performance management, and resource allocation.
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.
Establish Institute-wide technical standards, scripting guidelines, and validation protocols.
Evaluate emerging automation technologies and approaches and recommend adoption strategies.
Lead cross-functional collaboration with staff scientists, computational biologists, engineers, and operational teams.
Develop training materials, provide instruction on validated workflows, and foster team growth through mentoring, hiring, employee development, and performance management processes.
Technical Skills Required
Laboratory Automation Liquid Handling High-Throughput Molecular Assay Development
Benefits & Perks
Medical, dental, vision, and basic life insurance
401k plan
Paid time off
Nice to Have
Experience authoring verification protocols, SOPs, and validation documentation to industry or regulatory standards
Excellent communication and stakeholder management skills
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

Job Description

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.
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