Associate Director, Assay Development, Process Engineering – Brain Health

Allen Institute

Associate Director leading assay development and process engineering at the Allen Institute. Focusing on large-scale data generation pipelines for brain health research and therapeutic strategies.

Posted 5/23/2026full-timeSeattle • Washington • 🇺🇸 United StatesSenior💰 $183,050 - $240,200 per yearWebsite

About the role

Key responsibilities & impact

Lead, mentor, and manage a team of engineers and scientists, fostering a culture of collaboration, innovation, rigor and continuous improvement
Collaborate with senior leadership to develop and execute strategic plans for assay development and process engineering
Lead the design, integration, validation and implementation of novel molecular, microscopy and software components through successful pipeline implementation
Drive the development and implementation of engineering best practices, processes, and standards across assay development and end-to-end assay pipelines to ensure high-quality, reproducible deliverables
Oversee the design, development, and delivery of pipeline capabilities (assay workflows, automation, instrumentation/software integration, and supporting tools) for scientists, ensuring alignment with assay performance requirements and scientific use cases
Conduct technical assessments and guide complex assay pipeline implementations, ensuring scalable throughput, operational reliability, and appropriate security/privacy controls for the lab-to-data workflow
Ensure data integrity, quality, and governance for assay pipeline outputs (including sample metadata, QC metrics, provenance, and downstream handoffs) to enable reliable large-scale dataset generation
Partner with Product Management and cross-functional engineering teams to drive innovation and ensure seamless integration of assay workflows, instrumentation/software components, and data pipeline capabilities
Act as a technical advisor to key stakeholders, providing insights and recommendations to support decision-making and strategic planning
Oversee project timelines, budgets, and resource allocation to ensure successful delivery of assay development programs and supporting end-to-end assay pipeline capabilities
Identify and mitigate risks, manage project dependencies, and ensure alignment with organization goals and objectives
Stay current with industry trends, emerging technologies, and best practices in high-throughput assay development, workflow automation, instrumentation/software integration, and scalable lab-to-data pipelines
Champion the adoption of innovative tools, technologies, and methodologies that improve assay pipeline throughput, robustness, reproducibility, and data quality

Requirements

What you’ll need

Bachelors degree in computer science, engineering, molecular biology, neuroscience, or a related field
10+ years of experience in assay pipeline engineering (lab-to-data workflows), workflow automation and instrumentation/software integration, and/or high-throughput assay development, with at least three years in a leadership or management role
Strong technical background in development of industry-level molecular assays, including single cell and spatially resolved assays and platforms
Strong technical knowledge of highly multiplexed transcriptomic and/or proteomic spatial and single cell assays
Broad familiarity with molecular assay modalities beyond transcriptomics, including single-cell or fluid-based proteomics, lipidomics, and other relevant multi-omic assays
Proven experience managing cross-functional teams and delivering complex, large-scale assay development programs and end-to-end assay pipeline capabilities (including sample metadata, QC, and downstream handoffs)
Excellent communication, collaboration, and stakeholder management skills
Strong analytical and problem-solving skills, focusing on driving results and innovation.

Benefits

Comp & perks

Employees (and their families) are eligible to enroll in benefits per eligibility rules outlined in the Allen Institutes Benefits Guide.
These benefits include medical, dental, vision, and basic life insurance.
Employees are also eligible to enroll in the Allen Institutes 401k plan.
Paid time off is also available as outlined in the Allen Institutes Benefits Guide.

ATS Keywords

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Applicant Tracking System Keywords

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Hard Skills & Tools

assay pipeline engineeringworkflow automationinstrumentation integrationhigh-throughput assay developmentmolecular assaystranscriptomic assaysproteomic assayssingle-cell assaysspatially resolved assaysdata pipeline capabilities

Soft Skills

leadershipmentoringcollaborationcommunicationstakeholder managementanalytical skillsproblem-solvingproject managementrisk managementinnovation

Certifications

Bachelor's degree in computer scienceBachelor's degree in engineeringBachelor's degree in molecular biologyBachelor's degree in neuroscience