Associate Director, Assay Development and Process Engineering - Brain Health

About the role

The Allen Institute is launching a new accelerator on human brain health and disease. This initiative aims to dramatically accelerate our understanding of human brain structure and function, identify the molecular, cellular and circuit basis of disease progression, and pioneer new therapeutic strategies targeting vulnerable and affected cell types. Our mission focuses on taking a human-centric approach to understanding and treating disease, combining a large-scale open science discovery approach across multiple diseases, AI-based disease modeling, and translational programs in specific diseases to move from discovery to clinical application. We aim to make transformational change in understanding and treating brain disorders, the biggest health challenge of our time.

Responsibilities

• 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

• 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
• 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

Qualifications

• Ph.D. degree in a relevant technical discipline
• History of contributing software to open source and/or team-based projects
• Basic knowledge of neuroanatomy of mouse, monkey and human brains

Skills

• Technical expertise in assay pipeline engineering, workflow automation, and instrumentation/software integration
• Experience with high-throughput assay development, including single cell and spatially resolved assays
• Knowledge of molecular assay modalities beyond transcriptomics, including single-cell or fluid-based proteomics, lipidomics, and other relevant multi-omic assays
• Ability to lead and manage cross-functional teams
• Strong communication and stakeholder management skills
• Problem-solving and analytical skills

Benefits

• Medical, dental, vision, and basic life insurance
• Allen Institutes 401k plan
• Paid time off as outlined in the Allen Institutes Benefits Guide
• Details on the Allen Institutes benefits offering are located at the following link to the Benefits Guide: https://alleninstitute.org/careers/benefits

Pay

$183,050 - $240,200 annually *

* Final salary depends on the required education for the role, experience, level of skills relevant to the role, and work location, where applicable.

Schedule

This role is currently working onsite and is expected to work onsite for the majority of working hours. The primary work location for this role is 615 Westlake Ave N., with the flexibility to work remotely on a limited basis.

Travel

Occasional attendance and participation in national and international conferences may be required.