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Associate Director – Assay Development and Process Engineering

The mission of the Allen Institute is to unlock the complexities of bioscience and advance our knowledge to improve human health. Using an open science, multi-scale, team-oriented approach, the Allen Institute focuses on accelerating foundational research, developing standards and models, and cultivating new ideas to make a broad, transformational impact on science.

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.

The Associate Director, Assay Development and Process Engineering, will play a key leadership role within the organization, leading a team to develop and implement scalable high-information content assays that meet the needs of large-scale data generation pipelines for single cell molecular and spatially-resolved analysis of brain tissues or other biological samples. Reporting to the Executive Director, Strategy and Scientific Operations, the successful candidate will be highly experienced in industry-standard assay development, and motivated to work in a team environment with laboratory scientists and managers, engineers, and computational scientists to develop robust pipelines to generate large-scale datasets for scientific discovery. This role will be responsible for supporting internal scientists’ needs and staying at the forefront of technological innovation in relevant domains, managing a portfolio of technology development and implementation goals and working with similar functions across scientific units.

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

• 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

*Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects management’s assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.*

Required Education and Experience

• Bachelor’s 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

Preferred Experience

• 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

Work Environment

• Exposure to and handling of laboratory animals required
• Laboratory environment - possible chemical, biological, or other hazardous substances exposure
• Possible exposure to BioSafety Level 2 organisms, such as recombinant viruses

Animal Care Services

• Exposure to and handling of laboratory animals required
• Pre and post-operative care for mice
• Administration of compounds to mice (iv, ip, sc, po, im, ro, icv)
• Perform health assessments of mice
• Perform euthanasia and tissue collections
• Perform daily vivarium maintenance and/or closing procedures

Physical Demands

• Occasional lifting up to 30 pounds
• Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment.
• Push/pull up to 35 lbs
• Stooping, bending, crouching
• Reaching or climbing ladders

Position Type/Expected Hours of Work

• 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

Additional Eligibility Qualifications

• All employees who work with live animals must complete an Occupational Health medical history form and/or consultation with an Occupational Health Provider and receive clearance to work with animals. Depending on your health history and job responsibilities, an annual respiratory health screening and clearance to use a respirator may also be required.

Additional Comments

• **Please note, this opportunity offers relocation assistance**
• **Please note, this opportunity offers work visa sponsorship**

Annualized Salary Range

$183,050 - $240,200 *

* 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.