Allen Institute

Oversee operational structure and process management within Shared Resources, coordinate production efforts, and ensure alignment with financial and legal teams while fostering collaboration and continuous improvement in a scientific environment.

Title: Associate Director, Assay Development and Process Engineering - Brain Health Location: Seattle, WA United States Hybrid Job Description: 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 managements assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.* Required Education and Experience - 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 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 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. Details on the Allen Institutes benefits offering are located at the following link to the Benefits Guide:

Scientific Project and Alliance Manager Location: Seattle United States Job Description: Scientific Project and Alliance Manager Allen Institute, Brain Science The mission of the Allen Institute is to understand the principles that govern life, and to advance health. Our creative and multi-dimensional teams focus on answering some of the biggest questions in bioscience. We accelerate foundational research, catalyze bold ideas, develop tools and models, and openly share our science to make a broad, transformational impact on the world. The mission of the Allen Institute, Brain Science, is to accelerate the understanding of how the human brain works in health and disease. Using a big science approach, we generate useful public resources, drive technological and analytical advances, and discover fundamental brain properties. Built on the foundational knowledge of brain cell types, the mission of the Allen Institute, Brain Science, is to conduct a series of large-scale projects designed to create CAP (Complete, Accurate, Permanent) datasets and experimental tools; gain fundamental knowledge in the development, evolution, connectivity and function of brain cell types; move towards a better understanding of mammalian brain function in healthy and diseased conditions; and disseminate the data, knowledge and tools broadly with the community, to accelerate research across the neuroscience field. This position, reporting to the Director of Scientific Program Management, will support planning and execution of projects that are part of new scientific initiatives in Brain Science, such as the Mammalian Brain Lifespan, and Whole Mouse Brain Projectome & Connectome. 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 - In partnership with scientific co-leads for one to a few projects, serve as the Project Manager to ensure the successful execution of project deliverables - Support cross-functional teams throughout the project life cycle (planning and execution) - Plan and organize internal and external project meetings with clear agendas, expected outcomes, and follow-up on project-related actions - Plan and organize virtual and face-to-face meetings with external collaborators - Create, maintain, and disseminate project deliverables and timelines, using project management best practices and tools - Contribute to fiscal management of the project, including budget planning, resource forecasting, expenditure monitoring - Implement communication plans to promote effective dialogue among all team members - Ensure appropriate communication with all project stakeholders regarding timelines and status, deadlines, data requirements, and other project-related matters - Keep project milestones/deliverables on track, monitoring and identifying at-risk deliverables - Transparently communicate issues, and work with team members to identify options and implement mitigation strategies - Facilitate and support preparation for internal and external project reviews - Partner with scientific staff to develop competitive external funding applications (Federal and Private), including applications of significant complexity (multiple parties and administrative coordination). Ensure that Grants Management best practices are followed - Support post-award execution of externally funded efforts in audit-compliant fashion including contracts, sub-awardees, budget tracking/variance reporting, prior approval requests, carry forward requests and agency reporting - Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects managements assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned.* Required Education and Experience - Ph.D. degree in biological sciences, with a strong preference towards Neuroscience domain knowledge; or equivalent combination of degree and experience - Minimum of 1 year of experience as a Project Manager, beyond an academic research/post-doctoral setting for a Ph.D. degree holder, and a minimum of 6 years of experience for M.S. degree holder - Demonstrated experience with fiscal management of projects Preferred Education and Experience - 5 years of experience for Ph.D. degree holders and 6-10 years of experience for M.S. degree holders - Formal Project Management training and PMP certification is desirable - Experience planning, coordinating and launching a new initiative - A strong understanding of cell type characterization technologies (such as transcriptomics, spatial transcriptomics, morphology, anatomical tracing, and electrophysiology) is a plus - Results-oriented with a passion for delivering successful projects, with a proven track record of increasing teams velocity and effectiveness - Detail-focused and organized, with an understanding that communication and transparency are critical to achieving success - A collaborative leader with strong communication and collaboration skills; able to navigate challenging group dynamics with consensus-building skills, and to work effectively across scientific, technical and business interfaces - Able to set expectations (vertically and horizontally) and hold individuals and teams accountable - Advanced ability to translate scientific and technical subject matter into concise, clear communications that are understood by technical and non-technical leaders and constituents Physical Demands - Fine motor movements in fingers/hands to operate computers and other office equipment Position Type/Expected Hours of Work - 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. Travel - Possible travel to collaborator sites - Possible travel to national or international conferences Additional Comments - Please note, this opportunity offers relocation assistance - Please note, this opportunity does not offer visa sponsorship Annualized Salary Range $119,650 - $149,550 * - 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 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. Details on the Allen Institutes benefits offering are located at the following link to the Benefits Guide:

Title: Scientist II - Molecular and Proteomic Immunology Location: Seattle United States Job Description: Scientist II Molecular and Proteomic Immunology 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 mission of the Allen Institute for Immunology is to advance the fundamental understanding of human immunology through the study of immune health and diseases where excessive or impaired immune responses drive pathological processes. The Institute will employ a multi-disciplinary team approach in collaboration with academic centers of human immunology to generate novel mechanistic insights into the immune synapse in health and in diseases such as autoimmunity or oncology. The Institute will simultaneously provide a foundational data set and tools for future immunological research as well as a novel collaboration portal for the broader scientific community. The Allen Institute for Immunology is looking for an exceptional molecular immunologist (Scientist II) to join a team focused on using and developing molecular and/or proteomic approaches to comprehensively study the interactions of the immune system. Specific responsibilities will include the design and development of new assays, technologies, and in vitro and ex vivo immunologic studies along with the analysis and synthesis of data generated through our cellular, molecular and proteomic platforms or their derivatives. A flexible and creative mindset along with the ability to function in a team to bring projects to completion on a timeline is essential. The successful candidate will have a strong background in molecular and/or proteomic methodologies along with prior neuroscience and/or immunology experience. Strongest consideration will be given to candidates with a proven track record in identifying and progressing novel hypotheses forward in discovery research and technology development. This position is expected to last through December 2028 based on business needs and funding. 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 - Support the development and application of molecular and proteomic technologies to drive biological insight in the context of immunology. Examples include spatial and droplet based NGS platforms such as Xenium and 10x FLEX or REFLEX - Development of cellular engineering approaches for dissecting immune function. Examples could include molecular recorder systems and high throughput screens - Design, execute and analyze in vitro and ex vivo immunological studies utilizing cell lines, primary cells, and tissues to develop and test hypothesis, possibly including the utilization of genetic mouse models - Collaboration with a team to bring projects to completion on a timeline Note: Reasonable accommodations may be made to enable individuals with disabilities to perform the essential functions. This description reflects managements assignment of essential functions; it does not proscribe or restrict the tasks that may be assigned. Required Education and Experience - Ph.D. or equivalent combination of degree and experience in a life sciences discipline - 3+ years of postdoctoral experience Preferred Education and Experience - A strong background in molecular biology including NGS platforms - Experience in cellular immunology - Direct experience with advanced approaches in deconstructing immunologic mechanisms & testing hypotheses (e.g. targeted mutagenesis using CRISPR/Cas9, phenotypic screening, antibody-based immune modulation, lentiviral work, cell culture, etc.) - Proven success in troubleshooting and innovation on existing platforms, including publications and/or patents - Demonstrated ability to independently analyze data through coding languages (R, python, bash, version control) - Exceptional oral and written communication skills and ability to effectively present complicated concepts internally and externally in a cross-discipline environment Work Environment - Working in a laboratory environment with potential exposure to lasers, biohazards Physical Demands - Occasional lifting to 30 pounds - Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment - Stooping, bending, crouching Position Type/Expected Hours of Work - May need to work outside of standard working hours at times - 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 flexibility to work remotely on a limited basis. We are a Washington State employer; any remote work must be performed in Washington State. - This position is expected to last through December 2028, based on business needs and funding 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 may offer work visa sponsorship - Please note, this opportunity may offer relocation assistance Annualized Salary Range - $105,600 - $130,650 * - Final salary depends on required education for the role, experience, and level of skills relevant to the role, along with work location, where applicable. Benefits - 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. Details on the Allen Institutes benefits offering are located at the following link to the Benefits Guide: