Scientist I - Barcoded Connectomics

At the Allen Institute, we accelerate science for a healthier world through large-scale research designed to answer some of the most complex questions in biology. Our multidisciplinary teams generate foundational knowledge, tools, and data to understand how the brain, cells, and immune system work. We share our work openly so others can build on it, move faster, and ask bigger questions.

About the role

The Brain Science accelerator aims to produce three interlocking resources: cell type atlases that catalog every kind of brain cell across ages and species, connectomes that chart the brain's intricate wiring, and a knowledge platform that knits it all together with powerful analysis tools. Every dataset is freely shared to fuel discoveries worldwide.

We are seeking a Scientist I to join the Barcoded Connectomics team, which is focused on understanding the wiring logic of long-range connectivity in the brain. Led by Xiaoyin Chen, who developed BARseq, the team is advancing in situ sequencing and barcoded connectomics techniques to reveal the relationship between cell types, gene expression, and projections during development and across species.

The candidate will design and perform high-throughput transcriptomics and connectomics experiments, analyze large-scale datasets to uncover principles in brain wiring, and collaborate with teams specializing in sequencing, transcriptomics, and neuroanatomy. We welcome candidates from diverse scientific backgrounds and encourage them to include an optional short research proposal in their cover letter outlining questions they are interested in exploring.

Responsibilities

• Lead projects focused on understanding wiring rules of the brain using high-throughput techniques.
• Design and analyze high-throughput barcoded connectomics and transcriptomics experiments.
• Coordinate with other teams to acquire data.
• Maintain and improve software packages for data production and processing.
• Monitor and manage data acquisition, storage, and deposition.
• Publish and present findings in peer-reviewed journals and scientific conferences.
• Execute collaborative projects within the team, across teams, and/or with external collaborators.

Requirements

• Ph.D. or equivalent degree in STEM (e.g., Neuroscience, Biology, Computer Science, Mathematics, or related field); or equivalent combination of degree and experience.
• Experience in MATLAB and/or Python.
• Experience with lab-based research, experimental methods, and troubleshooting.

Preferred Qualifications

• Experience in molecular biology techniques and tissue culture.
• Five or more years of experience with MATLAB and/or Python.
• Five or more years of experience in Linux shell scripting and/or Micro-Manager.
• Five or more years of experience with fluorescent microscopy and confocal microscopy.

Work Environment

• Laboratory atmosphere with possible exposure to lasers, chemicals, biological, or other hazardous substances (PPE may be required).
• Exposure to BioSafety Level 2 materials, such as recombinant viruses.
• Potential exposure to and handling of live and fixed NHP tissues and mouse tissues.
• Potential exposure risk for bloodborne pathogens, e.g., Simian B virus.

Schedule

• Occasional evening and weekend hours required.
• This role is primarily onsite at 615 Westlake Ave N., with limited remote work flexibility.
• Occasional travel to partner sites for compliance oversight and attendance at national/international conferences required.

Additional Eligibility Qualifications

• All employees working with live animals must complete an Occupational Health medical history form and/or consultation and receive clearance.
• Depending on health history and job responsibilities, an annual respiratory health screening and respirator clearance may be required.

This opportunity offers relocation assistance and may provide work visa sponsorship.

Pay

Annualized salary range: $86,150 - $106,650. Final salary depends on education, experience, skills, and work location.

Benefits

• Medical, dental, vision, and basic life insurance.
• Eligibility to enroll in the Allen Institute’s 401k plan.
• Paid time off as outlined in the Benefits Guide.

Details on benefits are available at https://alleninstitute.org/careers/benefits.