Scientist - Barcoded Connectomics

Are you ready for new challenges and new opportunities? Join our team in Seattle!

Current job opportunities are posted here as they become available.

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 for 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 through the integration of experiments, modeling, and theory.

We are seeking a Scientist I to join the Barcoded Connectomics team. The Barcoded Connectomics team is broadly interested in understanding the wiring logic of long‑range connectivity in the brain. Led by Xiaoyin Chen, who developed BARseq, the team is developing 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 focus on designing and performing high-throughput transcriptomics and connectomics experiments and analyzing large‑scale datasets to reveal principles in brain wiring. In addition to working within the Barcoded Connectomics team, the candidate will benefit from interaction with other teams at the Allen Institute with complementary expertise in sequencing, transcriptomics, and neuroanatomy. We welcome candidates from diverse scientific backgrounds, who may bring their own questions and expertise into the field.

Candidates are encouraged to include an optional short research proposal as part of the cover letter describing question(s) they are interested in working on and why the Allen Institute is a good fit for such work.

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.

• Lead projects that focus 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

• Ph.D. or equivalent degrees in STEM (i.e. 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

• 2 years or more of experience in MATLAB and/or python
• 2 years or more of experience with lab‑based research, experimental methods and troubleshooting
• Experience in molecular biology techniques and tissue culture lab
• 5 years or more experience in Linux shell scripting and/or micromanager
• 5 years or more experience with fluorescent microscopy and confocal microscopy
• Laboratory atmosphere - possible exposure to laser, chemical, biological or other hazardous substance
• Exposure to Bio Safety Level 2 materials, such as recombinant viruses
• Potential exposure to and handling of live and fixed NHP tissues and mouse tissues