Scientist I - Barcoded Connectomics

The Allen Institute accelerates science for a healthier world through large-scale research designed to answer some of the most complex questions in biology. Our multi-disciplinary teams generate foundational knowledge, tools, and data to understand how our brain, cells, and immune system work. We share our work openly so others can build on it, move faster, and ask bigger questions. We drive discovery forward and create new possibilities for improving human health.

The goal of the Brain Science accelerator is 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, so discoveries made here fuel discoveries everywhere.

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

*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.*

• 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

• Experience in molecular biology techniques and tissue culture lab
• 5 years or more experience with MATLAB and/or python
• 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
• This may include wearing personnel protective equipment (PPE)
• 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

• Occasional evening and weekend hours required
• 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.

• Occasional travel to partner sites for compliance oversight required
• Attendance and participation in national and international conferences required

• 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

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

$86,150 - $106,650 *

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