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Scientist I - Barcoded Connectomics

Department: Brain Science Management

Scientist I – Barcoded Connectomics


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 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 integration of experiments, modeling and theory.

We are seeking an exceptionally creative and motivated Scientist I to join the Barcoded Connectomics team at the Allen Institute for Brain Science. 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 (Chen et al., 2019) and BARseq2 (Sun et al., 2021), the team is further developing in situ sequencing techniques and RNA barcoding-based neuroanatomical techniques (i.e. MAPseq and BARseq). Leveraging the cellular resolution and high throughput of these techniques, we aim to unravel the relationship between cell types, gene expression, and projections during development and across species.

The candidate will focus on developing in situ sequencing and/or barcoding-based techniques and applying them to understand how cell types and their connectivity diverge and expand across species. In addition to working within the Barcoded Connectomics team, the candidate will also benefit from interaction with other teams at the Allen Institute with complementary expertise in sequencing, transcriptomics, and neuroanatomy. We welcome candidates from diverse scientific background, who may bring their own questions and expertise into the field.

The Allen Institute believes that team science significantly benefits from the participation of diverse voices, experiences, and backgrounds. High-quality science can only be produced when it includes different perspectives. We are committed to increasing diversity across every team and encourage people from all backgrounds to apply for this role.

Essential Functions

  • Develop and apply in situ sequencing-based transcriptomics and neuroanatomical techniques.
  • Publish and present findings in peer-reviewed journals and scientific conferences.
  • Maintain clear and accurate communication with supervisor, team members, and external collaborators.

Note: Reasonable accommodation 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

  • PhD in neurobiology, molecular biology, chemistry, or related fields
  • Experience in MS Office programs and other relevant software programs (e.g. standard image analysis software etc.)

Preferred Education and Experience

  • Experience with and in-depth understanding of fluorescence microscopy
  • Proficiency in MATLAB, python, and/or R
  • Experience in molecular biology techniques and tissue culture lab
  • Strong publication record and consistent performance
  • Excellent communication skills

Work Environment

  • Laboratory atmosphere - possible exposure to chemical, biological, or other hazardous substances
  • Exposure to BioSafety Level 2 materials, such as recombinant viruses
  • Potential exposure to and handling of live and fixed NHP tissues
  • Potential exposure risk for bloodborne pathogens, e.g. Simian B virus

Physical Demands

  • Occasional lifting up to 30 pounds
  • Fine motor movements in fingers/hands to operate computers and other office equipment; lab equipment
  • Frequently required to sit, stand, walk, stoop, kneel or reach

Position Type/Expected Hours of Work

  • This role is currently working onsite and remotely when possible, due to COVID-19 and our focus on employee safety. We continue to evaluate the safest options for our employees.

Additional Eligibility Qualifications

  • In keeping with our focus on employee safety, all employees must be up to date with vaccinations against COVID-19 as a condition of employment unless a medical or religious accommodation is approved. All employees will be required to keep their vaccination status up to date according to CDC guidance

Additional Comments

  • 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
  • **Please note, this opportunity offers relocation assistance**


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.





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