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Scientist I - AAV Gene Therapy - Enhancer Optimization

Department: Human Cell Types

Scientist I – AAV Gene Therapy – Enhancer Optimization


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 to join the gene therapy program at the Allen Institute for Brain Science.  This program aims to develop and test new therapeutic AAVs to treat brain disorders including severe forms of epilepsy and other neurodevelopmental diseases using a novel AAV-based cell type-specific expression system. We are seeking a scientist to help design and build new enhancer-AAV-based therapeutics for application to neurodevelopmental and other disorders.  This scientist will work with a team to build on our platform for identification of enhancers that confer cell-type specificity in an AAV context, and develop, modify and optimize vectors for expression strength, specificity, temporal regulation, and therapeutic transgene expression in brain tissues. This scientist must have a strong background in molecular biology, genomics, experience with AAV vector generation, and should be experienced in applying state-of-the-art viral tools to the CNS.

In this role, the scientist will be part of a multidisciplinary team and expected to embrace a rapid and dynamic iterative tool development and testing approach to advance candidate vectors. They will be responsible for meeting goals and timelines as well as prompt and accurate reporting of progress to the group and external collaborators. This individual must have a strong track record and be excited by the prospect of joining a team-science environment at the Allen Institute for Brain Science to help develop new gene therapies for brain diseases.

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

  • Working with bioinformatics team to identify and evaluate critical genomics datasets for enhancer discovery and select putative enhancer elements for testing in an AAV system
  • Design and construction of AAV vectors using standard molecular techniques
  • Modification of expression cassettes to deliver customized gene expression of reporters and therapeutic transgenes
  • Efficiently track developments in the field that may improve vector performance, such as viral capsid improvements and mechanisms to enhance, refine, or regulate gene expression in AAV.
  • Evaluation of therapeutic transgene expression in brain tissue using IHC, mFISH, and fluorescence microscopy
  • Validation of transgene expression in mouse and primate tissues
  • Rapid and transparent communication of all results
  • Take on complex problems and come up with novel solutions in a timeline, milestone-driven and team-centric environment
  • Presentation of results internally, externally and through publications
  • Coordinate with commercial partners on enhancer development and testing

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.

Required Education and Experience

  • PhD or equivalent combination of degree and experience in genomics, neurobiology, virology, or related fields
  • Experience in MS Office programs and other relevant software programs (eg standard DNA sequence analysis, image analysis, etc.)

Preferred Education and Experience

  • PhD and 3-5 years experience in neurobiology, molecular biology, epigenetics, virology, or related fields
  • Single-cell epigenetic or transcriptomic analysis (eg. snATAC-seq, snRNA-seq)
  • High proficiency in molecular biology
  • Building, purifying, and applying AAV viruses in animals
  • Construction of AAVs with novel expression control (using different control elements)
  • Proficiency in brain staining and imaging using fluorescence and confocal microscopy
  • Experience independently solving problems and establishing new procedures and processes.
  • Excellent organizational and communication skills
  • Experience leading projects, designing research projects, and mentoring others
  • Strong publication record

Work Environment

  • Laboratory atmosphere - possible exposure to chemical, biological or other hazardous substances
  • Frequently required to sit, stand, walk, stoop, kneel or reach
  • Possible exposure to BioSafety Level 2 organisms, such as recombinant viruses

Physical Demands

  • Occasional lifting to 30 pounds
  • Fine motor movements in fingers/hands to operate computers and other office equipment; lab equipment
  • Exposure and handling of laboratory animals required

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
  • This position is funded through a sponsored research collaboration

Additional Comments

  • **Please note, this opportunity offers work visa sponsorship and 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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