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Scientist I - Transgenic mouse line development - Genetic Tools

Department: Molecular Genetics

Scientist I – Transgenic mouse line development


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.

The Genetic Tools team (led by Tanya Daigle) within the Molecular Genetics department (led by Bosiljka Tasic) at the Allen Institute for Brain Science generates high-precision genetic tools to effectively target, monitor, and manipulate distinct cell types within the mouse brain. These genetic tools enable the analysis of the structure and function of neural circuits within the brain and represent foundational resources for the neuroscience community.

We aim to generate transgenic mouse driver lines to target a diversity of neocortical and thalamic cell types and to develop reporter lines in parallel for functional experiments. We have built many successful transgene expression platforms (most recently Daigle and Madisen et al., Cell 2018) and have demonstrated these tools can be combined with one another and enhancer-based AAVs (Graybuck and Daigle, et al., Neuron 2021) to target a diversity of cell types. We seek an exceptional experimentalist to further these platforms and develop intersectional genetic approaches for cell type targeting. The candidate scientist should have a strong background in molecular and cellular neuroscience and mouse genetics and be able to lead efforts to build and validate transgenic mouse lines. They will design and build targeting vectors, manage production activities, systematically characterize the lines, and help manage our transgenic portfolio. This individual should be highly efficient, thrive in a fast-paced, team environment, and be excited about developing leading-edge genetic tools for brain cell types. This work is currently supported by two BRAIN grants, one awarded to Hongkui Zeng and the other awarded to Karel Svoboda, as well as support from the Allen Institute for Neural Dynamics.

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.

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.

Essential Functions

  • Utilize existing in-house analysis tools to explore single-cell genomics data (scRNA-seq) and identify marker genes for brain regions and cell types
  • Design and construct complex targeting vectors using standard molecular cloning techniques
  • Work with external cores to produce transgenic mice and oversee breeding of internal mouse colonies
  • Evaluate transgene expression in the brain using biochemical techniques, fluorescence microscopy, immunohistochemistry (IHC), and multiplex fluorescence in situ hybridization (mFISH)
  • Manage characterization efforts conducted by our core teams and coordinate activities with key stakeholders
  • Evaluate new tools, components, and targeting strategies for implementation in transgenic mouse line production
  • Communicate results rapidly and with a high level of transparency to internal teams and collaborators
  • Manage deposition of tools and data to public repositories
  • Lead publications, contribute to grant applications, and preparation of intellectual property (IP)-related materials

Required Education and Experience

  • Ph.D. in Neurobiology, Genetics, Biochemistry or related fields; or equivalent combination of degree and experience
  • Experience with molecular cloning techniques and with DNA construction software (Geneious or Vector NTI)
  • Experience with MS office programs and other related software (Adobe products and software for basic image analysis)
  • Ability to work at the bench >80% of the time

Preferred Education and Experience

  • Deep experience with molecular cloning techniques and targeting vector generation
  • Experience generating mouse lines
  • Experience with complex breeding strategies and characterizing mouse models
  • Experience characterizing gene expression in the mouse brain
  • Proficient in mouse brain tissue sectioning, staining (IHC), fluorescence imaging (epi and confocal), protein and image analysis
  • Outstanding oral and written communication skills
  • Experience working in milestone-driven environment with aggressive timelines
  • Highly self-motivated, experienced research scientist with a positive attitude and ability to work independently to solve problems
  • Experience designing and leading research projects
  • Strong publication record

Work Environment

  • Will enter laboratory environment, including potential exposure to lasers, biohazards

Physical Demands

  • Fine motor movements in fingers/hands to operate computers and other office equipment; repetitive motion with lab equipment

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 Comments

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


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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