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Scientist I - Bio-realistic Modeling of Reconstructed Cortical Tissue

Department: 2230 - Modeling and Theory
Location: Seattle

Scientist I Bio-realistic Modeling of Reconstructed Cortical Tissue

Our mission at the Allen Institute is to advance our understanding of how the brain works in health and disease. Using a team science approach, we strive to discover how the brain implements fundamental computations through the integration of technological innovation, cutting-edge experiments, modeling, and theory.

The Allen Institute is seeking exceptional candidates for a BRAIN Initiative-funded position of Scientist in our Seattle-based multidisciplinary organization. The Scientist will join the computational team of Anton Arkhipov and will focus on data analysis and modeling of structure, activity, and computations in mouse cortical circuits.

This project will take advantage of unprecedented experimental datasets from the Allen Institute that contain a systematic characterization of synaptic connections between the cell types ( and a connectome of individual neurons coupled with dense recordings of activity in the mouse visual cortex ( The Scientist will work collaboratively with colleagues to integrate these data into new, highly realistic network models of cortical circuits, use the models to explore theoretical predictions, and provide them as a resource to fuel future theoretical, modeling, and experimental work in the community.

Our computational team collaborates closely with experimentalists to build systematic classifications of structure and function of the mouse visual cortex based on high-throughput recordings in vitro (e.g., Gouwens et al., Nature Neurosci., 2019; Gouwens et al., Cell, in press, 2020, and in vivo (e.g., Siegle et al., Nature, in press, 2020,  Using systematically constructed models of neurons from diverse types, we are building and simulating data-driven, highly realistic models of the mouse visual cortex (Arkhipov et al., PLOS Comp. Bio., 2018; Billeh et al., Neuron, 2020; The team also develops and disseminates modeling software (;

Join us to analyze world-class experimental data and build the next generation of brain models!

Essential Functions

  • Collaborate with in-house experimentalists to analyze data from the synaptic physiology and 2-photon calcium imaging/electron microscopy connectomics datasets.
  • Use these data to build and simulate models of cortical circuits, in order to study mechanisms connecting circuit structure and function.
  • Publish/present findings in peer-reviewed journals/scientific conferences.

Required Education and Experience

  • PhD degree in Neuroscience, Physics, Applied Mathematics, or related fields.
  • 0-2 years of post-doctoral experience.
  • Strong publication record.
  • Track record of scientific excellence and independent thinking.

Preferred Education and Experience

  • Experience in computational neuroscience and/or systems neuroscience is preferred, but other strong applicants will be considered (with background in computational physics, biophysics, and related disciplines).
  • Candidates with strong background in experimental systems neuroscience, willing to switch to computational work, are encouraged to apply.
  • Experience with scientific programming (e.g., in Python) and sharing/collaborative development of software (e.g., GitHub) is a plus.

Physical Demands

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

Position Type/Expected Hours of Work

  • This role is currently able to work remotely due to COVID-19 and our focus on employee safety; this may change, and you may be required to work onsite at our South Lake Union office as safety restrictions are lifted in relation to COVID-19.

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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