Shanahan Foundation Fellowship

The Shanahan Foundation Fellowship at the Interface of Data and Neuroscience

The Shanahan Foundation Fellowship at the Interface of Data and Neuroscience is co-hosted by the Allen Institute and the University of Washington (through its eScience Institute and the Computational Neuroscience Center) and directed by Christof Koch, Ph.D., Chief Scientist for the MindScope Program at the Allen Institute. This post-graduate fellowship is funded by the Shanahan Family Foundation, as part of their mission to empower people and accelerate scientific discovery, and by the Allen Institute.

"We wanted to create the opportunity for fresh perspectives to join neuroscience. This fellowship is intended to give upcoming leaders in quantitative fields the opportunity to uncover new insights in the massive neuroscience datasets produced by the Allen Institute."

— The Shanahan Family

The brain is the most complex piece of organized matter in the known universe. Now, with burgeoning advances in brain science methodology—Neuropixels probes that can record from 1000 neurons at once, massive optical calcium imaging in behaving animals, transcriptional data relating to 100s of distinct neuronal cell types, and a growing consensus on data on common standards across laboratories—the field is flooded with data that need interpretation. The skills of data scientists are essential to help springboard the field to the next stage of discoveries.

To that end, the Shanahan Foundation Fellowship was created to bring fresh perspectives into the field, encouraging data scientists to work together with leading neuroscientists at the Allen Institute and at UW.


We are looking for post-graduate quantitative scientists who want to use their expertise to make a difference in the field of neuroscience. The Allen Institute is unique in its ability to produce vast data sets on the brain (see our existing datasets and other resources). We have invested in the infrastructure and pipeline needed to produce standardized, reproducible survey-styled data that is ripe for analysis. Since 2003, Allen Institute neuroscience teams have generated large-scale, cutting-edge brain atlases and other resources to advance the field and our knowledge about the brain.

Neuroscientists at the Allen Institute are at the forefront of the field, bringing our unique principles of Big, Team and Open Science to bear on the challenge of understanding the brain and, ultimately, what it means to be human. Together with our collaborators at the UW Computational Neuroscience Center and eScience Institute, we provide quantitative scientists with the ideal opportunity and resources to mine for novel insights and discoveries in the field of neuroscience.

This three-year data science fellowship program has the following five aims:

  • Integrate Data Scientists into Neuroscience Research – The Fellowship will serve to promote the application of statistical, computational, machine learning or other data science methods to neuroscience by recruiting scientists with a Ph.D. (or equivalent) in a quantitative field such as computer science, electrical engineering, physics, mathematics or biology.

  • Challenge Traditional Approaches to Neuroscience – Fellows are encouraged to develop novel research programs which push the boundaries of both data and neuroscience. Fellows will have independence in selection and focus of research direction with the Allen Institute and University of Washington throughout their fellowship term.

  • Provide Multidisciplinary, Multi-organizational Co-Mentorship – Each fellow will be matched with two mentors (one from the Allen Institute and one from University of Washington).

  • Network and Community Building – The Allen Institute and UW will facilitate the growth of fellows’ scientific and professional networks with ongoing opportunities to meet and interact with peers and established scientists.

  • Career Development – First-year fellows will take the Allen Institute’s Summer Workshop on the Dynamic Brain course and serve as teaching assistants for the course in their second year. It is expected that fellows will present their research at relevant professional gatherings, such as the annual Neural Computation and Engineering Connection event, Cosyne, NeurIPS (formerly NIPS), and the Society for Neuroscience conference.

The Fellowship Experience

You do not need experience in neuroscience to apply. The goal of the fellowship is to provide opportunities to non-traditional applicants who other postdoctoral fellowships in neuroscience would not typically fund. The fellowship has been purposefully designed to give fellows the time and mentorship needed to get up to speed in a new field and new data collection techniques and methods. 

At the beginning of the three-year fellowship, fellows will identify a mentor at the Allen Institute, where the fellows will be based. Fellows will also select a co-mentor at the University of Washington who will provide additional guidance on a project designed by the fellow, focused on quantitative analysis of neuroscience data available through the Allen Institute’s vast data banks – ranging from molecular, genomic, transcriptional, physiological, morphological, anatomical and functional whole-brain level in the brains of mice, non-human primates and humans or through analysis of data generated by ongoing laboratory work.

Fellows will participate in the career development program at the University of Washington’s eScience Institute and the UW  Computational Neuroscience Center. The eScience Institute offers regular workshops on topics such as cloud computing, python and reproducibility. New fellows will attend the annual Summer Workshop on the Dynamic Brain where they will begin learning how to apply data science skills to neuroscience data and questions. Throughout the three years of the fellowship, fellows will be supported in developing a network in the neuroscience field and sharing their progress with peers at conferences. Each fellow will have the opportunity to mentor a fully-funded UW undergraduate or postbaccalaureate research assistant who helps with their research for 3-12 months. Up to three fellows will be selected to begin in Fall 2022. 

Fellows will be Allen Institute employees (Scientist I or Scientist II) with salary commensurate to years of experience. They will also receive an affiliate postdoctoral appointment at UW.  Each fellow will have $10,000 per year to fund travel to conferences, computer hardware, books or other research expenses. Some relocation expenses can also be reimbursed. 

The choice of the final advisor/co-advisor will be accomplished during the first year of this fellowship.  

Applicant Eligibility

Applicants must be scientists with a Ph.D. (or equivalent) in a quantitative field such as computer science, electrical engineering, physics, mathematics or biology with a background in statistical, computational, machine learning or other data science methods,or who will have completed their Ph.D. by the start of the fellowship program. Ph.D. should have been awarded in the last 3 years.  

One goal of the fellowship is to build a network of collaborators, as such, priority will be given to applicants who are not currently postdoctoral fellows or scientists at the University of Washington or the Allen Institute respectively.

We believe high-quality science can only be produced when it includes different perspectives. We are building an environment of diversity and inclusion and encourage people from all backgrounds to apply for this fellowship.

Required Application Materials

  • A curriculum vitae from the applicant

  • Two (2) Letters of support from other colleagues or mentors

  • A one-page personal statement from the applicant describing their history, activities and interests as an individual (especially those outside of science) which may give the committee a greater sense of you as a person and your ability to simultaneously interact with and challenge traditional scientific fields.

  • A two-to-three page research statement from the applicant describing their prior research, interests in applying data science to the field of neuroscience, potential research interests (including tools they are familiar with) and how this fellowship aligns with their career goals.

Applications for the Fall 2022 cohort are closed. The next round expected of applications will open in Sept/October 2022.

Questions? Please reach out to