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Shanahan Foundation Fellowship

The Shanahan Foundation Fellowship at the Interface of Data and Neuroscience

Neuroscience has a treasure trove of data waiting to be explored.

The Allen Institute is a leader in collecting large-scale, standardized datasets on the brain, working since 2003 to refine the data collection techniques needed to understand biology’s most complex system. Our data banks are ready and waiting. The next stage of discovery depends on experts from diverse technical backgrounds coming together to uncover new insights.

The Shanahan Foundation Fellowship at the Interface of Data and Neuroscience was created to provide freedom and flexibility to promising young scientists from diverse fields, as they work alongside neuroscientists at the Allen Institute and University of Washington. The three-year fellowship provides Ph.D.s from data science, computer science, physics, mathematics, and many other fields the mentorship and support to pursue their own research interests with our data.

Applications for the Fall 2025 cohort are closed.

Shanahan Fellows group photo 2022
Group photo of Shanahan Fellows in at the 2022 Summer Workshop on the Dynamic Brain at Friday Harbor Labs on San Juan Island.

“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

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"An exciting opportunity to make fundamental discoveries."

The Shanahan Foundation Fellowship at the Interface of Data and Neuroscience, funded, in part, by the Shanahan Family Foundation, was created to bring diverse, non-neuroscience perspectives to the neuroscience field. This is a collaborative program between the Allen Institute and the University of Washington. Fellows will work with mentors to develop novel research programs using the Allen Institute’s large data banks to push the boundaries of both data and neuroscience.

Shanahan Fellowship Alumni

Overview

  • 3-year program for recent Ph.D.s to explore complex data in neuroscience at the Allen Institute and University of Washington
  • Neuroscience experience not needed—we’re seeking applicants with expertise in computer science, data science, engineering, mathematics, physics, and many other fields
  • Designed to provide increased freedom to explore a new research area and data of interest, through the Allen Institute’s vast data banks. Includes a discretionary fund for each fellow
  • Participation in the 2-week Summer Workshop on the Dynamic Brain course in the San Juan Islands
  • Mentorship from leading Allen Institute and UW investigators. Fellows are hired as an Allen Institute employee with a starting salary of $104,000 annually, immigration support and benefits package

Shanahan Fellowship Details

You do not need experience in neuroscience to apply. Applicants must be scientists with a Ph.D. (or equivalent) or who will have completed their Ph.D. by the start of the fellowship. The Ph.D. should have been awarded in the last 3 years. The fellowship is appropriate for Ph.D.s in a quantitative field such as computer science, electrical engineering, physics, mathematics, or biology. They should have a strong background in statistical, computational, machine learning, or other data science methods. Up to three fellows will be selected each year. International applicants are eligible to apply and we provide immigration support.

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Applications must include:

  • A curriculum vitae (CV) from the applicant
  • Two (2) Letters of support from your mentor and other professors and scientists you have worked with
  • 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.

Direct questions to shanahan.fellow@alleninstitute.org.

Shanahan Fellowship Publications

Nature Neuroscience

Integrated multimodal cell atlas of Alzheimer’s disease

Oct 14, 2024

Mariano I. Gabitto, Kyle J. Travaglini, Victoria M. Rachleff, Eitan S. Kaplan, Brian Long, Jeanelle Ariza, Yi Ding, Joseph T. Mahoney, Nick Dee, Jeff Goldy, Erica J. Melief, Anamika Agrawal, Omar Kana, Xingjian Zhen, Samuel T. Barlow, Krissy Brouner, Jazmin Campos, John Campos, Ambrose J. Carr, Tamara Casper, Rushil Chakrabarty, Michael Clark, Jonah Cool, Rachel Dalley, Martin Darvas, Song-Lin Ding, Tim Dolbeare, Tom Egdorf, Luke Esposito, Rebecca Ferrer, Lynn E. Fleckenstein, Rohan Gala, Amanda Gary, Emily Gelfand, Jessica Gloe, Nathan Guilford, Junitta Guzman, Daniel Hirschstein, Windy Ho, Madison Hupp, Tim Jarsky, Nelson Johansen, Brian E. Kalmbach, Lisa M. Keene, Sarah Khawand, Mitchell D. Kilgore, Amanda Kirkland, Michael Kunst, Brian R. Lee, Mckaila Leytze, Christine L. Mac Donald, Jocelin Malone, Zoe Maltzer, Naomi Martin, Rachel McCue, Delissa McMillen, Gonzalo Mena, Emma Meyerdierks, Kelly P. Meyers, Tyler Mollenkopf, Mark Montine, Amber L. Nolan, Julie K. Nyhus, Paul A. Olsen, Maiya Pacleb, Chelsea M. Pagan, Nicholas Peña, Trangthanh Pham, Christina Alice Pom, Nadia Postupna, Christine Rimorin, Augustin Ruiz, Giuseppe A. Saldi, Aimee M. Schantz, Nadiya V. Shapovalova, Staci A. Sorensen, Brian Staats, Matt Sullivan, Susan M. Sunkin, Carol Thompson, Michael Tieu, Jonathan T. Ting, Amy Torkelson, Tracy Tran, Nasmil J. Valera Cuevas, Sarah Walling-Bell, Ming-Qiang Wang, Jack Waters, Angela M. Wilson, Ming Xiao, David Haynor, Nicole M. Gatto, Suman Jayadev, Shoaib Mufti, Lydia Ng, Shubhabrata Mukherjee, Paul K. Crane, Caitlin S. Latimer, Boaz P. Levi, Kimberly A. Smith, Jennie L. Close, Jeremy A. Miller, Rebecca D. Hodge, Eric B. Larson, Thomas J. Grabowski, Michael Hawrylycz, C. Dirk Keene, Ed S. Lein

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bioRxiv

Functional connectomics reveals general wiring rule in mouse visual cortex

Oct 14, 2024

Zhuokun Ding, Paul G. Fahey, Stelios Papadopoulos, Eric Y. Wang, Brendan Celii, Christos Papadopoulos, Andersen Chang, Alexander B. Kunin, Dat Tran, Jiakun Fu, Zhiwei Ding, Saumil Patel, Lydia Ntanavara, Rachel Froebe, Kayla Ponder, Taliah Muhammad, J. Alexander Bae, Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Manuel A. Castro, Erick Cobos, Sven Dorkenwald, Leila Elabbady, Akhilesh Halageri, Zhen Jia, Chris Jordan, Dan Kapner, Nico Kemnitz, Sam Kinn, Kisuk Lee, Kai Li, Ran Lu, Thomas Macrina, Gayathri Mahalingam, Eric Mitchell, Shanka Subhra Mondal, Shang Mu, Barak Nehoran, Sergiy Popovych, Casey M. Schneider-Mizell, William Silversmith, Marc Takeno, Russel Torres, Nicholas L. Turner, William Wong, Jingpeng Wu, Wenjing Yin, Szi-chieh Yu, Dimitri Yatsenko, Emmanouil Froudarakis, Fabian Sinz, Krešimir Josić, Robert Rosenbaum, H. Sebastian Seung, Forrest Collman, Nuno Maçarico da Costa, R. Clay Reid, Edgar Y. Walker, Xaq Pitkow, Jacob Reimer, Andreas S. Tolias

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Nature

Neuronal wiring diagram of an adult brain

Oct 01, 2024

Sven Dorkenwald, Arie Matsliah, Amy R. Sterling, Philipp Schlegel, Szi-Chieh Yu, Claire E. McKellar, Albert Lin, Marta Costa, Katharina Eichler, Yijie Yin, Will Silversmith, Casey Schneider-Mizell, Chris S. Jordan, Derrick Brittain, Akhilesh Halageri, Kai Kuehner, Oluwaseun Ogedengbe, Ryan Morey, Jay Gager, Krzysztof Kruk, Eric Perlman, Runzhe Yang, David Deutsch, Doug Bland, Marissa Sorek, Ran Lu, Thomas Macrina, Kisuk Lee, J. Alexander Bae, Shang Mu, Barak Nehoran, Eric Mitchell, Sergiy Popovych, Jingpeng Wu, Zhen Jia, Manuel A. Castro, Nico Kemnitz, Dodam Ih, Alexander Shakeel Bates, Nils Eckstein, Jan Funke, Forrest Collman, Davi D. Bock, Gregory S. X. E. Jefferis, H. Sebastian Seung, Mala Murthy, FlyWire Consortium

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Nature

A Drosophila computational brain model reveals sensorimotor processing

Oct 01, 2024

Philip K. Shiu, Gabriella R. Sterne, Nico Spiller, Romain Franconville, Andrea Sandoval, Joie Zhou, Neha Simha, Chan Hyuk Kang, Seongbong Yu, Jinseop S. Kim, Sven Dorkenwald, Arie Matsliah, Philipp Schlegel, Szi-chieh Yu, Claire E. McKellar, Amy Sterling, Marta Costa, Katharina Eichler, Alexander Shakeel Bates, Nils Eckstein, Jan Funke, Gregory S. X. E. Jefferis, Mala Murthy, Salil S. Bidaye, Stefanie Hampel, Andrew M. Seeds, Kristin Scott

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Nature

Network statistics of the whole-brain connectome of Drosophila

Oct 01, 2024

Albert Lin, Runzhe Yang, Sven Dorkenwald, Arie Matsliah, Amy R. Sterling, Philipp Schlegel, Szi-chieh Yu, Claire E. McKellar, Marta Costa, Katharina Eichler, Alexander Shakeel Bates, Nils Eckstein, Jan Funke, Gregory S. X. E. Jefferis, Mala Murthy

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Nature

The fly connectome reveals a path to the effectome

Oct 01, 2024

Dean A. Pospisil, Max J. Aragon, Sven Dorkenwald, Arie Matsliah, Amy R. Sterling, Philipp Schlegel, Szi-chieh Yu, Claire E. McKellar, Marta Costa, Katharina Eichler, Gregory S. X. E. Jefferis, Mala Murthy, Jonathan W. Pillow

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Nature

Whole-brain annotation and multi-connectome cell typing of Drosophila

Oct 01, 2024

Philipp Schlegel, Yijie Yin, Alexander S. Bates, Sven Dorkenwald, Katharina Eichler, Paul Brooks, Daniel S. Han, Marina Gkantia, Marcia dos Santos, Eva J. Munnelly, Griffin Badalamente, Laia Serratosa Capdevila, Varun A. Sane, Alexandra M. C. Fragniere, Ladann Kiassat, Markus W. Pleijzier, Tomke Stürner, Imaan F. M. Tamimi, Christopher R. Dunne, Irene Salgarella, Alexandre Javier, Siqi Fang, Eric Perlman, Tom Kazimiers, Sridhar R. Jagannathan, Arie Matsliah, Amy R. Sterling, Szi-chieh Yu, Claire E. McKellar, Marta Costa, H. Sebastian Seung, Mala Murthy, Volker Hartenstein, Davi D. Bock, Gregory S. X. E. Jefferis

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bioRxiv

B-BIND: Biophysical Bayesian Inference for Neurodegenerative Dynamics

Jul 31, 2024

Anamika Agrawal, Victoria Mallett Rachleff, Kyle J Travaglini, Shubhabrata Mukherjee, Paul K. Crane, Michael Hawrylycz, C. Dirk Keene, Ed Lein, Gonzalo E. Mena, Mariano I. Gabitto

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Nature

Connectomic reconstruction of a female Drosophila ventral nerve cord

Jul 01, 2024

Anthony Azevedo, Ellen Lesser, Jasper S. Phelps, Brandon Mark, Leila Elabbady, Sumiya Kuroda, Anne Sustar, Anthony Moussa, Avinash Khandelwal, Chris J. Dallmann, Sweta Agrawal, Su-Yee J. Lee, Brandon Pratt, Andrew Cook, Kyobi Skutt-Kakaria, Stephan Gerhard, Ran Lu, Nico Kemnitz, Kisuk Lee, Akhilesh Halageri, Manuel Castro, Dodam Ih, Jay Gager, Marwan Tammam, Sven Dorkenwald, Forrest Collman, Casey Schneider-Mizell, Derrick Brittain, Chris S. Jordan, Michael Dickinson, Alexandra Pacureanu, H. Sebastian Seung, Thomas Macrina, Wei-Chung Allen Lee, John C. Tuthill

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Nonlinear Dynamics

Beyond expectations: residual dynamic mode decomposition and variance for stochastic dynamical systems

Feb 01, 2024

Matthew J. Colbrook, Qin Li, Ryan V. Raut, Alex Townsend

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bioRxiv

Hierarchical Bayesian inference to model continuous phenotypical progression in Alzheimer’s Disease

Jan 01, 2024

Anamika Agrawal, Victoria Mallett Rachleff, Kyle J. Travaglini, Shubhabrata Mukherjee, Paul Crane, Michael Hawrylycz, C. Dirk Keene, Ed Lein, Gonzalo E. Mena, Mariano I. Gabitto

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IEEE Journal on Selected Areas in Information Theory

Information-Theoretic Tools to Understand Distributed Source Coding in Neuroscience

Jan 01, 2024

Ariel K. Feldman, Praveen Venkatesh, Douglas J. Weber, Pulkit Grover

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bioRxiv: The Preprint Server for Biology

Arousal as a universal embedding for spatiotemporal brain dynamics

Dec 21, 2023

Ryan V. Raut, Zachary P. Rosenthal, Xiaodan Wang, Hanyang Miao, Zhanqi Zhang, Jin-Moo Lee, Marcus E. Raichle, Adam Q. Bauer, Steven L. Brunton, Bingni W. Brunton, J. Nathan Kutz

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Neurology

Temporal dynamics of triphasic waves and generalized periodic discharges (P10-1.012)

Apr 25, 2023

George Plummer, Ryan Raut, Bingni Brunton, Shahin Hakimian

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