Ryan Raut | Washington University in St. Louis

About

Hello! I am a computational researcher seeking to understand principles of the living, dynamic brain—how activity is continuously generated, orchestrated across space and time, and woven into a broader whole that actively realizes a functioning organism. I look to uncover hidden rules and constraints that shape these internal dynamics, allowing their complexity to be distilled into simpler underlying principles.

In practice, this means extracting structure from complex data—placing my research at the intersection of systems neuroscience, dynamical systems, and machine learning. I pursue this work in collaboration with experimentalists recording brain activity and behavior across scales and species, ultimately building toward holistic accounts of brain function.

** I am in the process of starting up a research group (and real website…stay tuned), and in general am always eager to hear from folks with similar interests. So, do feel free to reach out! **

Bio

I am currently an Instructor at Washington University School of Medicine. Prior to St. Louis, I was a Shanahan Foundation Fellow at the Allen Institute and the University of Washington, Seattle, spending much of my time at the AI Institute in Dynamic Systems. Before that, I completed my PhD in neuroscience with Marcus Raichle at Washington University in St. Louis.

Papers

For the most up-to-date listing, please visit my Google Scholar page.

Raut, R.V., Rosenthal, Z.P., Wang, X., Miao, H., Zhang, Z., Lee, J.M., Raichle, M.E., Bauer, A.Q., Brunton, B.W., Brunton, S.L., Kutz, J.N. Arousal as a universal embedding for spatiotemporal brain dynamics. bioRxiv. [paper][code]
Colbrook, M.J., Li, Q., Raut, R.V., Townsend, A. (2024). Beyond expectations: residual dynamic mode decomposition and variance for stochastic dynamical systems. Nonlinear Dynamics, 112 (3), 2037-2061 [paper]
Jacobs, M., Brunton, B.W., Brunton, S.L., Kutz, J.N., Raut, R.V. (2023). HyperSINDy: deep generative modeling of nonlinear stochastic governing equations. arXiv preprint arXiv:2310.04832. [paper]
Luckett, P.H., Lee, J.J., Park, K.Y., Raut, R.V., Meeker, K.L., Gordon, E.M., Snyder, A.Z., Ances, B.M., Leuthardt, E.C., Shimony, J.S. (2023). Resting state network mapping in individuals using deep learning. Frontiers in Neurology, 13, p.1055437. [paper]
*Carroll, C.M., *Stanley, M., Raut, R.V., Constantino, N.J., Irmen, R.E., Mitra, A., Snipes, J.A., Raichle, M.E., Holtzman, D.M., Gould, R.W., Kishida, K.T., Macauley, S.L. (2022). Acute hyper-and hypoglycemia uncouples the metabolic cooperation between glucose and lactate to disrupt sleep. bioRxiv, pp.2022-09. [paper]
Raut, R.V., Snyder, A.Z., Mitra, A., Yellin, D.M., Fujii, N., Malach, R., Raichle, M.E. (2021). Global waves synchronize the brain’s functional systems with fluctuating arousal. Science Advances, 7 (30), eabf2709. [paper][code]
Rosenthal, Z.P., Raut, R.V., Snyder, A.Z., Culver, J.P., Raichle, M.E., Lee, J. (2021). Peripheral sensory stimulation elicits global slow waves by recruiting somatosensory cortex bilaterally. Proceedings of the National Academy of Sciences, 118 (8), e2021252118. [paper]
Raut, R.V., Snyder, A.Z., Raichle, M.E. (2020). Hierarchical dynamics as a macroscopic organizing principle of the human brain. Proceedings of the National Academy of Sciences, 117 (34), 20890-20897. [paper][code]
Gordon, E.M., Laumann, T.O., Marek, S., Raut, R.V., Gratton, C., Gilmore, A.W., Newbold, D.J., Greene, D.J., Coalson, R.S., Snyder, A.Z., Schlaggar, B.L., Petersen, S.E., Dosenbach, N.U.F., Nelson, S.M. (2020). Default mode network streams for coupling to language and control systems. Proceedings of the National Academy of Sciences, 117 (29), 17308-17319. [paper]
Newbold, D.J., Laumann, T.O., Hoyt, C.R., Hampton, J.M., Montez, D.F., Raut, R.V., Ortega, M., Mitra, A., Nielsen, A.N., Miller, D.B., Adeyemo, B., Nguyen, A.L., Scheidter, K.M., Tanenbaum, A.B., Van, A.N., Marek, S., Schlaggar, B.L., Carter, A.R., Greene, D.J., Gordon, E.M., Raichle, M.E., Petersen, S.E., Snyder, A.Z., Dosenbach, N.U.F. (2020). Plasticity and spontaneous activity pulses in disused human brain circuits. Neuron, 107, 580-589. [paper]
Sylvester, C.M., Yu, Q., Srivastava, A.B., Marek, S., Zheng, A., Alexopoulos, D., Smyser, C.D., Shimony, J.S., Ortega, M., Dierker, D.L., Patel, G.H., Nelson, S.M., Gilmore, A.W., McDermott, K.B., Berg, J.J., Drysdale, A.T., Perino, M., Snyder, A.Z., Raut, R.V., Laumann, T.O., Gordon, E., Barch, D.M., Rogers, C.E., Greene, D.J., Raichle, M.E., Dosenbach, N.U.F. (2020). Individual-specific functional connectivity of the amygdala: A substrate for precision psychiatry. Proceedings of the National Academy of Sciences, 177 (7), 3808-3818. [paper]
Rosenthal, Z.P., Raut, R.V., Yan, P., Koko, D., Kraft, A.W., Czerniewski, L., Acland, B., Mitra, A., Snyder, L.H., Bauer, A.Q., Snyder, A.Z., Culver, J.P., Raichle, M.E., Lee, J. (2020). Local perturbations of cortical excitability propagate differentially through large-scale functional networks. Cerebral Cortex, 30 (5), 3352-3369. [paper]
Seitzman, B.A., Gratton, C., Marek, S., Raut, R.V., Dosenbach, N.U.F., Schlaggar, B.L., Petersen, S.E., Greene, D.J. (2020). A set of functionally-defined brain regions with improved representation of the subcortex and cerebellum. NeuroImage, 206, 116-290. [paper]
Raut, R.V., Mitra, A., Marek, S., Ortega, M., Snyder, A.Z., Tanenbaum, A., Laumann, T.O., Dosenbach, N.U.F., Raichle, M.E. (2020). Organization of propagated intrinsic brain activity in individual humans. Cerebral Cortex, 30 (3), 1716-1734. [paper][code]
Raut, R.V., Mitra, A., Snyder, A.Z., Raichle, M.E. (2019). On time delay estimation and sampling error in resting-state fMRI. NeuroImage, 194, 211-227. [paper][code]
Raichle, M.E., Raut, R.V., Mitra, A. (2019). Brain networks: How many types are there?, in The Neocortex. Singer, W., Sejnowski, T., Rakic, P. eds. Strüngmann Forum Reports (27), Lupp, J.R. series ed. MIT Press, MA, 97-108. [paper]
Marek, S., Siegel, J.S., Gordon, E.M., Raut, R.V., Gratton, C., Newbold, D.J., Ortega, M., Laumann, T.O., Miller, D.B., Zheng, A., Lopez, K.C., Berg., J.J., Coalson, R.S., Nguyen, A.L., Dierker, D., Van., A.N., Hoyt, C.R., McDermott, K.B., Norris, S.A., Shimony, J.S., Snyder, A.Z., Nelson, S.M., Barch, D.M., Schlaggar, B.L., Raichle, M.E., Petersen, S.E., Greene, D.J., Dosenbach, N.U.F. (2018) Spatial and temporal organization of the individual human cerebellum. Neuron, 100 (4), 977-993. [paper]
Nair, V.A., Raut, R.V., Prabhakaran, V. (2017). Investigating the BOLD fMRI response to a verbal fluency task in early stroke before and after hemodynamic scaling. Frontiers in Neurology, 8-23. [paper]
Raut, R.V., Nair, V.A., Sattin, J.A., Prabhakaran, V. (2016). Hypercapnic evaluation of vascular reactivity in healthy aging and acute stroke via functional MRI. NeuroImage: Clinical, 12, 173-179. [paper]
DeYoe, E.A. & Raut, R.V. (2014). Visual mapping using blood oxygen level dependent functional magnetic resonance imaging. Neuroimag Clin N Am, 24, 573-584. [paper]