Publications

Google Scholar [link]

Code repository [github]

Sanchez-Romero, R., Akyuz, S., & Krekelberg, B. (2025). EFMouse: A toolbox to model stimulation-induced electric fields in the mouse brain. PLOS Computational Biology, 21(9): e1013471 [link] [EFMouse github] 

Peterson, K.L., Sanchez-Romero, R., Mill, R.D., & Cole, M. W. (2025).  Regularized partial correlation provides reliable functional connectivity estimates while correcting for widespread confounding. Imaging Neuroscience [link] [github]  

Cocuzza, C. V., Sanchez-Romero, R., Ito, T., Mill, R. D., Keane, B. P., & Cole, M. W. (2024). Distributed network flows generate localized category selectivity in human visual cortex. PLOS Computational Biology, 20(10), e1012507. [link] [github]

Podvalny, E., Sanchez-Romero, R., & Cole, M. W. (2024). Functionality of arousal-regulating brain circuitry at rest predicts human cognitive abilities. Cerebral Cortex, 34(5), bhae192. [link]

Sanchez-Romero, R., Ito, T., Mill, R. D., Hanson, S. J., & Cole, M. W. (2023). Causally informed activity flow models provide mechanistic insight into network-generated cognitive activations. NeuroImage, 278, 120300. [link] [DirectedActflow github]

Andrews, B., Ramsey, J., Sanchez Romero, R., Camchong, J., & Kummerfeld, E. (2023). Fast scalable and accurate discovery of dags using the best order score search and grow shrink trees. Advances in Neural Information Processing Systems, 36, 63945-63956. [link] [github] 

Hanson, S.J., Sanchez-Romero, R., Valdes-Sosa, P.A., & Biswal, B.B. (Editors). (2023). Research Topics: Brain Connectivity, Dynamics and Complexity. Frontiers in Human Neuroscience and Computational Neuroscience. [link]

Peterson, K. L., Sanchez-Romero, R., Mill, R. D., & Cole, M. W. (2023). Regularized partial correlation provides reliable functional connectivity estimates while correcting for widespread confounding. bioRxiv, 2023-09. [link]

Cole, M. W., Ito, T., Cocuzza, C., & Sanchez-Romero, R. (2021). The functional relevance of task-state functional connectivity. Journal of Neuroscience, 41(12), 2684-2702. [link] [github]

Cocuzza, C. V., Sanchez-Romero, R., & Cole, M. W. (2022). Protocol for activity flow mapping of neurocognitive computations using the Brain Activity Flow Toolbox. STAR Protocols, 3(1), 101094. [link] [Actflow Toolbox github]

Sanchez-Romero, R., & Cole, M. W. (2021). Combining multiple functional connectivity methods to improve causal inferences. Journal of Cognitive Neuroscience, 33(2), 180-194. [link] [CombinedFC github]

Huang, B., Zhang, K., Zhang, J., Ramsey, J., Sanchez-Romero, R., Glymour, C., & Schölkopf, B. (2020). Causal discovery from heterogeneous/nonstationary data. Journal of Machine Learning Research, 21(89), 1-53. [link] [code part of causal-learn github]

Reid, A. T., Headley, D. B., Mill, R. D., Sanchez-Romero, R., Uddin, L. Q., Marinazzo, D., ... & Calhoun, V. (2019). Advancing functional connectivity research from association to causation. Nature neuroscience, 1-10. [link] 

Sanchez-Romero, R., Ramsey, J. D., Zhang, K., Glymour, M. R., Huang, B., & Glymour, C. (2019). Estimating feedforward and feedback effective connections from fMRI time series: Assessments of statistical methods. Network Neuroscience, 3(2), 274-306. [link] [data repository] [Two-Step algorithm github] (*Early versions of this work were presented as posters in the 7th International Workshop on Pattern Recognition in Neuroimaging, Toronto 2017 [poster], and in the Atlantic Causal Inference Conference, Pittsburgh 2018 [poster])

Sanchez-Romero, R., Ramsey, J.D., Zhang, K., & Glymour, C. (2019). Identification of Effective Connectivity Subregions. arXiv. [link]

Huang, B., Zhang, K., Sanchez-Romero, R., Ramsey, J., Glymour, M., & Glymour, C. (2019). Diagnosis of Autism Spectrum Disorder by Causal Influence Strength Learned from Resting- State fMRI Data. arXiv. [link]

Glymour, C., & Sanchez-Romero, R., (2018). Helmholtz’s Vision: Underdetermination, Behavior and the Brain. In M. Sprevak & M. Colombo (Eds.), The Routledge Handbook of the Computational Mind. Routledge. [link]

Ramsey, J., Zhang, K., Glymour, M.R.K., Sanchez-Romero, R., Huang, B., Ebert-Uphoff, I., Samarasinghe S., Barnes, E.A., & Glymour, C., (2018). Tetrad – A Toolbox for Causal Discovery. In Proceedings of the 8th International Workshop on Climate Informatics. [link]

Ramsey, J.D., Glymour, M., Sanchez-Romero, R., & Glymour, C. (2017). A million variables and more: The Fast Equivalence Greedy Search algorithm for learning high dimensional graphical causal models, with an Application to functional magnetic resonance images. International Journal of Data Science and Analytics. [link] (*This paper was presented as a poster in the Conference on Complex Systems, Cancun MX, 2017 [poster])

Huang, B., Zhang, K., Zhang, J., Sanchez-Romero, R., Glymour, C., & Scholkopf, B. (2017, November). Behind Distribution Shift: Mining Driving Forces of Changes and Causal Arrows. In 2017 IEEE International Conference on Data Mining (ICDM) (pp. 913-918). IEEE. [link]

Sanchez-Romero, R., Ramsey, J. D., Liang, J. C., & Glymour, C. (2017). Identification of Mechanisms of Functional Signaling Between Human Hippocampus Regions. bioRxiv. [biorXiv]

Sanchez-Romero, R., Ramsey, J. D., Liang, J. C., Jarbo, K., & Glymour, C. (2016). Estimation of Voxelwise Effective Connectivities: Applications to High Connectivity Sub-Regions within Hippocampal and within Corticostriatal Networks. bioRxiv, 039057. [biorXiv]. (*This paper was presented as a poster in the Society for Neuroscience Meeting, Chicago 2015. [poster])

Glymour, M., Sanchez-Romero, R., Ramsey, J.D., Zhang, K., Huang, B., Glymour C., (2016). Fusiform and Cerebellum rs-fMRI Connectivity Implicated in ASD. Poster presented in the Cognitive Neuroscience Society Meeting, New York, 2016. [poster]

Ramsey, J. D., Sanchez-Romero, R., & Glymour, C. (2014). Non-Gaussian methods and high-pass filters in the estimation of effective connections. NeuroImage, 84, 986-1006. [link] (*This paper was presented as a poster in the Fourth Biennial Conference in Resting State / Brain Connectivity, Boston 2014. [poster])

Sanchez-Romero, R. (2012). Formation of Variables for Brain Connectivity. MS Thesis. Carnegie Mellon University. [pdf]