List of Peer-Reviewed Papers

Ikeda, S., Kawano, K., Watanabe,  S., Yamashita, O., & Kawahara, Y. (2022). Predicting behavior through dynamic modes in resting-state fMRI data. NeuroImage, Vol.247, p.118801

Takeda, Y., Hiroe, N., & Yamashita, O. (2021). Whole-brain propagating patterns in human resting-state brain activities. NeuroImage, Vol.245, p.118711

Hayashi, R., Yamashita, O., Yamada, T., Kawaguchi, H., & Higo, N. (2021). Diffuse Optical Tomography Using fNIRS Signals Measured from the Skull Surface of the Macaque Monkey. Cerebral Cortex Communications.

Tanaka, S.C., Yamashita, A., Yahata, N.,Yamashita, O., Kawato, M., & Imamizu, H.  A multi-site, multi-disorder resting-state magnetic resonance image database. Scientific Data 8, 227 (2021).

Maikusa, N., Zhu, Y., Uematsu, A., Yamashita, A., Saotome, K., Okada, N., …, Yamashita, O., Tanaka C. S. & Koike, S. (2021). Comparison of traveling‐subject and ComBat harmonization methods for assessing structural brain characteristics. Human Brain Mapping.

Tokuda, T., Yamashita, O., Sakai, Y., & Yoshimoto, J. (2021). Clustering of multiple psychiatric disorders using functional connectivity in the data-driven brain subnetworkFrontiers in Psychiatry, 1428.

Tokuda, T., Yamashita, O., & Yoshimoto, J. (2021). Multiple clustering for identifying subject clusters and brain sub-networks using functional connectivity matrices without vectorization. Neural Networks142, 269-287.

Yamashita, A., Sakai, Y., Yamada, T., Yahata, N., Kunimatsu, A., Okada, N., … Yamashita, O & Imamizu, H. (2021). Common Brain Networks Between Major Depressive-Disorder Diagnosis and Symptoms of Depression That Are Validated for Independent Cohorts. Frontiers in Psychiatry12, 888.

Suzuki, K., & Yamashita, O. (2021). MEG current source reconstruction using a meta-analysis fMRI prior. NeuroImage, 118034.

Koike, S., Tanaka, S. C., Okada, T., Aso, T., Yamashita, A., Yamashita, O., … & Hayashi, T. (2021). Brain/MINDS beyond human brain MRI project: A protocol for multi-level harmonization across brain disorders throughout the lifespan. NeuroImage: Clinical, 102600.

Yamashita, A., Sakai, Y., Yamada, T., Yahata, N., Kunimatsu, A., Okada, N., … Yamashita, O & Imamizu, H. (2020). Generalizable brain network markers of major depressive disorder across multiple imaging sites. PLoS biology18(12), e3000966.

Yanagisawa, T., Fukuma, R., Seymour, B., Tanaka, M., Hosomi, K., Yamashita, O., … & Saitoh, Y. (2020). BCI training to move a virtual hand reduces phantom limb pain: A randomized crossover trial. Neurology95(4), e417-e426.

Shiraishi, Y., Kawahara, Y., Yamashita, O., Fukuma, R., Yamamoto, S., Saitoh, Y., … & Yanagisawa, T. (2020). Neural decoding of electrocorticographic signals using dynamic mode decomposition. Journal of Neural Engineering. 17, 3.

Aihara, T., Shimokawa, T., Ogawa, T., Okada, Y., Ishikawa, A., Inoue, Y.,  Yamashita, O. (2020). Resting-State Functional Connectivity Estimated With Hierarchical Bayesian Diffuse Optical Tomography. Frontiers in neuroscience14, 32.

Sanger, T. D., Yamashita, O., Kawato, M. (2020). Expansion coding and computation in the cerebellum: 50 years after the Marr–Albus codon theory. The Journal of Physiology598(5), 913-928.

Endo, H., Hiroe, N., Yamashita, O. (2020). Evaluation of resting spatio-temporal dynamics of a neural mass model using resting fMRI connectivity and EEG microstates. Frontiers in Computational Neuroscience, 13, 91.

Takeda Y., Itahashi T., Sato M., Yamashita O. (2019), Estimating repetitive spatiotemporal patterns from many subjects’ resting-state fMRIs, NeuroImage,  Vol 2-3,  p. 116182,

Yamashita A, Yahata N, Itahashi T, Lisi G, Yamada T, Ichikawa N, …, Yamashita O., Imamizu H. (2019) Harmonization of resting-state functional MRI data across multiple imaging sites via the separation of site differences into sampling bias and measurement bias. PLoS Biol 17(4): e3000042

Takeda Y., Suzuki K., Kawato M., Yamashita O. (2019), MEG Source Imaging and Group Analysis Using VBMEG, Frontiers in Neuroscience, 13, 241

Shimokawa, T., Ishii, T., Takahashi, Y., Mitani, Y., Mifune, H., Chubashi, S., Satoh, M., Oba, Y., Adachi, K., Sugawara, S., Yamashita, O. (2019), Development of multi-directional functional near-infrared spectroscopy system for human neuroimaging studiesBiomedical Optics Express, Vol. 11, No. 3, pp.1393-1404

Filatova, O., Yang, Y., Dewald, J., Tian, R., Maceira-Elvira, P., Takeda, Y., Kwakkel, G., Yamashita, O., van der Helm FCT (2018), Dynamic information flow based on EEG and diffusion MRI in stroke: a proof-of-principle study, Frontiers in Neural Circuits, Vol.12, Article 79

Sato M, Yamashita O, Sato Ma, Miyawaki Y (2018) Information spreading by a combination of MEG source estimation and multivariate pattern classification. PLoS ONE 13(6): e0198806.

Ogawa T, Aihara T, Shimokawa T, and Yamashita O (2018), “Large-scale brain network associated with creative insight: combined voxel-based morphometry and resting-state functional connectivity analyses”, Scientific Reports, 8:6477

Aihara T, Ogawa T, Shimokawa T, and Yamashita O (2017), “Anodal transcranial direct current stimulation of the right anterior temporal lobe did not significantly affect verbal insight.” PLoS One, 12(9): e0184749

Hirayama J, Hyvärinen A, Kiviniemi V, Kawanabe M, Yamashita O (2016), “Characterizing Variability of Modular Brain Connectivity with Constrained Principal Component Analysis.”  PLoS One, 21;11(12):e0168180

Sato T, Nambu I, Takeda K, Aihara T, Yamashita O, Isogaya Y, Inoue Y, Otaka Y, Wada Y, Kawato M, Sato MA, Osu R. (2016), “Reduction of global interference of scalp-hemodynamics in functional near-infrared spectroscopy using short distance probes.” Neuroimage, 141(1), 120-132

Shimokawa T., Ishii T., Takahashi Y., Sugawara S., Sato M., and Yamashita O. (2016), “Diffuse optical tomography using multi-directional sources and detectors.” Biomedical Optics Express 7, 2623-2640

Yamashita O.,Shimokawa T., Aisu R., Amita T., Inoue Y., Sato M. (2016), “Multi-subject and multi-task experimental validation of the hierarchical Bayesian diffuse optical tomography algorithm.”  NeuroImage135, 287-299

Takeda, Y., Hiroe, N., Yamashita, O., Sato, M., (2016), “Estimating repetitive spatiotemporal patterns from resting-state brain activity data.”  NeuroImage133, 251-265

Hoang H, Yamashita O, Tokuda IT, Sato M, Kawato M and Toyama K (2015), “Segmental Bayesian estimation of gap-junctional and inhibitory conductance of inferior olive neurons from spike trains with complicated dynamics”, Front. Comput. Neurosci9:56.

Fukushima M, Yamashita O, Knosche TR, Sato M (2015), “MEG source reconstruction based on identification of directed source interactions on whole-brain anatomical networks”, NeuroImage, Volume 105, 408-427

Yamashita O, Shimokawa T, Kosaka T, Amita T, Inoue Y, and Sato M (2014), “Hierarchical Bayesian Model for Diffuse Optical Tomography of the Human Brain: Human Experimental Study” (open access, need registration to the journal),Journal of Advanced Computational Intelligence and Intelligent Informatics, Vol.18, No.6 pp. 1026-1033

Shimokawa T, Kosaka T, Yamashita O, Hiroe N, Amita T, Inoue Y, and Sato M (2013), “Extended hierarchical Bayesian diffuse optical tomography for removing sclap artifact”, Biomedical Optics Express Vol.4, 2411-2432

Shimokawa T, Kosaka T, Yamashita O, Hiroe N, Amita T, Inoue Y, and Sato M (2012),
“Hierarchical Bayesian estimation improves depth accuracy and spatial resolution of diffuse optical tomography”, Optics Express, Vol.20, 20427-20446

Yanagisawa T*, Yamashita O*, Hirata M, Kishima H, Saitoh Y, Goto T, Yoshimine T, and Kamitani Y (2012),“Regulation of motor representation by phase–amplitude coupling in the sensorimotor cortex.” Journal of  Neuroscience, vol.32(44):15467-75  (*equal contribution)

Fukushima M, Yamashita O, Kanemura A, Ishii S, Kawato M, and Sato M (2012),”A State-Space Modeling Approach for Localization of Focal Current Sources From MEG”. IEEE Transaction on Biomed. Eng., Vol.59,1561-1571

Bosch J, Riera J, Biscay R, Wong K, Galka G, Yamashita O, Sadatao N, Kawashima R, Aubert E, Rodriguez R, Valdes-Sosa P, Miwakeichi F, Ozaki T (2010), “Spatio-temporal correlations from fMRI time series based on the NN-ARx model”, Journal of Integrative Neuroscience, Vol.9, pp.381-406

Fujiwara Y, Yamashita O, Kawawaki D, Doya K, Kawato M, Toyama K and Sato M (2009), “A hierarchical Bayesian method to resolve an inverse problem of MEG contaminated with eye movement artifacts”. NeuroImage, Vol.45, pp.393-409

Miyawaki Y, Uchida H, Yamashita O, Sato M, Morito Y, Tanabe H, Sadato N, Kamitani Y (2008), “Visual image reconstruction from human brain activity using a combination of multiscale local image decoders”. Neuron, Vol.60(5):915-29.

Yoshioka T, Toyama K, Kawato M, Yamashita O, Nishina S, Yamagishi N, Sato M (2008), “Evaluation of hierarchical Bayesian method through retinotopic brain activities reconstruction from fMRI and MEG signals”. Neuroimage. Vol.42(4):1397-413.

Yamashita O, Sato M, Yoshioka T, Tong F, Kamitani Y (2008). “Sparse estimation automatically selects voxels relevant for the decoding of fMRI activity patterns”. Neuroimage. Vol.42(4):1414-29.

Shibata K, Yamagishi N, Goda N, Yoshioka T, Yamashita O, Sato M and Kawato M (2008), “The Effects of Feature Attention on Prestimulus Cortical Activity in the Human Visual System”, Cerebral Cortex, Vol.18, pp.1664-75

Wong K, Galka A, Yamashita O and Ozaki T (2006), “Modelling non-stationary variance in EEG time series by state space GARCH model”,Computers in Biology and Medicine, Vol. 36, Issue 12, pp.1327-1335

Yamashita O, Sadato N, Okada T and Ozaki T (2005), “Evaluating frequency-wise directed connectivity of BOLD signals applying relative power contribution with the linear multivariate time-series models”, NeuroImage, Vol.25, Issue 2, pp.478-490

Galka A, Yamashita O and Ozaki T (2004), “GARCH modelling of covariance in dynamical estimation of inverse solutions”, Physics Letters A, Vol. 333, Issues 3-4, 6, pp.261-268

Riera J, Bosch J, Yamashita O, Kawashima R, Sadato N, Okada T and Ozaki T (2004), “fMRI activation maps based on the NNARx model”, NeuroImage, Vol. 23, Issue 2, pp.680-697

Galka A, Yamashita O, Ozaki T, Biscay R and Valdes-Sosa P (2004), “A solution to the dynamical inverse problem of EEG generation using spatiotemporal Kalman filtering”, NeuroImage, Vol.23, Issue 2, pp.435-453

Yamashita O, Galka A, Ozaki T, Biscay R and Valdes-Sosa P (2004), “Recursive Penalized Least Squares Solution for Dynamical Inverse Problems of EEG Generation”, Human Brain Mapping, Vol.21, Issue 4, pp.221-235


List of Peer-reviewed Conference papers

Bai, W., Tokuda, T., Yamashita, O., & Yoshimoto, J. (2020, December). Reconstructing Temporal Dynamics of fMRI Time Series via Encoded Contextual Information. In 2020 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (pp. 968-971). IEEE.

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