• S Choi, D Hike, R Pohmann, N Avdievich, K Scheffler, X Yu Alpha-180 spin-echo based line-scanning method for high resolution laminar-specific fMRI bioRxiv, 2023.05. 09.540065
  • Grandjean J, Desrosiers-Gregoire G, Anckaerts C, …, Yu X, …, Hess A. A consensus protocol for functional connectivity analysis in the rat brain. Nat Neurosci. 2023 04; 26(4):673-681. PMID: 36973511.
  • Choi S, Chen Y, Zeng H, Biswal B, Yu X. Identifying the distinct spectral dynamics of laminar-specific interhemispheric connectivity with bilateral line-scanning fMRI. J Cereb Blood Flow Metab. 2023 Jul; 43(7):1115-1129. PMID: 36803280; PMCID: PMC10291453.
  • Castaneda-Vega S, Beer-Hammer S, Leiss V, Napieczynska H, Vuozzo M, Schmid AM, Zeng H, He Y, Kohlhofer U, Gonzalez-Menendez I, Quintanilla-Martinez L, Hempel JM, Gollasch M, Yu X, Pichler BJ, Nürnberg B. Cerebrovascular Gi Proteins Protect Against Brain Hypoperfusion and Collateral Failure in Cerebral Ischemia. Mol Imaging Biol. 2023 04; 25(2):363-374. PMID: 36074223; PMCID: PMC10006265.


  • Zhou, X.A.; Jiang, Y.; Napadow, V.; Yu, X. Challenges and Perspectives of Mapping Locus Coeruleus Activity in the Rodent with High-Resolution fMRI. Brain Sci. 2022, 12, 1085.
  • Zeng H, Jiang Y, Beer-Hammer S, Yu X. Awake Mouse fMRI and Pupillary Recordings in the Ultra-High Magnetic Field. Front Neurosci. 2022; 16:886709. PMID: 35903811.
  • Duy PQ, Weise SC, Marini C, Li XJ, Liang D, Dahl PJ, Ma S, Spajic A, Dong W, Juusola J, Kiziltug E, Kundishora AJ, Koundal S, Pedram MZ, Torres-Fernández LA, Händler K, De Domenico E, Becker M, Ulas T, Juranek SA, Cuevas E, Hao LT, Jux B, Sousa AMM, Liu F, Kim SK, Li M, Yang Y, Takeo Y, Duque A, Nelson-Williams C, Ha Y, Selvaganesan K, Robert SM, Singh AK, Allington G, Furey CG, Timberlake AT, Reeves BC, Smith H, Dunbar A, DeSpenza T, Goto J, Marlier A, Moreno-De-Luca A, Yu X, Butler WE, Carter BS, Lake EMR, Constable RT, Rakic P, Lin H, Deniz E, Benveniste H, Malvankar NS, Estrada-Veras JI, Walsh CA, Alper SL, Schultze JL, Paeschke K, Doetzlhofer A, Wulczyn FG, Jin SC, Lifton RP, Sestan N, Kolanus W, Kahle KT. Impaired neurogenesis alters brain biomechanics in a neuroprogenitor-based genetic subtype of congenital hydrocephalus. Nat Neurosci. 2022 04; 25(4):458-473. PMID: 35379995.
  • Choi S, Zeng H, Chen Y, Sobczak F, Qian C, Yu X. Laminar-Specific Functional Connectivity Mapping with Multi-Slice Line-Scanning fMRI. Cereb Cortex. 2022 Feb 02. PMID: 35107125.
  • Chen Y, Wang Q, Choi S, Zeng H, Takahashi K, Qian C, Yu X. Focal fMRI signal enhancement with implantable inductively coupled detectors. Neuroimage. 2022 02 15; 247:118793. PMID: 34896291.


  • X Chen, Y Jiang, S Choi, R Pohmann, K Scheffler, D Kleinfeld, X Yu,Assessment of single-vessel cerebral blood velocity by phase contrast fMRI, PLoS Biology 19 (9), e3000923
  • Sobczak F, Pais-Roldán P, Takahashi K, Yu X. Decoding the brain state-dependent relationship between pupil dynamics and resting state fMRI signal fluctuation. Elife. 2021 Aug 31; 10. PMID: 34463612.
  • Raimondo L, Knapen T, Oliveira LAF, Yu X, Dumoulin SO, van der Zwaag W, Siero JCW. A line through the brain: implementation of human line-scanning at 7T for ultra-high spatiotemporal resolution fMRI. J Cereb Blood Flow Metab. 2021 Aug 20; 271678X211037266. PMID: 34415208.
  • “Functional magnetic resonance imaging.” Yu, Xin and Pais-Roldán, Patricia. Imaging Modalities for Biological and Preclinical Research: A Compendium, Volume 2: In vivo preclinical imaging, multimodality imaging and outlook; Edited by Andreas Walter, Julia Mannheim and Garmel J Caruana. IOP Publishing. Parts II–IV.
  • A Suite of Neurophotonic Tools to Underpin the Contribution of Internal Brain States in fMRI. Philipp Mächler, Thomas Broggini, Celine Mateo, Martin Thunemann, Natalie Fomin-Thunemann, Patrick R Doran, Ikbal Sencan, Kivilcim Kilic, Michèle Desjardins, Hana Uhlirova, Mohammad A Yaseen, David A Boas, Andreas A Linninger, Massimo Vergassola, Xin Yu, Laura D Lewis, Jonathan R Polimeni, Bruce R Rosen, Sava Sakadžić, Richard B Buxton, Martin Lauritzen, David Kleinfeld, Anna Devor. Current Opinion in Biomedical Engineering. doi: 10.1016/j.cobme.2021.100273
  • Predicting the fmri signal fluctuation with recurrent neural networks trained on vascular network dynamics. Filip Sobczak, Yi He, Terrence J Sejnowski, Xin Yu. Cerebral cortex. doi: 10.1093/cercor/bhaa260


  • Wireless Powered Encoding and Broadcasting of Frequency Modulated Detection Signals. Wei Qian, Xin Yu, Chunqi Qian. IEEE Access. DOI: 10.1109/ACCESS.2020.3035938
  • High spatiotemporal vessel-specific hemodynamic mapping with multi-echo single-vessel fMRI. Yi He, Maosen Wang, Xin Yu. Journal of Cerebral Blood Flow & Metabolism. doi:
  • Real-Time fMRI Brain Mapping in Animals. Sangcheon Choi, Kengo Takahashi, Yuanyuan Jiang, Sascha Köhler, Hang Zeng, Qi Wang, Yan Ma, Xin Yu. Journal of Visualized Experiments. DOI:10.3791/61463
  • Ultra-slow oscillations in fMRI and Resting-State connectivity: neuronal and vascular contributions and technical confounds. Patrick J Drew, Celine Mateo, Kevin L Turner, Xin Yu, David Kleinfeld. Neuron. doi:
  • Mapping the Brain-Wide Network Effects by Optogenetic Activation of the Corpus Callosum. Y Chen, F Sobczak, P Pais Roldán, C Schwarz, AP Koretsky, X Yu. Cereb Cortex. doi:10.1093/cercor/bhaa164
  • Wireless Reconfigurable RF Detector Array for Focal and Multiregional Signal Enhancement. Wei Qian, Xin Yu, Chunqi Qian. Ieee Access. doi: 10.1109/ACCESS.2020.3011905
  • Indexing brain state-dependent pupil dynamics with simultaneous fMRI and optical fiber calcium recording. Patricia Pais-Roldán, Kengo Takahashi, Filip Sobczak, Yi Chen, Xiaoning Zhao, Hang Zeng, Yuanyuan Jiang, Xin Yu. Proceedings of the National Academy of Sciences. doi:
  • Visualizing cortical response to optogenetic stimulation and sensory inputs using multispectral handheld optoacoustic imaging. Saak V Ovsepian, Yuanyuan Jiang, Thomas CP Sardella, Jaber Malekzadeh-Najafabadi, Neal C Burton, Xin Yu, Vasilis Ntziachristos. Photoacoustics. doi:
  • A CMOS NMR needle for probing brain physiology with high spatial and temporal resolution. Jonas Handwerker, Marlon Pérez-Rodas, Michael Beyerlein, Franck Vincent, Armin Beck, Nicolas Freytag, Xin Yu, Rolf Pohmann, Jens Anders, Klaus Scheffler. Nature methods. doi:


  • Mapping optogenetically-driven single-vessel fMRI with concurrent neuronal calcium recordings in the rat hippocampus. Xuming Chen, Filip Sobczak, Yi Chen, Yuanyuan Jiang, Chunqi Qian, Zuneng Lu, Cenk Ayata, Nikos K Logothetis, Xin Yu. Nature communications. doi:
  • MRI-guided robotic arm drives optogenetic fMRI with concurrent Ca 2+ recording. Yi Chen, Patricia Pais-Roldan, Xuming Chen, Michael H Frosz, Xin Yu. Nature communications. doi:
  • Multimodal assessment of recovery from coma in a rat model of diffuse brainstem tegmentum injury. Patricia Pais-Roldán, Brian L Edlow, Yuanyuan Jiang, Johannes Stelzer, Ming Zou, Xin Yu. Neuroimage. doi:


  • Identifying respiration-related aliasing artifacts in the rodent resting-state fMRI. Patricia Pais-Roldán, Bharat Biswal, Klaus Scheffler, Xin Yu. Frontiers in neuroscience. doi:
  • Ultra-slow single-vessel BOLD and CBV-based fMRI spatiotemporal dynamics and their correlation with neuronal intracellular calcium signals. Yi He, Maosen Wang, Xuming Chen, Rolf Pohmann, Jonathan R Polimeni, Klaus Scheffler, Bruce R Rosen, David Kleinfeld, Xin Yu. Neuron. doi:
  • Brain-state dependent astrocytic Ca2+ signals are coupled to both positive and negative BOLD-fMRI signals. Maosen Wang, Yi He, Terrence J Sejnowski, Xin Yu. Proceedings of the National Academy of Sciences. doi:


  • Peripheral sensory deprivation restores critical-period-like plasticity to adult somatosensory thalamocortical inputs. Seungsoo Chung, Ji-Hyun Jeong, Sukjin Ko, Xin Yu, Young-Hwan Kim, John TR Isaac, Alan P Koretsky. Cell reports. doi:
  • When photons meet protons: Optogenetics, Calcium signal detection, and fMRI in small animals. Xin Yu. Small Animal Imaging. doi:


  • High magnetic field induced otolith fusion in the zebrafish larvae. Patricia Pais-Roldán, Ajeet Pratap Singh, Hildegard Schulz, Xin Yu. Scientific reports. doi: 10.1038/srep24151
  • Sensory and optogenetically driven single-vessel fMRI. Xin Yu, Yi He, Maosen Wang, Hellmut Merkle, Stephen J Dodd, Afonso C Silva, Alan P Koretsky. Nature methods. doi:


  • Live nephron imaging by MRI. Chunqi Qian, Xin Yu, Nikorn Pothayee, Stephen Dodd, Nadia Bouraoud, Robert Star, Kevin Bennett, Alan Koretsky. American Journal of Physiology-Renal Physiology. doi:
  • Interhemispheric plasticity protects the deafferented somatosensory cortex from functional takeover after nerve injury. Xin Yu, Alan P Koretsky. Brain connectivity. doi:
  • Deciphering laminar-specific neural inputs with line-scanning fMRI. Xin Yu, Chunqi Qian, Der-yow Chen, Stephen J Dodd, Alan P Koretsky. Nature methods. doi:


  • Wireless amplified nuclear MR detector (WAND) for high-spatial-resolution MR imaging of internal organs: preclinical demonstration in a rodent model. Chunqi Qian, Xin Yu, Der-Yow Chen, Stephen Dodd, Nadia Bouraoud, Nikorn Pothayee, Yun Chen, Scott Beeman, Kevin Bennett, Joseph Murphy-Boesch, Alan Koretsky. Radiology. doi:


  • Thalamocortical inputs show post-critical-period plasticity. Xin Yu, Seungsoo Chung, Der-Yow Chen, Shumin Wang, Stephen J Dodd, Judith R Walters, John TR Isaac, Alan P Koretsky. Neuron. doi:
  • Direct imaging of macrovascular and microvascular contributions to BOLD fMRI in layers IV–V of the rat whisker–barrel cortex. Xin Yu, Daniel Glen, Shumin Wang, Stephen Dodd, Yoshiyuki Hirano, Ziad Saad, Richard Reynolds, Afonso C Silva, Alan P Koretsky. Neuroimage. doi:


  • Morphological and functional midbrain phenotypes in Fibroblast Growth Factor 17 mutant mice detected by Mn-enhanced MRI. Xin Yu, Brian J Nieman, Anamaria Sudarov, Kamila U Szulc, Davood J Abdollahian, Nitin Bhatia, Anil K Lalwani, Alexandra L Joyner, Daniel H Turnbull. Neuroimage. doi:


  • 3D mapping of somatotopic reorganization with small animal functional MRI. Xin Yu, Shumin Wang, Der-Yow Chen, Stephen Dodd, Artem Goloshevsky, Alan P Koretsky. Neuroimage. doi:


  • Statistical mapping of sound-evoked activity in the mouse auditory midbrain using Mn-enhanced MRI. Xin Yu, Jing Zou, James S Babb, Glyn Johnson, Dan H Sanes, Daniel H Turnbull. Neuroimage. doi:


  • Large-scale reorganization of the tonotopic map in mouse auditory midbrain revealed by MRI. Xin Yu, Dan H Sanes, Orlando Aristizabal, Youssef Zaim Wadghiri, Daniel H Turnbull. Proceedings of the National Academy of Sciences. doi:


  • Cellular MRI contrast via coexpression of transferrin receptor and ferritin. Abby E Deans, Youssef Zaim Wadghiri, Lisa M Bernas, Xin Yu, Brian K Rutt, Daniel H Turnbull. Magnetic Resonance in Medicine: An Official Journal of the International Society for Magnetic Resonance in Medicine. doi:


  • In vivo auditory brain mapping in mice with Mn-enhanced MRI. Xin Yu, Youssef Zaim Wadghiri, Dan H Sanes, Daniel H Turnbull. Nature neuroscience. doi:


  • Manganese‐enhanced magnetic resonance imaging (MEMRI) of mouse brain development. Youssef Zaim Wadghiri, Jeffrey A Blind, Xiaohong Duan, Clement Moreno, Xin Yu, Alexandra L Joyner, Daniel H Turnbull. NMR in Biomedicine: An International Journal Devoted to the Development and Application of Magnetic Resonance In Vivo. doi:


  • Morphine and endomorphins differentially regulate μ-opioid receptor mRNA in SHSY-5Y human neuroblastoma cells. Xin Yu, Xin Mao, Allan D Blake, Wen Xin Li, Sulie L Chang. Journal of Pharmacology and Experimental Therapeutics. DOI: