Journal Publications
- Li Y, Joaquim MR, Pickup S, Song HK, Zhou R, Fan Y. Learning ADC maps from accelerated radial k-space diffusion-weighted MRI in mice using a deep CNN-transformer model. Magn Reson Med. 2024 Jan;91(1):105-117. doi: 10.1002/mrm.29833. Epub 2023 Aug 20. PMID: 37598398; PMCID: PMC10691280.
- Wen J, Nasrallah IM, Abdulkadir A, Satterthwaite TD, Yang Z, Erus G, Robert-Fitzgerald T, Singh A, Sotiras A, Boquet-Pujadas A, Mamourian E, Doshi J, Cui Y, Srinivasan D, Skampardoni I, Chen J, Hwang G, Bergman M, Bao J, Veturi Y, Zhou Z, Yang S, Dazzan P, Kahn RS, Schnack HG, Zanetti MV, Meisenzahl E, Busatto GF, Crespo-Facorro B, Pantelis C, Wood SJ, Zhuo C, Shinohara RT, Gur RC, Gur RE, Koutsouleris N, Wolf DH, Saykin AJ, Ritchie MD, Shen L, Thompson PM, Colliot O, Wittfeld K, Grabe HJ, Tosun D, Bilgel M, An Y, Marcus DS, LaMontagne P, Heckbert SR, Austin TR, Launer LJ, Espeland M, Masters CL, Maruff P, Fripp J, Johnson SC, Morris JC, Albert MS, Bryan RN, Resnick SM, Fan Y, Habes M, Wolk D, Shou H, Davatzikos C. Genomic loci influence patterns of structural covariance in the human brain. Proc Natl Acad Sci U S A. 2023 Dec 26;120(52):e2300842120. doi: 10.1073/pnas.2300842120. Epub 2023 Dec 21. PMID: 38127979; PMCID: PMC10756284.
- Keller AS, Pines AR, Shanmugan S, Sydnor VJ, Cui Z, Bertolero MA, Barzilay R, Alexander-Bloch AF, Byington N, Chen A, Conan GM, Davatzikos C, Feczko E, Hendrickson TJ, Houghton A, Larsen B, Li H, Miranda-Dominguez O, Roalf DR, Perrone A, Shetty A, Shinohara RT, Fan Y, Fair DA, Satterthwaite TD. Personalized functional brain network topography is associated with individual differences in youth cognition. Nat Commun. 2023 Dec 18;14(1):8411. doi: 10.1038/s41467-023-44087-0. PMID: 38110396; PMCID: PMC10728159.
- Dannhauer M, Gomez LJ, Robins PL, Wang D, Hasan NI, Thielscher A, Siebner HR, Fan Y, Deng ZD. Electric field modeling in personalizing TMS interventions. Biol Psychiatry. 2023 Dec 5:S0006-3223(23)01752-3. doi: 10.1016/j.biopsych.2023.11.022. Epub ahead of print. PMID: 38061463.
- Cheng H, Gao L, Jing R, Hou B, Guo X, Yao Y, Feng M, Xing B, Feng F, Fan Y. Reversibility of Impaired Large-Scale Functional Brain Networks in Cushing's Disease after Surgery Treatment: A Longitudinal Study. Neuroendocrinology. 2023 Nov 1. doi: 10.1159/000534789. Epub ahead of print. PMID: 37913760
- Jing R, Lin X, Ding Z, Chang S, Shi L, Liu L, Wang Q, Si J, Yu M, Zhuo C, Shi J, Li P, Fan Y, Lu L. Heterogeneous brain dynamic functional connectivity patterns in first-episode drug-naive patients with major depressive disorder. Hum Brain Mapp. 2023 Jun 1;44(8):3112-3122. doi: 10.1002/hbm.26266. Epub 2023 Mar 15. PMID: 36919400; PMCID: PMC10171501
- Ostrowski DA, Logan JR, Antony M, Broms R, Weiss DA, Van Batavia J, Long CJ, Smith AL, Zderic SA, Edwins RC, Pominville RJ, Hannick JH, Woo LL, Fan Y, Tasian GE, Weaver JK. Automated Society of Fetal Urology (SFU) grading of hydronephrosis on ultrasound imaging using a convolutional neural network. J Pediatr Urol. 2023 Oct;19(5):566.e1-566.e8. doi: 10.1016/j.jpurol.2023.05.014. Epub 2023 May 26. PMID: 37286464.
- Lee SH, Geng H, Arnold J, Caruana R, Fan Y, Rosen MA, Apte AP, Deasy JO, Bradley JD, Xiao Y. Interpretable Machine Learning for Choosing Radiation Dose-volume Constraints on Cardio-pulmonary Substructures Associated with Overall Survival in NRG Oncology RTOG 0617. Int J Radiat Oncol Biol Phys. 2023 Jun 19: S0360-3016(23)00591-6. doi: 10.1016/j.ijrobp.2023.06.009. Epub ahead of print. PMID: 37343707
- Sarthak Pati, Siddhesh P. Thakur, İbrahim Ethem Hamamcı, Ujjwal Baid, Bhakti Baheti, Megh Bhalerao, Orhun Güley, Sofia Mouchtaris, David Lang, Spyridon Thermos, Karol Gotkowski, Camila González, Caleb Grenko, Alexander Getka, Brandon Edwards, Micah Sheller, Junwen Wu, Deepthi Karkada, Ravi Panchumarthy, Vinayak Ahluwalia, Chunrui Zou, Vishnu Bashyam, Yuemeng Li, Babak Haghighi, Rhea Chitalia, Shahira Abousamra, Tahsin M. Kurc, Aimilia Gastounioti, Sezgin Er, Mark Bergman, Joel H. Saltz, Yong Fan, Prashant Shah, Anirban Mukhopadhyay, Sotirios A. Tsaftaris, Bjoern Menze, Christos Davatzikos, Despina Kontos, Alexandros Karargyris, Renato Umeton, Peter Mattson, Spyridon Bakas. GaNDLF: the generally nuanced deep learning framework for scalable end-to-end clinical workflows. Commun Eng 2, 23 (2023).
- Dwyer DB, Chand GB, Pigoni A, Khuntia A, Wen J, Antoniades M, Hwang G, Erus G, Doshi J, Srinivasan D, Varol E, Kahn RS, Schnack HG, Meisenzahl E, Wood SJ, Zhuo C, Sotiras A, Shinohara RT, Shou H, Fan Y, Schaulfelberger M, Rosa P, Lalousis PA, Upthegrove R, Kaczkurkin AN, Moore TM, Nelson B, Gur RE, Gur RC, Ritchie MD, Satterthwaite TD, Murray RM, Di Forti M, Ciufolini S, Zanetti MV, Wolf DH, Pantelis C, Crespo-Facorro B, Busatto GF, Davatzikos C, Koutsouleris N, Dazzan P. Psychosis brain subtypes validated in first-episode cohorts and related to illness remission: results from the PHENOM consortium. Mol Psychiatry. 2023 May;28(5):2008-2017. doi: 10.1038/s41380-023-02069-0. Epub 2023 May 5. PMID: 37147389; PMCID: PMC10575777.
- Hwang G, Wen J, Sotardi S, Brodkin ES, Chand GB, Dwyer DB, Erus G, Doshi J, Singhal P, Srinivasan D, Varol E, Sotiras A, Dazzan P, Kahn RS, Schnack HG, Zanetti MV, Meisenzahl E, Busatto GF, Crespo-Facorro B, Pantelis C, Wood SJ, Zhuo C, Shinohara RT, Shou H, Fan Y, Di Martino A, Koutsouleris N, Gur RE, Gur RC, Satterthwaite TD, Wolf DH, Davatzikos C. Assessment of Neuroanatomical Endophenotypes of Autism Spectrum Disorder and Association With Characteristics of Individuals With Schizophrenia and the General Population. JAMA Psychiatry. 2023 May 1;80(5):498-507. doi: 10.1001/jamapsychiatry.2023.0409. Erratum in: JAMA Psychiatry. 2023 May 17;: PMID: 37017948; PMCID: PMC10157419.
- Shah C, Srinivasan D, Erus G, Kurella Tamura M, Habes M, Detre JA, Haley WE, Lerner AJ, Wright CB, Wright JT Jr, Oparil S, Kritchevsky SB, Punzi HA, Rastogi A, Malhotra R, Still CH, Williamson JD, Bryan RN, Fan Y, Nasrallah IM. Intensive Blood Pressure Management Preserves Functional Connectivity in Patients with Hypertension from the Systolic Blood Pressure Intervention Randomized Trial. AJNR Am J Neuroradiol. 2023 May;44(5):582-588. doi: 10.3174/ajnr.A7852. Epub 2023 Apr 27. PMID: 37105682; PMCID: PMC10171386.
- Li H, Srinivasan D, Zhuo C, Cui Z, Gur RE, Gur RC, Oathes DJ, Davatzikos C, Satterthwaite TD, Fan Y. Computing personalized brain functional networks from fMRI using self-supervised deep learning. Med Image Anal. 2023 Jan 21;85:102756. doi: 10.1016/j.media.2023.102756. Epub ahead of print. PMID: 36706636.
- Weaver JK, Martin-Olenski M, Logan J, Broms R, Antony M, Van Batavia J, Weiss DA, Long CJ, Smith AL, Zderic SA, Huang J, Fan Y, Tasian GE. Deep Learning of Videourodynamics to Classify Bladder Dysfunction Severity in Patients with Spina Bifida. J Urol. 2023 Feb 14:101097JU0000000000003267. doi: 10.1097/JU.0000000000003267. Epub ahead of print. PMID: 36787376.
- Zhou Z, Li H, Srinivasan D, Abdulkadir A, Nasrallah I, Wen J, Doshi J, Erus G, Mamourian E, Bryan NR, Wolk DA, Beason-Held L, Resnick SM, Satterthwaite TD, Davatzikos C, Shou H, Fan Y; ISTAGING Consortium. Multiscale functional connectivity patterns of the aging brain learned from harmonized rsfMRI data of the multi-cohort iSTAGING study. Neuroimage. 2023 Jan 30:119911. doi: 10.1016/j.neuroimage.2023.119911. Epub ahead of print. PMID: 36731813.
- Cynthia H. Y. Fu, Guray Erus, Yong Fan, Mathilde Antoniades, Danilo Arnone, Stephen R. Arnott, Taolin Chen, Ki Sueng Choi, Cherise Chin Fatt, Benicio N. Frey, Vibe G. Frokjaer, Melanie Ganz, Jose Garcia, Beata R. Godlewska, Stefanie Hassel, Keith Ho, Andrew M. McIntosh, Kun Qin, Susan Rotzinger, Matthew D. Sacchet, Jonathan Savitz, Haochang Shou, Ashish Singh, Aleks Stolicyn, Irina Strigo, Stephen C. Strother, Duygu Tosun, Teresa A. Victor, Dongtao Wei, Toby Wise, Rachel D. Woodham, Roland Zahn, Ian M. Anderson, J. F. William Deakin, Boadie W. Dunlop, Rebecca Elliott, Qiyong Gong, Ian H. Gotlib, Catherine J. Harmer, Sidney H. Kennedy, Gitte M. Knudsen, Helen S. Mayberg, Martin P. Paulus, Jiang Qiu, Madhukar H. Trivedi, Heather C. Whalley, Chao-Gan Yan, Allan H. Young, Christos Davatzikos, AI-based dimensional neuroimaging system for characterizing heterogeneity in brain structure and function in major depressive disorder: COORDINATE-MDD consortium design and rationale. BMC Psychiatry 23, 59 (2023). https://doi.org/10.1186/s12888-022-04509-7
- J.K. Weaver, J. Logan, R. Broms, M. Antony, M. Rickard, L. Erdman, R. Edwins, R. Pominville, J. Hannick, L. Woo, B. Viteri, N. D’Souza, S. Viswanath, C. Flask, A. Lorenzo, Y. Fan, G.E. Tasian, Deep Learning of Renal Scans in Children with Antenatal Hydronephrosis, Journal of Pediatric Urology, 2023, https://doi.org/10.1016/j.jpurol.2022.12.017
- Adam Pines, Arielle S. Keller, Bart Larsen, Maxwell Bertolero, Arian Ashourvan, Dani S. Bassett, Matthew Cieslak, Sydney Covitz, Yong Fan, Eric Feczko, Audrey Houghton, Amanda R. Rueter, Manish Saggar, Golia Shafiei, Tinashe M. Tapera, Jacob Vogel, Sarah M. Weinstein, Russell T. Shinohara, Leanne M. Williams, Damien A. Fair, Theodore D. Satterthwaite, Development of top-down cortical propagations in youth, Neuron,
2023, https://doi.org/10.1016/j.neuron.2023.01.014 - Lin X, Jing R, Chang S, Liu L, Wang Q, Zhuo C, Shi J, Fan Y, Lu L, Li P. Understanding the heterogeneity of dynamic functional connectivity patterns in first-episode drug naïve depression using normative models. J Affect Disord. 2023 Apr 14;327:217-225. doi: 10.1016/j.jad.2023.01.109. Epub 2023 Feb 2. PMID: 36736793.
- Sydnor VJ, Larsen B, Seidlitz J, Adebimpe A, Alexander-Bloch AF, Bassett DS, Bertolero MA, Cieslak M, Covitz S, Fan Y, Gur RE, Gur RC, Mackey AP, Moore TM, Roalf DR, Shinohara RT, Satterthwaite TD. Intrinsic activity development unfolds along a sensorimotor-association cortical axis in youth. Nat Neurosci. 2023 Apr;26(4):638-649. doi: 10.1038/s41593-023-01282-y. Epub 2023 Mar 27. PMID: 36973514; PMCID: PMC10406167.
- Li H, De Deng Z, Oathes D, Fan Y. Computation of transcranial magnetic stimulation electric fields using self-supervised deep learning. Neuroimage. 2022 Oct 21:119705. doi: 10.1016/j.neuroimage.2022.119705. Epub ahead of print. PMID: 36280099.
- Shanmugan S, Seidlitz J, Cui Z, Adebimpe A, Bassett DS, Bertolero MA, Davatzikos C, Fair DA, Gur RE, Gur RC, Larsen B, Li H, Pines A, Raznahan A, Roalf DR, Shinohara RT, Vogel J, Wolf DH, Fan Y, Alexander-Bloch A, Satterthwaite TD. Sex differences in the functional topography of association networks in youth. Proc Natl Acad Sci U S A. 2022 Aug 16;119(33):e2110416119. doi: 10.1073/pnas.2110416119. Epub 2022 Aug 8. PMID: 35939696.
- Romanello Joaquim, Miguel, Emma E. Furth, Yong Fan, Hee Kwon Song, Stephen Pickup, Jianbo Cao, Hoon Choi, Mamta Gupta, Quy Cao, Russell Shinohara, Deirdre McMenamin, Cynthia Clendenin, Thomas B. Karasic, Jeffrey Duda, James C. Gee, Peter J. O’Dwyer, Mark A. Rosen, and Rong Zhou. 2022. "DWI Metrics Differentiating Benign Intraductal Papillary Mucinous Neoplasms from Invasive Pancreatic Cancer: A Study in GEM Models" Cancers 14, no. 16: 4017. https://doi.org/10.3390/cancers14164017
- Babajide R, Lembrikova K, Ziemba J, Ding J, Li Y, Fermin AS, Fan Y, Tasian GE. Automated Machine Learning Segmentation and Measurement of Urinary Stones on CT Scan. Urology. 2022 Jul 28:S0090-4295(22)00626-4. Epub ahead of print. PMID: 35908740. doi: https://doi.org/10.1016/j.urology.2022.07.029
- Zaixu Cui, Hongming Li, Cedric H Xia, Bart Larsen, Azeez Adebimpe, Graham L Baum, Matt Cieslak, Raquel E Gur, Ruben C Gur, Tyler M Moore, Desmond J Oathes, Aaron F Alexander-Bloch, Armin Raznahan, David R Roalf, Russell T Shinohara, Daniel H Wolf, Christos Davatzikos, Danielle S Bassett, Damien A Fair, Yong Fan, Theodore D Satterthwaite: Individual Variation in Functional Topography of Association Networks in Youth. Neuron, 106(2):340-353.e8, April 2020
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Yong Fan, Yong Liu, Hong Wu, Yihui Hao, Haihong Liu, Zhening Liu, and Tianzi Jiang: Discriminant analysis of functional connectivity patterns on Grassmann manifold. Neuroimage 56(4): 2058-67, Jun 2011.