Publications

Journal Publications

  • Bashyam VM, Erus G, Doshi J, Habes M, Nasrallah I, Truelove-Hill M, Srinivasan D, Mamourian L, Pomponio R, Fan Y, Launer LJ, Masters CL, Maruff P, Zhuo C, Völzke H, Johnson SC, Fripp J, Koutsouleris N, Satterthwaite TD, Wolf D, Gur RE, Gur RC, Morris J, Albert MS, Grabe HJ, Resnick S, Bryan RN, Wolk DA, Shou H, Davatzikos C. MRI signatures of brain age and disease over the lifespan based on a deep brain network and 14 468 individuals worldwide. Brain. 2020 Jul 1;143(7):2312-2324. doi: 10.1093/brain/awaa160. Erratum in: Brain. 2021 Feb 12;144(1):e12. PMID: 32591831; PMCID: PMC7364766.
  • Beer JC, Tustison NJ, Cook PA, Davatzikos C, Sheline YI, Shinohara RT, Linn KA; Alzheimer’s Disease Neuroimaging Initiative. Longitudinal ComBat: A method for harmonizing longitudinal multi-scanner imaging data. Neuroimage. 2020 Oct 15;220:117129. doi: 10.1016/j.neuroimage.2020.117129. Epub 2020 Jul 5. PMID: 32640273; PMCID: PMC7605103.
  • Srinivasan D, Erus G, Doshi J, Wolk DA, Shou H, Habes M, Davatzikos C; Alzheimer’s Disease Neuroimaging Initiative; BLSA; iSTAGING. A comparison of Freesurfer and multi-atlas MUSE for brain anatomy segmentation: Findings about size and age bias, and inter-scanner stability in multi-site aging studies. Neuroimage. 2020 Dec;223:117248. doi: 10.1016/j.neuroimage.2020.117248. Epub 2020 Aug 27. PMID: 32860881.
  • Peng B, Yao X, Risacher SL, Saykin AJ, Shen L, Ning X; ADNI. Cognitive biomarker prioritization in Alzheimer’s Disease using brain morphometric data. BMC Med Inform Decis Mak. 2020 Dec 2;20(1):319. doi: 10.1186/s12911-020-01339-z. PMID: 33267852; PMCID: PMC7709267.
  • Choi SE, Mukherjee S, Gibbons LE, Sanders RE, Jones RN, Tommet D, Mez J, Trittschuh EH, Saykin A, Lamar M, Rabin L, Foldi NS, Sikkes S, Jutten RJ, Grandoit E, Mac Donald C, Risacher S, Groot C, Ossenkoppele R; Alzheimer’s Disease Neuroimaging Initiative, Crane PK. Development and validation of language and visuospatial composite scores in ADNI. Alzheimers Dement (N Y). 2020 Dec 5;6(1):e12072. doi: 10.1002/trc2.12072. PMID: 33313380; PMCID: PMC7718716.
  • Jo T, Nho K, Risacher SL, Saykin AJ; Alzheimer’s Neuroimaging Initiative. Deep learning detection of informative features in tau PET for Alzheimer’s disease classification. BMC Bioinformatics. 2020 Dec 28;21(Suppl 21):496. doi: 10.1186/s12859-020-03848-0. PMID: 33371874; PMCID: PMC7768646.
  • Kim M, Bao J, Liu K, Park BY, Park H, Baik JY, Shen L. A structural enriched functional network: An application to predict brain cognitive performance. Med Image Anal. 2021 Jul;71:102026. doi: 10.1016/j.media.2021.102026. Epub 2021 Mar 4. PMID: 33848962; PMCID: PMC8184595.
  • Wu J, Dong Q, Gui J, Zhang J, Su Y, Chen K, Thompson PM, Caselli RJ, Reiman EM, Ye J, Wang Y. Predicting Brain Amyloid Using Multivariate Morphometry Statistics, Sparse Coding, and Correntropy: Validation in 1,101 Individuals From the ADNI and OASIS Databases. Front Neurosci. 2021 Aug 6;15:669595. doi: 10.3389/fnins.2021.669595. PMID: 34421510; PMCID: PMC8377280.
  • Bashyam VM, Doshi J, Erus G, Srinivasan D, Abdulkadir A, Singh A, Habes M, Fan Y, Masters CL, Maruff P, Zhuo C, Völzke H, Johnson SC, Fripp J, Koutsouleris N, Satterthwaite TD, Wolf DH, Gur RE, Gur RC, Morris JC, Albert MS, Grabe HJ, Resnick SM, Bryan NR, Wittfeld K, Bülow R, Wolk DA, Shou H, Nasrallah IM, Davatzikos C; iSTAGING and PHENOM consortia. Deep Generative Medical Image Harmonization for Improving Cross-Site Generalization in Deep Learning Predictors. J Magn Reson Imaging. 2021 Sep 25. doi: 10.1002/jmri.27908. Epub ahead of print. PMID: 34564904.
  • Panitch R, Hu J, Chung J, Zhu C, Meng G, Xia W, Bennett DA, Lunetta KL, Ikezu T, Au R, Stein TD, Farrer LA, Jun GR. Integrative brain transcriptome analysis links complement component 4 and HSPA2 to the APOE ε2 protective effect in Alzheimer disease. Mol Psychiatry. 2021 Oct;26(10):6054-6064. doi: 10.1038/s41380-021-01266-z. Epub 2021 Sep 3. PMID: 34480088; PMCID: PMC8758485. 
  • Tosun D, Veitch D, Aisen P, Jack CR, Jagust WJ, Petersen RC, Saykin AJ, Bollinger J, Ovod V, Mawuenyega KG, Bateman RJ, Shaw LM, Trojanowski JQ, Blennow K, Zetterberg H, Weiner MW. Detection of β-amyloid positivity in Alzheimer’s Disease Neuroimaging Initiative participants with demographics, cognition, MRI and plasma biomarkers. Brain Commun. 2021; 3(2):fcab008. PMID: 33842885. PMCID: PMC8023542
  • Rubinski A, Tosun D, Franzmeier N, Neitzel J, Frontzkowski L, Weiner M, Ewers M. Lower cerebral perfusion is associated with tau-PET in the entorhinal cortex across the Alzheimer’s continuum. Neurobiol Aging. 2021 06; 102:111-118. PMID: 33765424. PMCID: PMC8205941 
  • Ashford MT, Veitch DP, Neuhaus J, Nosheny RL, Tosun D, Weiner MW. The search for a convenient procedure to detect one of the earliest signs of Alzheimer’s disease: A systematic review of the prediction of brain amyloid status. Alzheimers Dement. 2021 05; 17(5):866-887. PMID: 33583100 
  • Branislav Kovacech , Stanislav Katina , Reinhold Schmidt , Philip Scheltens , Eva Kontsekova , Stefan Ropele , Lubica Fialova , Milica Kramberger , Natalia Paulenka-Ivanovova , Miroslav Smisek , Jozef Hanes , Eva Stevens , Andrej Kovac , Stanislav Sutovsky , Vojtech Parrak , Peter Koson , Michal Prcina , Jaroslav Galba , Martin Cente , Tomas Hromadka , Peter Filipcik , Juraj Piestansky , Maria Samcova , Carmen Prenn-Gologranc , Roman Sivak , Lutz Frölich , Michal Fresser , Martin Rakusa , John Harrison , Jakub Hort , Professor Markus Otto , Duygu Tosun , Matej Ondrus , Bengt Winblad , Michal Novak , Norbert Zilka. ADAMANT: a placebo-controlled randomised phase 2 study of AADvac1, an active immunotherapy against pathological tau protein in Alzheimer’s disease. Nat Aging 1, 521–534 (2021). 
  • Powell F, Tosun D, Raj A, Alzheimer’s Disease Neuroimaging Initiative. Network-constrained technique to characterize pathology progression rate in Alzheimer’s disease. Brain Commun. 2021; 3(3):fcab144. PMID: 34704025. PMCID: PMC8376686 
  • Veitch DP, Weiner MW, Aisen PS, Beckett LA, DeCarli C, Green RC, Harvey D, Jack CR, Jagust W, Landau SM, Morris JC, Okonkwo O, Perrin RJ, Petersen RC, Rivera-Mindt M, Saykin AJ, Shaw LM, Toga AW, Tosun D, Trojanowski JQ, Alzheimer’s Disease Neuroimaging Initiative. Using the Alzheimer’s Disease Neuroimaging Initiative to improve early detection, diagnosis, and treatment of Alzheimer’s disease. Alzheimers Dement. 2021 Sep 28. PMID: 34581485 
  • Tosun D, Demir Z, Veitch DP, Weintraub D, Aisen P, Jack CR, Jagust WJ, Petersen RC, Saykin AJ, Shaw LM, Trojanowski JQ, Weiner MW, Alzheimer’s Disease Neuroimaging Initiative. Contribution of Alzheimer’s biomarkers and risk factors to cognitive impairment and decline across the Alzheimer’s disease continuum. Alzheimers Dement. 2021 Oct 14. PMID: 34647694. PMCID: PMC9014819 
  • Yang Z, Nasrallah IM, Shou H, Wen J, Doshi J, Habes M, Erus G, Abdulkadir A, Resnick SM, Albert MS, Maruff P, Fripp J, Morris JC, Wolk DA, Davatzikos C; iSTAGING Consortium; Baltimore Longitudinal Study of Aging (BLSA); Alzheimer’s Disease Neuroimaging Initiative (ADNI). A deep learning framework identifies dimensional representations of Alzheimer’s Disease from brain structure. Nat Commun. 2021 Dec 3;12(1):7065. doi: 10.1038/s41467-021-26703-z. PMID: 34862382; PMCID: PMC8642554.
  • Shishegar R, Cox T, Rolls D, Bourgeat P, Doré V, Lamb F, Robertson J, Laws SM, Porter T, Fripp J, Tosun D, Maruff P, Savage G, Rowe CC, Masters CL, Weiner MW, Villemagne VL, Burnham SC. Using imputation to provide harmonized longitudinal measures of cognition across AIBL and ADNI. Sci Rep. 2021 12 10; 11(1):23788. PMID: 34893624. PMCID: PMC8664816
  • Myoraku A, Klein G, Landau S, Tosun D, Alzheimer’s Disease Neuroimaging Initiative. Regional uptakes from early-frame amyloid PET and 18F-FDG PET scans are comparable independent of disease state. Eur J Hybrid Imaging. 2022 Jan 18; 6(1):2. PMID: 35039928. PMCID: PMC8763988 
  • Jun GR, You Y, Zhu C, Meng G, Chung J, Panitch R, Hu J, Xia W; Alzheimer’s Disease Genetics Consortium, Bennett DA, Foroud TM, Wang LS, Haines JL, Mayeux R, Pericak-Vance MA, Schellenberg GD, Au R, Lunetta KL, Ikezu T, Stein TD, Farrer LA. Protein phosphatase 2A and complement component 4 are linked to the protective effect of APOE ɛ2 for Alzheimer’s disease. Alzheimers Dement. 2022 Feb 9:10.1002/alz.12607. doi: 10.1002/alz.12607. Epub ahead of print. PMID: 35142023; PMCID: PMC9360190.
  • Ushizima D, Chen Y, Alegro M, Ovando D, Eser R, Lee W, Poon K, Shankar A, Kantamneni N, Satrawada S, Junior EA, Heinsen H, Tosun D, Grinberg LT. Deep learning for Alzheimer’s disease: Mapping large-scale histological tau protein for neuroimaging biomarker validation. Neuroimage. 2022 03; 248:118790. PMID: 34933123. PMCID: PMC8983026 
  • ​​Bashyam VM, Doshi J, Erus G, Srinivasan D, Abdulkadir A, Singh A, Habes M, Fan Y, Masters CL, Maruff P, Zhuo C, Völzke H, Johnson SC, Fripp J, Koutsouleris N, Satterthwaite TD, Wolf DH, Gur RE, Gur RC, Morris JC, Albert MS, Grabe HJ, Resnick SM, Bryan NR, Wittfeld K, Bülow R, Wolk DA, Shou H, Nasrallah IM, Davatzikos C; iSTAGING and PHENOM consortia. Deep Generative Medical Image Harmonization for Improving Cross-Site Generalization in Deep Learning Predictors. J Magn Reson Imaging. 2022 Mar;55(3):908-916. doi: 10.1002/jmri.27908. Epub 2021 Sep 25. PMID: 34564904; PMCID: PMC8844038.
  • Jo T, Nho K, Bice P, Saykin AJ; Alzheimer’s Disease Neuroimaging Initiative. Deep learning-based identification of genetic variants: application to Alzheimer’s disease classification. Brief Bioinform. 2022 Mar 10;23(2):bbac022. doi: 10.1093/bib/bbac022. PMID: 35183061; PMCID: PMC8921609.
  • Vogel JW, Tosun D. Multiple Cortical to Striatal Accumulation Trajectories of ß-Amyloid: Do All Roads Lead to Rome? Neurology. 2022 Mar 25. PMID: 35338076
  •  Stocks J, Popuri K, Heywood A, Tosun D, Alpert K, Beg MF, Rosen H, Wang L; Alzheimer’s Disease Neuroimaging Initiative. Network-wise concordance of multimodal neuroimaging features across the Alzheimer’s disease continuum. Alzheimers Dement (Amst). 2022 Apr 26;14(1):e12304. doi: 10.1002/dad2.12304. PMID: 35496375; PMCID: PMC9043119.

Conference Papers

SIPAIM 2022

  • Gadewar S, Ramesh A, Liu M, Ba Gari I, Nir TM, Thompson PT, Jahanshad N. Predicting individual brain MRIs at any age using style encoding generative adversarial networks. Accepted to SIPAIM 2022.

MICCAI 2022 + Workshops

  • Haddad E, Javid S, Dhinagar N, Zhu AH, Lam P, Ba Gari I, Gupta A, Thompson PM, Nir TM, Jahanshad, N. Lifestyle factors that promote brain structural resilience in individuals with genetic risk factors for dementia. Presented at MLCN – MICCAI Workshop 2022.

MICCAI 2021

  • ZhangY , Zhan L, Wu S, Thompson PM, Huang H. Disentangled and Proportional Representation Learning for Multi-View Brain Connectomes (2021). Medical Image Computing and Computer Assisted Interventions (MICCAI), pp. 508-518. PMID: 35449787 PMCID: PMC9020272 DOI: 10.1007/978-3-030-87234-2_48
  • Liu M, Maiti P, Thomopoulos SI, Zhu A, Chai Y, Kim H, Jahanshad N (2021). Style Transfer Using Generative Adversarial Networks for Multi-Site MRI Harmonization. MICCAI 2021. Preprint available on bioRxiv 2021.03.17.435892; doi: https://doi.org/10.1101/2021.03.17.435892

ISBI 2021

  • Ficiarà E, Crespi V, Gadewar SP, Thomopoulos SI, Boyd J, Thompson PM, Jahanshad N, Pizzagalli F, and the Alzheimer’s Disease Neuroimaging Initiative (2021). Predicting Progression from Mild Cognitive Impairment to Alzheimer’s Disease using MRI-based Cortical Features and a Two-State Markov Model, ISBI 2021. https://ieeexplore.ieee.org/document/9434143/. 
  • Gupta U, Pradeep K. Lam, Greg Ver Steeg, Paul M. Thompson (2021). Improved Brain Age Estimation With Slice-based Set Networks, ISBI 2021. https://ieeexplore.ieee.org/document/9434081/. 
  • Stripelis D, José Luis Ambite, Pradeep Lam, Paul Thompson (2021). Scaling Neuroscience Research Using Federated Learning, ISBI 2021. https://ieeexplore.ieee.org/document/9433925/. 

MIDL 2021

  • Gupta U, Stripelis D, Lam PK, Thompson PM, Ambite JL, ver Steeg G. Membership Inference Attacks on Deep Regression Models for Neuroimaging, submitted to MIDL 2021. Preprint available at: arXiv. doi: arXiv:2105.02866

SIPAIM 2021

  • Sinha S, Thomopoulos SI, Lam P, Muir A, Thompson PM (2021). Alzheimer’s Disease Classification Accuracy is Improved by MRI Harmonization based on Attention-Guided Generative Adversarial Networks Proceedings Volume 12088, 17th International Symposium on Medical Information Processing and Analysis; https://doi.org/10.1117/12.2606155. 
  • Stripelis D*, Saleem H*, Ghai* T, Dhinagar N* , Gupta U, Anastasiou C, Ver Steeg G, Ravi S, Naveed N, Thompson PM, Ambite JL (2021). Secure Neuroimaging Analysis using Federated Learning with Homomorphic Encryption. Proceedings Volume 12088, 17th International Symposium on Medical Information Processing and Analysis; https://doi.org/10.1117/12.2606256.   
  • Dhinagar NJ, Thomopoulos SI, Owens-Walton C, Stripelis D, Ambite JL, Ver Steeg G, Weintraub D, Cook P, McMillan C, Thompson PM (2021). 3D convolutional neural networks for classification of Alzheimer’s and Parkinson’s disease with T1-weighted brain MRI. Proceedings Volume 12088, 17th International Symposium on Medical Information Processing and Analysis; https://doi.org/10.1117/12.2606297.  
  • Thomopoulos SI, Nir TM, Villalon-Reina JE, Zavaliangos-Petropulu A, Maiti P, Zheng H, Nourollahimoghadam E, Jahanshad N, Thompson PM, for the Alzheimer’s Disease Neuroimaging Initiative (2021). Diffusion MRI Metrics and their Relation to Dementia Severity: Effects of Harmonization Approaches. Proceedings Volume 12088, 17th International Symposium on Medical Information Processing and Analysis; https://doi.org/10.1117/12.2606337. 

BIBM 2021

  • Kim M, Kim J, Qu J, Huang H, Sohn KA, Long Q, Kim D, Shen L. (2021) Interpretable temporal graph neural network for prognostic prediction of Alzheimer’s disease using longitudinal neuroimaging data. BIBM’21: IEEE Int. Conf. on Bioinformatics and Biomedicine, pp. 1381-1384, Virtual Conference, Dec 9-12, 2021. https://ieeexplore.ieee.org/document/9669504

PSB 2022

  • Bao J, Wen Z, Kim M, Zhao X, Lee BN, Jung SH, Davatzikos C, Saykin AJ, Thompson PM, Kim D, Zhao Y, Shen L, for the ADNI. (2022) Identifying highly heritable brain amyloid phenotypes through mining Alzheimer’s imaging and sequencing biobank data. Pac Symp Biocomput. 2022;27:109-20. https://pubmed.ncbi.nlm.nih.gov/34890141/

EMBC 2022

  • Chandio BQ, Chattopadhyay T, Owens-Walton C, Reina JEV, Nabulsi L, Thomopoulos SI, Garyfallidis E, Thompson PM. FiberNeat: Unsupervised White Matter Tract Filtering. 2022 44th Annual International Conference of the IEEE Engineering in Medicine & Biology Society (EMBC), 2022, pp. 5055-5061. doi: 10.1109/EMBC48229.2022.9870877. PMID: 36085780.  https://ieeexplore.ieee.org/document/9870877.

ISBI 2022

  • Chandio BQ, Chattopadhyay T, Owens-Walton C, Villalon Reina JE, Nabulsi L, Thomopoulos SI, Garyfallidis E, Thompson PM (2022). FIBERNEAT: Unsupervised Streamline Clustering and White Matter Tract Filtering in Latent Space. ISBI 2022.
  • Sinha S, Thomopoulos SI, Lam P, Muir A, Thompson PM (2022). Improving Alzheimer’s Disease Classification using Attention-Guided Neural Networks and MRI Domain Adaptation. ISBI 2022.
  • Tang HT, Guo L, Fu XY, Qu B, Thompson PM, Huang H, Zhan L. Hierarchical Brain Embedding Using Explainable Graph Learning. ISBI 2022. https://ieeexplore.ieee.org/document/9761543  

MICCAI 2022