Publications

Full list of publications available on Google Scholar.

• Mitigation of outcome conflation in predicting patient outcomes using electronic health records
  S.M. Reincke, C. Espinosa, P. Chung, T. James, E. Berson, N. Aghaeepour
  Journal of the American Medical Informatics Association, 2025
• Benchmarking of pre-training strategies for electronic health record foundation models
  S. Mataraso, S. D'Souza, D. Seong, E. Berson, C. Espinosa, N. Aghaeepour
  JAMIA Open, 2025
• Deep learning-based cell type profiles reveal signatures of Alzheimer's disease resilience and resistance
  E. Berson, A. Perna, S. Bukhari, Y. Kim, L. Xue, D. Seong, S. Mataraso, M. Ghanem, A.L. Chang, K.S. Montine, et al.
  Brain, 2025
• A machine learning approach to leveraging electronic health records for enhanced omics analysis
  S.J. Mataraso, C.A. Espinosa, D. Seong, S.M. Reincke, E. Berson, J.D. Reiss, Y. Kim, M. Ghanem, C-H. Shu, T. James, et al.
  Nature Machine Intelligence, 2025
• Generating pregnant patient biological profiles by deconvoluting clinical records with electronic health record foundation models
  D. Seong, S. Mataraso, C. Espinosa, E. Berson, S.M. Reincke, L. Xue, C. Kashiwagi, Y. Kim, C-H. Shu, P. Chung, et al.
  Briefings in Bioinformatics, 2024
• Unlocking human immune system complexity through AI
  E. Berson, P. Chung, C. Espinosa, T.J. Montine, N. Aghaeepour
  Nature Methods, 2024
• Mediterranean vs. Western diet effects on the primate cerebral cortical pre-synaptic proteome: Relationships with the transcriptome and multi-system phenotypes
  E. Berson, B.M. Frye, C.R. Gajera, G. Saarunya, A. Perna, T. Phongpreecha, S. Shome, J.D. Negrey, N. Aghaeepour, T.J. Montine, et al.
  Alzheimer's & Dementia, 2025
• Epigenomic profile of GBA1 in Parkinson's disease
  E. Berson, R. Zaghroun, M. Santoro, S. Bukhari, D. Seong, C-H. Shu, A. Perna, T. James, K.S. Montine, G.E. Serrano, et al.
  Parkinsonism & Related Disorders, 2025
• Single-cell peripheral immunoprofiling of lewy body and Parkinson's disease in a multi-site cohort
  T. Phongpreecha, K. Mathi, B. Cholerton, E.J. Fox, N. Sigal, C. Espinosa, M. Reincke, P. Chung, L-J. Hwang, C.R. Gajera, et al.
  Molecular Neurodegeneration, 2024
• Intra- and post-pandemic impact of the COVID-19 outbreak on Stanford Health Care
  T. Phongpreecha, E. Berson, L. Xue, S. Shome, G. Saarunya, J. Fralick, B.G. Ruiz-Tagle, A. Foody, A.L. Chin, M. Lim, et al.
  Academic Pathology, 2024
• Human cerebrospinal fluid single exosomes in Parkinson's and Alzheimer's diseases
  K. Yakabi, E. Berson, K.S. Montine, S.C. Bendall, M.J. MacCoss, K.L. Poston, T.J. Montine
  bioRxiv, 2023
• Deep representation learning identifies associations between physical activity and sleep patterns during pregnancy and prematurity
  N.G. Ravindra, C. Espinosa, E. Berson, T. Phongpreecha, P. Zhao, M. Becker, A.L. Chang, S. Shome, I. Marić, D. De Francesco, et al.
  npj Digital Medicine, 2023
• Whole genome deconvolution unveils Alzheimer's resilient epigenetic signature
  E. Berson, A. Sreenivas, T. Phongpreecha, A. Perna, F.C. Grandi, L. Xue, N.G. Ravindra, N. Payrovnaziri, S. Mataraso, Y. Kim, et al.
  Nature Communications, 2023
• Understanding the molecular basis of resilience to Alzheimer's disease
  K.S. Montine, E. Berson, T. Phongpreecha, Z. Huang, N. Aghaeepour, J.Y. Zou, M.J. MacCoss, T.J. Montine
  Frontiers in Neuroscience, 2023
• Quantitative estimate of cognitive resilience and its medical and genetic associations
  T. Phongpreecha, D. Godrich, E. Berson, C. Espinosa, Y. Kim, B. Cholerton, A.L. Chang, S. Mataraso, S.A. Bukhari, A. Perna, et al.
  Alzheimer's Research & Therapy, 2023
• Cross-species comparative analysis of single presynapses
  E. Berson, C.R. Gajera, T. Phongpreecha, A. Perna, S.A. Bukhari, M. Becker, A.L. Chang, D. De Francesco, C. Espinosa, N.G. Ravindra, et al.
  Scientific Reports, 2023
• Large-scale correlation network construction for unraveling the coordination of complex biological systems
  M. Becker, H. Nassar, C. Espinosa, I.A. Stelzer, D. Feyaerts, E. Berson, N.H. Bidoki, A.L. Chang, G. Saarunya, A. Culos, et al.
  Nature Computational Science, 2023
• Prediction of neuropathologic lesions from clinical data
  T. Phongpreecha, B. Cholerton, S. Bukhari, A.L. Chang, D. De Francesco, M. Thuraiappah, D. Godrich, A. Perna, M.G. Becker, N.G. Ravindra, et al.
  Alzheimer's & Dementia, 2023
• Intuitive facial animation editing based on a generative RNN framework
  E. Berson, C. Soladié, N. Stoiber
  Computer Graphics Forum, 2020
• Real-time cleaning and refinement of facial animation signals
  E. Berson, C. Soladie, N. Stoiber
  Proceedings of the 4th International Conference on Graphics and Signal Processing, 2020
• A robust interactive facial animation editing system
  E. Berson, C. Soladié, V. Barrielle, N. Stoiber
  Proceedings of the 12th ACM SIGGRAPH Conference on Motion, Interaction and Games, 2019
• Collecting, analyzing and predicting socially-driven image interestingness
  E. Berson, N. Duong, C-H. Demarty
  27th European Signal Processing Conference (EUSIPCO), 2019
• Multimodality and deep learning when predicting media interestingness
  E. Berson, C-H. Demarty, N. Duong
  Proc. MediaEval 2017 Workshop, 2017