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Joost B.M. Wagenaar, PhD

Assistant Professor of Biostatistics and Epidemiology at the Hospital of the University of Pennsylvania
Assistant Director for Cloud Computing, Institute for Biomedical Informatics, University of Pennsylvania, Philadelphia, PA
Director of the Neuroengineering Data Ecosystem,, Center for Neuroengineering and Therapeutics, University of Pennsylvania, Philadelphia, PA
Department: Biostatistics and Epidemiology

Contact information
University of Pennsylvania
Department of Biostatistics, Epidemiology and Informatics
3700 Hamilton Walk
Philadelphia, PA 19104
BS (Electrical Engineering)
University of Twente, 2002.
MS (Electrical Engineering)
University of Twente, 2005.
Ph.D. (Bioengineering)
University of Pittsburgh, 2011.
Post-Graduate Training
Postdoc, Translational Neuroengineering, University of Pennsylvania, 2011-2012.
University of Pittsburgh/Carnegie Mellon University, Pittsburgh, PA, USA Center for the Neural Basis of Cognition (CNBC) Graduate Training Program, 2011.
Perelman School of Medicine, Philadelphia PA, USA Supervisory Skills certificate, 2013.
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Description of Research Expertise

Dr. Wagenaar’s research focuses on the mechanisms of data integration and sustainable scientific collaboration through technology. The challenges of integrating complex scientific data are accompanied by a need for novel, scalable and sustainable software infrastructure to support these efforts. He has worked on multiple platform technologies to support scientific data management, analysis and peer reviewed scientific data distribution at scale with a focus on the FAIR (Findability, Accessibility, Interoperability, Reusability) principles of data sharing.

His academic efforts include 1) the development of scalable HIPAA compliant platform technologies for scientific data management, 2) the development of methods and tools for streaming and analyzing high-bandwidth, high channel count neuroscience time-series data at scale, 3) methods and tools for integrating scientific data and metadata, and 4) statistical modeling of information from populations of sensory neurons.

Dr. Wagenaar leads the development of the Pennsieve data management platform, which is leveraged as the data core for the NIH SPARC initiative and is used broadly by the neuroscience community. Dr. Wagenaar joined the University of Pennsylvania in 2021. In addition to his appointment within the DBEI, he is affiliated with the Center for Neuroengineering and Therapeutics and the Institute for Biomedical Informatics at Penn.

Selected Publications

Mahyar Osanlouy, Anita Bandrowski, Bernard de Bono, David Brooks, Antonino M. Cassarà, Richard Christie, Nazanin Ebrahimi, Tom Gillespie, Jeffrey S. Grethe, Leonardo A. Guercio, Maci Heal, Mabelle Lin, Niels Kuster, Maryann E. Martone, Esra Neufeld, David P. Nickerson, Elias G. Soltani, Susan Tappan, Joost B. Wagenaar, Katie Zhuang, Peter J. Hunter: The SPARC DRC: Building a Resource for the Autonomic Nervous System Community. Frontiers in Physiology 12(693735), Jun 2021 Notes: DOI=10.3389/fphys.2021.693735 ISSN=1664-042X.

Joost Wagenaar, Esra Neufeld, Peter Hunter, Niels Kuster: The SPARC Data Resource Center: A Systematic Approach to Collaborative, Sustainable, and FAIR Neurosciences Applied to Bioelectronic Medicine. Federation of European Neuroscience Societies (FENS) 2020.

Baldassano, S., Williams Roberson, S., Balu, R., Scheid, B., Bernabei, J., Pathmanathan, J., Oom- men, B., Leri, D., Echauz, J., Gelfand, M., Kadakia Bhalla, P., Hill, C., Christini, A., Wagenaar, J., Litt,B.: IRIS: A Modular Platform for Continuous Monitoring and Caretaker Notification in the Intensive Care Unit. IEEE Journal of Biomedical and Health Informatics 24(8): 2389-2397, Aug 2020.

Ramirez-Zamora, A., Giordano, J. J., Boyden, E. S., Gunduz, A., Starr, P.A., Sheth, S.A., McIntyre, C.C., Fox, M.D. Vitek, J.L., Vedam-Mai, V., Almeida, L., Bronte-Stewart, H.M., Mayberg, H.S., Pouratian, N., Gittis, A., Singer, A.C., Creed, M.C., L ́azaro-Mun ̃oz, G., Richardson, M.R., Rossi, M.A., Cendejas-Zaragoza, L., D’Haese, P., Chiong, W., Gilron, R., Chizeck, H., Ko, A., Baker, K.B., Wagenaar, J., Harel, N., Deeb, W., Foote, K.D., Okun, M. S.: Proceedings of the Sixth Deep Brain Stimulation Think Tank Modulation of Brain Networks and Application of Advanced Neuroimaging, Neurophysiology, and Optogenetics. Frontiers in Neuroscience 13: 936, Sept 2019.

L.A. Guercio, M. Hollenbeck, J.B. Wagenaar: Blackfynn: Rapid multimodal data integration for the neurosciences. Society for Neuroscience 2018.

Ono, T., Wagenaar, J., Giorgi, F.S., Fabera, P., Hanaya, R., Jefferys, J., Moyer, J.T., Harte-Hargrove, L.C., Galanopoulou, A.S.: A companion to the preclinical common data elements and case report forms for rodent EEG studies. A report of the TASK3 EEG Working Group of the ILAE/AES Joint Translational Task Force. Epilepsia Open 3: 90-103, Sep 2018.

Davis, K.A., Devries, S.P., Krieger, A., Mihaylova, T., Minecan, D., Litt, B., Wagenaar, J.B., Stacey, W.C.: The effect of increased intracranial EEG sampling rates in clinical practice. Clinical Neuro- physiology 129(2): 360-367, Nov 2018.

Steven N Baldassano, Benjamin H Brinkmann, Hoameng Ung, Tyler Blevins, Erin C Conrad, Kent Leyde, Mark J Cook, Ankit N Khambhati, Joost B Wagenaar, Gregory A Worrell, Brian Litt: Crowdsourcing seizure detection: algorithm development and validation on human implanted device recordings. Brain 140(6): 1680-1691, Jun 2017.

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Last updated: 03/01/2024
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