Alexandra Badea

Associate Professor in Radiology

I have a joint appointment in Radiology and Neurology and my research focuses on neurological conditions like Alzheimer’s disease. I work on imaging and analysis to provide a comprehensive characterization of the brain. MRI is particularly suitable for brain imaging, and diffusion tensor imaging is an important tool for studying brain microstructure, and the connectivity amongst gray matter regions.  

I am interested in image segmentation, morphometry and shape analysis, as well as in integrating information from MRI with genetics, and behavior. Our approaches  target: 1) phenotyping the neuroanatomy using imaging; 2) uncovering the link between structural and functional changes, the genetic bases, and environmental factors. I am interested in generating methods and tools for comprehensive phenotyping.

We use high-performance cluster computing to accelerate our image analysis. We use compressed sensing image reconstruction, and process large image arrays using deformable registration, perform segmentation based on multiple image contrasts including diffusion tensor imaging, as well as voxel, and graph analysis for connectomics.

At BIAC  my efforts focus on developing multivariate biomarkers and identifying vulnerable networks based on genetic risk for Alzheimer's disease.

My enthusiasm comes from the possibility to extend from single to integrative multivariate and network based analyses to obtain a comprehensive picture of normal development and aging, stages of disease, and the effects of treatments.  I am working on multivariate image analysis and predictive modeling approaches to help better understand early biomarkers for human disease indirectly through mouse models, as well as directly in human studies. 

I am dedicated to supporting an increase in female presence in STEM fields, and love working with students. The Bass Connections teams involve undergraduate students in research, providing them the opportunity to do independent research studies and get involved with the community. These students have for example takes classes such as:

BME 394: Projects in Biomedical Engineering (GE)
BME 493: Projects in Biomedical Engineering (GE)
ECE 899: Special Readings in Electrical Engineering
NEUROSCI 493: Research Independent Study 1

Appointments and Affiliations

  • Associate Professor in Radiology
  • Associate Professor in the Department of Neurology
  • Assistant Professor of Biomedical Engineering
  • Member of the Center for Brain Imaging and Analysis

Contact Information

Education

  • Ph.D. University of Patras (Greece), 2003

Research Interests

Alzheimer's Disease, Brain Imaging, MRI, Connectivity, Multivariate Biomarkers, Image Analysis, Neurological Conditions. 

Courses Taught

  • BME 394: Projects in Biomedical Engineering (GE)
  • BME 493: Projects in Biomedical Engineering (GE)
  • BME 494: Projects in Biomedical Engineering (GE)
  • BRAINSOC 395-1: Bass Connections in Brain and Society: Interdisciplinary Team Projects
  • BRAINSOC 395: Bass Connections in Brain and Society: Interdisciplinary Team Projects
  • BRAINSOC 395T: Bass Connections in Brain & Society Research Team
  • BRAINSOC 396-1: Bass Connections in Brain and Society 2: Interdisciplinary Team Projects
  • BRAINSOC 396: Bass Connections in Brain and Society 2: Interdisciplinary Team Projects
  • BRAINSOC 396T: Bass Connections in Brain & Society Research Team
  • BRAINSOC 397-1: Bass Connections in Brain and Society 3: Interdisciplinary Team Projects
  • BRAINSOC 397: Bass Connections in Brain and Society 3: Interdisciplinary Team Projects
  • BRAINSOC 397T: Bass Connections in Brain & Society Research Team
  • BRAINSOC 398-1: Bass Connections in Brain and Society 4: Interdisciplinary Team Projects
  • BRAINSOC 398: Bass Connections in Brain and Society 4: Interdisciplinary Team Projects
  • BRAINSOC 398T: Bass Connections in Brain & Society Research Team
  • BRAINSOC 795T: Bass Connections in Brain & Society Research Team
  • BRAINSOC 796T: Bass Connections in Brain & Society Research Team
  • ECE 899: Special Readings in Electrical Engineering
  • EGR 393: Research Projects in Engineering
  • MEDPHY 791: Independent Study in Medical Physics
  • NEUROSCI 493: Research Independent Study 1
  • NEUROSCI 494: Research Independent Study 2

In the News

Representative Publications

  • Wu, Teresa, Min Hyeok Bae, Min Zhang, Rong Pan, and Alexandra Badea. “A prior feature SVM-MRF based method for mouse brain segmentation.” Neuroimage 59, no. 3 (February 1, 2012): 2298–2306. https://doi.org/10.1016/j.neuroimage.2011.09.053.
  • Poot, Martin, Alexandra Badea, Robert W. Williams, and Martien J. Kas. “Identifying human disease genes through cross-species gene mapping of evolutionary conserved processes.” Plos One 6, no. 5 (May 4, 2011): e18612. https://doi.org/10.1371/journal.pone.0018612.
  • Bowden, Douglas M., G Allan Johnson, Laszlo Zaborsky, William D. K. Green, Eider Moore, Alexandra Badea, Mark F. Dubach, and Fred L. Bookstein. “A symmetrical Waxholm canonical mouse brain for NeuroMaps.” J Neurosci Methods 195, no. 2 (February 15, 2011): 170–75. https://doi.org/10.1016/j.jneumeth.2010.11.028.
  • Johnson, G Allan, Alexandra Badea, and Yi Jiang. “Quantitative neuromorphometry using magnetic resonance histology.” Toxicol Pathol 39, no. 1 (January 2011): 85–91. https://doi.org/10.1177/0192623310389622.
  • Johnson, G Allan, Alexandra Badea, Jeffrey Brandenburg, Gary Cofer, Boma Fubara, Song Liu, and Jonathan Nissanov. “Waxholm space: an image-based reference for coordinating mouse brain research.” Neuroimage 53, no. 2 (November 1, 2010): 365–72. https://doi.org/10.1016/j.neuroimage.2010.06.067.
  • Badea, Alexandra, G Allan Johnson, and Joanna L. Jankowsky. “Remote sites of structural atrophy predict later amyloid formation in a mouse model of Alzheimer's disease.” Neuroimage 50, no. 2 (April 1, 2010): 416–27. https://doi.org/10.1016/j.neuroimage.2009.12.070.
  • Badea, Alexandra, G Allan Johnson, and Robert W. Williams. “Genetic dissection of the mouse CNS using magnetic resonance microscopy.” Curr Opin Neurol 22, no. 4 (August 2009): 379–86. https://doi.org/10.1097/WCO.0b013e32832d9b86.
  • Bae, Min Hyeok, Rong Pan, Teresa Wu, and Alexandra Badea. “Automated segmentation of mouse brain images using extended MRF.” Neuroimage 46, no. 3 (July 1, 2009): 717–25. https://doi.org/10.1016/j.neuroimage.2009.02.012.
  • Badea, A., G. A. Johnson, and R. W. Williams. “Genetic dissection of the mouse brain using high-field magnetic resonance microscopy.” Neuroimage 45, no. 4 (May 1, 2009): 1067–79. https://doi.org/10.1016/j.neuroimage.2009.01.021.
  • Sharief, Anjum A., Alexandra Badea, Anders M. Dale, and G Allan Johnson. “Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy.” Neuroimage 39, no. 1 (January 1, 2008): 136–45. https://doi.org/10.1016/j.neuroimage.2007.08.028.
  • Driehuys, Bastiaan, John Nouls, Alexandra Badea, Elizabeth Bucholz, Ketan Ghaghada, Alexandra Petiet, and Laurence W. Hedlund. “Small animal imaging with magnetic resonance microscopy.” Ilar J 49, no. 1 (2008): 35–53. https://doi.org/10.1093/ilar.49.1.35.
  • Badea, A., A. A. Ali-Sharief, and G. A. Johnson. “Morphometric analysis of the C57BL/6J mouse brain.” Neuroimage 37, no. 3 (September 1, 2007): 683–93. https://doi.org/10.1016/j.neuroimage.2007.05.046.
  • Johnson, G Allan, Anjum Ali-Sharief, Alexandra Badea, Jeffrey Brandenburg, Gary Cofer, Boma Fubara, Sally Gewalt, Laurence W. Hedlund, and Lucy Upchurch. “High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology.” Neuroimage 37, no. 1 (August 1, 2007): 82–89. https://doi.org/10.1016/j.neuroimage.2007.05.013.
  • Badea, Alexandra, Peter J. Nicholls, G Allan Johnson, and William C. Wetsel. “Neuroanatomical phenotypes in the reeler mouse.” Neuroimage 34, no. 4 (February 15, 2007): 1363–74. https://doi.org/10.1016/j.neuroimage.2006.09.053.
  • Ali, Anjum A., Anders M. Dale, Alexandra Badea, and G Allan Johnson. “Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain.” Neuroimage 27, no. 2 (August 15, 2005): 425–35. https://doi.org/10.1016/j.neuroimage.2005.04.017.
  • Badea, Alexandra, George K. Kostopoulos, and Andreas A. Ioannides. “Surface visualization of electromagnetic brain activity.” J Neurosci Methods 127, no. 2 (August 15, 2003): 137–47. https://doi.org/10.1016/s0165-0270(03)00100-6.