Alexandra Badea | Scholars@Duke

Alexandra Badea
Associate Professor in Radiology

My interest lies primarily in using MR microscopy to image the rodent brain, including its vasculature, so as to provide comprehensive morphometric phenotyping. I study the morphometry of the rodent brain, its anatomical variability in normal states, and also in human disease models. These studies require several steps: imaging protocols for optimal contrast, brain segmentation, registration, statistical analysis, and atlasing. Ultimately we should be able to quantify changes during normal development, aging, disease progression and to assess treatment effect in a quantitative fashion. By combining imaging data with behavioral and genetic tools we have a truly interdisciplinary approach in our translational studies.

Current Appointments & Affiliations

Associate Professor in Radiology, Radiology, Clinical Science Departments 2018
Assistant Professor of Biomedical Engineering, Biomedical Engineering, Pratt School of Engineering 2017

Contact Information

Box 3302 Duke University Medic, Durham, NC 27710
Center For In Vivo Microscopy, Room 139 Bryan Research Building, Durham, NC 27710
alexandra.badea@duke.edu (919) 684-7654
See my Duke Radiology Page - Click Here
See my Duke University School of Medicine Page - Click Here

Background
Education, Training, & Certifications
- Ph.D., University of Patras (Greece) 2003
Duke Appointment History
- Associate Professor in Radiology, Radiology, Clinical Science Departments 2017 - 2018
- Assistant Professor of Radiology, Radiology, Clinical Science Departments 2011 - 2017
- Medical Instructor in the Department of Radiology, Radiology, Clinical Science Departments 2010
Research
Selected Grants
- The Duke Preclinical Research Resources for Quantitative Imaging Biomarkers awarded by National Institutes of Health 2017 - 2022
- Sex and APOE genotype interact to alter immune regulated metabolism in AD awarded by National Institutes of Health 2017 - 2019
- Training in Medical Imaging awarded by National Institutes of Health 2003 - 2019
- Using MRI To Visualize Regional Therapy Response In Idiopathic Pulmonary Fibrosis awarded by National Institutes of Health 2015 - 2019
- Quantitative MR Microscopy of Phenotypic Biomarkers in Alzheimer's Disease awarded by National Institutes of Health 2013 - 2018
- Immune regulated amino acid pathways in Alzheimer's Disease awarded by National Institutes of Health 2016 - 2018
- Serial Block Face Scanning Electron Microscope awarded by National Institutes of Health 2016 - 2018
Publications & Artistic Works
Selected Publications
- Academic Articles
  - Wang, N, Anderson, RJ, Badea, A, Cofer, G, Dibb, R, Qi, Y, and Johnson, GA. "Whole mouse brain structural connectomics using magnetic resonance histology." Brain Structure & Function 223, no. 9 (December 2018): 4323-4335. Full Text
  - Nouls, JC, Badea, A, Anderson, RBJ, Cofer, GP, and Allan Johnson, G. "Diffusion tensor imaging using multiple coils for mouse brain connectomics." Nmr in Biomedicine 31, no. 6 (June 2018): e3921-null. Full Text
  - Badea, A, Kamnaksh, A, Anderson, RJ, Calabrese, E, Long, JB, and Agoston, DV. "Repeated mild blast exposure in young adult rats results in dynamic and persistent microstructural changes in the brain." Neuroimage. Clinical 18 (January 11, 2018): 60-73. Full Text
  - Graña, GD, Hutson, KA, Badea, A, Pappa, A, Scott, W, and Fitzpatrick, DC. "The organization of frequency and binaural cues in the gerbil inferior colliculus." The Journal of comparative neurology 525, no. 9 (June 2017): 2050-2074. Full Text
  - Anderson, RJ, Cook, JJ, Delpratt, NA, Nouls, JC, Gu, B, McNamara, JO, Avants, BB, Johnson, GA, and Badea, A. "An HPC Pipeline with Validation Framework for Small Animal Multivariate Brain Analysis (SAMBA)." CoRR abs/1709.10483 (2017).
  - Badea, A, Kane, L, Anderson, RJ, Qi, Y, Foster, M, Cofer, GP, Medvitz, N, Buckley, AF, Badea, AK, Wetsel, WC, and Colton, CA. "The fornix provides multiple biomarkers to characterize circuit disruption in a mouse model of Alzheimer's disease." Neuroimage 142 (November 2016): 498-511. Full Text
  - Bhagat, SL, Qiu, S, Caffall, ZF, Wan, Y, Pan, Y, Rodriguiz, RM, Wetsel, WC, Badea, A, Hochgeschwender, U, and Calakos, N. "Mouse model of rare TOR1A variant found in sporadic focal dystonia impairs domains affected in DYT1 dystonia patients and animal models." Neurobiology of disease 93 (September 2016): 137-145. Full Text
  - Wang, X, Bey, AL, Katz, BM, Badea, A, Kim, N, David, LK, Duffney, LJ, Kumar, S, Mague, SD, Hulbert, SW, Dutta, N, Hayrapetyan, V, Yu, C, Gaidis, E, Zhao, S, Ding, J-D, Xu, Q, Chung, L, Rodriguiz, RM, Wang, F, Weinberg, RJ, Wetsel, WC, Dzirasa, K, Yin, H, and Jiang, Y-H. "Altered mGluR5-Homer scaffolds and corticostriatal connectivity in a Shank3 complete knockout model of autism." Nature Communications 7 (May 10, 2016): 11459-null. Full Text Open Access Copy
  - Calabrese, E, Badea, A, Cofer, G, Qi, Y, and Johnson, GA. "A Diffusion MRI Tractography Connectome of the Mouse Brain and Comparison with Neuronal Tracer Data." Cerebral Cortex (New York, N.Y. : 1991) 25, no. 11 (November 2015): 4628-4637. Full Text Open Access Copy
  - Calabrese, E, Badea, A, Coe, CL, Lubach, GR, Shi, Y, Styner, MA, and Johnson, GA. "A diffusion tensor MRI atlas of the postmortem rhesus macaque brain." Neuroimage 117 (August 2015): 408-416. Full Text
  - Borg, JS, Vu, M-A, Badea, C, Badea, A, Johnson, GA, and Dzirasa, K. "Localization of Metal Electrodes in the Intact Rat Brain Using Registration of 3D Microcomputed Tomography Images to a Magnetic Resonance Histology Atlas." Eneuro 2, no. 4 (July 2015). Full Text Open Access Copy
  - Lorenzo, DN, Badea, A, Davis, J, Hostettler, J, He, J, Zhong, G, Zhuang, X, and Bennett, V. "A PIK3C3-ankyrin-B-dynactin pathway promotes axonal growth and multiorganelle transport." The Journal of Cell Biology 207, no. 6 (December 2014): 735-752. Full Text
  - Calabrese, E, Badea, A, Coe, CL, Lubach, GR, Styner, MA, and Johnson, GA. "Investigating the tradeoffs between spatial resolution and diffusion sampling for brain mapping with diffusion tractography: time well spent?." Human brain mapping 35, no. 11 (November 2014): 5667-5685. Full Text
  - Johnson, GA, Calabrese, E, Little, PB, Hedlund, L, Qi, Y, and Badea, A. "Quantitative mapping of trimethyltin injury in the rat brain using magnetic resonance histology." Neurotoxicology 42 (May 2014): 12-23. Full Text Open Access Copy
  - Ashbrook, DG, Delprato, A, Grellmann, C, Klein, M, Wetzel, R, Overall, RW, and Badea, A. "Transcript co-variance with Nestin in two mouse genetic reference populations identifies Lef1 as a novel candidate regulator of neural precursor cell proliferation in the adult hippocampus." Frontiers in Neuroscience 8 (January 2014): 418-null. Full Text
  - Johnson, GA, Badea, A, Calabrese, E, Liu, C, and Xie, L. "Magnetic resonance histology: cool images- but who cares?." TOXICOLOGY LETTERS 221 (August 28, 2013): S50-S50. Full Text Link to Item
  - Clark, D, Badea, A, Johnson, GA, and Badea, CT. "Constructing a 4D murine cardiac micro-CT atlas for automated segmentation and phenotyping applications." Progress in Biomedical Optics and Imaging Proceedings of Spie 8669 (June 3, 2013). Full Text
  - Calabrese, E, Badea, A, Watson, C, and Johnson, GA. "A quantitative magnetic resonance histology atlas of postnatal rat brain development with regional estimates of growth and variability." Neuroimage 71 (May 1, 2013): 196-206. Full Text Link to Item
  - Badea, A, and Johnson, GA. "Magnetic resonance microscopy." Studies in Health Technology and Informatics 185 (January 2013): 153-184. (Review)
  - Badea, A, Gewalt, S, Avants, BB, Cook, JJ, and Johnson, GA. "Quantitative mouse brain phenotyping based on single and multispectral MR protocols." Neuroimage 63, no. 3 (November 15, 2012): 1633-1645. Full Text Link to Item
  - Clark, D, Badea, A, Liu, Y, Johnson, GA, and Badea, CT. "Registration-based segmentation of murine 4D cardiac micro-CT data using symmetric normalization." Physics in Medicine and Biology 57, no. 19 (October 2012): 6125-6145. Full Text
  - Driehuys, B, Nouls, J, Badea, A, Bucholz, E, Ghaghada, K, Petiet, A, and Hedlund, LW. "Small animal imaging with magnetic resonance microscopy." Ilar Journal 53, no. 1 (September 11, 2012): 35-53.
  - Johnson, GA, Calabrese, E, Badea, A, Paxinos, G, and Watson, C. "A multidimensional magnetic resonance histology atlas of the Wistar rat brain." Neuroimage 62, no. 3 (September 2012): 1848-1856. Full Text Link to Item
  - Wu, T, Bae, MH, Zhang, M, Pan, R, and Badea, A. "A prior feature SVM-MRF based method for mouse brain segmentation." Neuroimage 59, no. 3 (February 1, 2012): 2298-2306. Full Text Link to Item
  - Badea, A, and Johnson, GA. "Magnetic resonance microscopy." Analytical Cellular Pathology (Amsterdam) 35, no. 4 (January 2012): 205-227. (Review) Full Text Open Access Copy
  - Poot, M, Badea, A, Williams, RW, and Kas, MJ. "Identifying human disease genes through cross-species gene mapping of evolutionary conserved processes. (Published online)" PLoS One 6, no. 5 (May 4, 2011): e18612-. Full Text Link to Item
  - Bowden, DM, Johnson, GA, Zaborsky, L, Green, WDK, Moore, E, Badea, A, Dubach, MF, and Bookstein, FL. "A symmetrical Waxholm canonical mouse brain for NeuroMaps." J Neurosci Methods 195, no. 2 (February 15, 2011): 170-175. Full Text Link to Item
  - Johnson, GA, Badea, A, and Jiang, Y. "Quantitative neuromorphometry using magnetic resonance histology." Toxicol Pathol 39, no. 1 (January 2011): 85-91. Full Text Link to Item
  - Johnson, GA, Badea, A, Brandenburg, J, Cofer, G, Fubara, B, Liu, S, and Nissanov, J. "Waxholm space: an image-based reference for coordinating mouse brain research." Neuroimage 53, no. 2 (November 1, 2010): 365-372. Full Text Link to Item
  - Badea, A, Johnson, GA, and Jankowsky, JL. "Remote sites of structural atrophy predict later amyloid formation in a mouse model of Alzheimer's disease." Neuroimage 50, no. 2 (April 1, 2010): 416-427. Full Text Link to Item
  - Badea, A, Johnson, GA, and Williams, RW. "Genetic dissection of the mouse CNS using magnetic resonance microscopy." Curr Opin Neurol 22, no. 4 (August 2009): 379-386. (Review) Full Text Link to Item
  - Bae, MH, Pan, R, Wu, T, and Badea, A. "Automated segmentation of mouse brain images using extended MRF." Neuroimage 46, no. 3 (July 1, 2009): 717-725. Full Text Link to Item
  - Badea, A, Johnson, GA, and Williams, RW. "Genetic dissection of the mouse brain using high-field magnetic resonance microscopy." Neuroimage 45, no. 4 (May 1, 2009): 1067-1079. Full Text Link to Item
  - Driehuys, B, Nouls, J, Badea, A, Bucholz, E, Ghaghada, K, Petiet, A, and Hedlund, LW. "Small animal imaging with magnetic resonance microscopy." Ilar Journal 49, no. 1 (January 2008): 35-53. (Review) Full Text
  - Sharief, AA, Badea, A, Dale, AM, and Johnson, GA. "Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy." Neuroimage 39, no. 1 (January 1, 2008): 136-145. Full Text Link to Item
  - Badea, A, Ali-Sharief, AA, and Johnson, GA. "Morphometric analysis of the C57BL/6J mouse brain." Neuroimage 37, no. 3 (September 2007): 683-693. Full Text
  - Johnson, GA, Ali-Sharief, A, Badea, A, Brandenburg, J, Cofer, G, Fubara, B, Gewalt, S, Hedlund, LW, and Upchurch, L. "High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology." Neuroimage 37, no. 1 (August 1, 2007): 82-89. Full Text Link to Item
  - Badea, A, Nicholls, PJ, Johnson, GA, and Wetsel, WC. "Neuroanatomical phenotypes in the reeler mouse." Neuroimage 34, no. 4 (February 2007): 1363-1374. Full Text
  - Ali, AA, Dale, AM, Badea, A, and Johnson, GA. "Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain." Neuroimage 27, no. 2 (August 15, 2005): 425-435. Full Text Link to Item
  - Badea, A, Kostopoulos, GK, and Ioannides, AA. "Surface visualization of electromagnetic brain activity." J Neurosci Methods 127, no. 2 (August 15, 2003): 137-147. Link to Item
- Conference Papers
  - Johnson, GA, Anderson, RJ, Cook, JJ, Long, C, and Badea, A. "Image-processing pipelines: Applications in magnetic resonance histology." January 1, 2016. Full Text
  - Johnson, GA, Badea, A, Calabrese, E, Liu, C, and Xie, L. "Magnetic resonance histology—Applications in toxicology." September 2014. Full Text
  - Bowsher, JE, Yuan, H, Hedlund, LW, Turkington, TG, Akabani, G, Badea, A, Kurylo, WC, Wheeler, CT, Cofer, GP, Dewhirst, MW, and Johnson, GA. "Utilizing MRI information to estimate F18-FDG distributions in rat flank tumors." 2004.

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Education, Training, & Certifications

Duke Appointment History

Selected Grants

Selected Publications

Academic Articles

Conference Papers