Shen, C., S. Wang, A. Badea, C. E. Priebe, and J. T. Vogelstein. “Discovering the signal subgraph: An iterative screening approach on graphs.” Pattern Recognition Letters 184 (August 1, 2024): 97–102. https://doi.org/10.1016/j.patrec.2024.06.011.

Stout, Jacques, Robert J. Anderson, Ali Mahzarnia, Zay Han, Kate Beck, Jeffrey Browndyke, Kim Johnson, Richard J. O’Brien, and Alexandra Badea. “Mapping the impact of age and APOE risk factors for late onset Alzheimer's disease on long range brain connections through multiscale bundle analysis.,” June 28, 2024. https://doi.org/10.1101/2024.06.24.599407.

Stout, Jacques A., Ali Mahzarnia, Rui Dai, Robert J. Anderson, Scott Cousins, Jie Zhuang, Eleonora M. Lad, et al. “Accelerated Brain Atrophy, Microstructural Decline and Connectopathy in Age-Related Macular Degeneration.” Biomedicines 12, no. 1 (January 10, 2024). https://doi.org/10.3390/biomedicines12010147.

Mahzarnia, Ali, Michael W. Lutz, and Alexandra Badea. “A Continuous Extension of Gene Set Enrichment Analysis Using the Likelihood Ratio Test Statistics Identifies Vascular Endothelial Growth Factor as a Candidate Pathway for Alzheimer's Disease via ITGA5.” J Alzheimers Dis 97, no. 2 (2024): 635–48. https://doi.org/10.3233/JAD-230934.

Nadkarni, Rohan, Zay Yar Han, Robert J. Anderson, Alex J. Allphin, Darin P. Clark, Alexandra Badea, and Cristian T. Badea. “High-resolution hybrid micro-CT imaging pipeline for mouse brain region segmentation and volumetric morphometry.” PLoS One 19, no. 5 (2024): e0303288. https://doi.org/10.1371/journal.pone.0303288.

Moon, Hae Sol, Ali Mahzarnia, Jacques Stout, Robert J. Anderson, Madison Strain, Jessica T. Tremblay, Zay Yar Han, et al. “Multivariate investigation of aging in mouse models expressing the Alzheimer's protective APOE2 allele: integrating cognitive metrics, brain imaging, and blood transcriptomics.” Brain Struct Funct 229, no. 1 (January 2024): 231–49. https://doi.org/10.1007/s00429-023-02731-x.

Moon, H. S., A. Mahzarnia, J. Stout, R. J. Anderson, Z. Y. Han, C. T. Badea, and A. Badea. “Predicting brain age and associated structural networks in mouse models with humanized APOE alleles using integrative and interpretable graph neural networks.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12927, 2024. https://doi.org/10.1117/12.3005695.

Mahzarnia, Ali, Michael W. Lutz, and Alexandra Badea. “A Continuous Extension of Gene Set Enrichment Analysis using the Likelihood Ratio Test Statistics Identifies VEGF as a Candidate Pathway for Alzheimer's disease.” BioRxiv, August 26, 2023. https://doi.org/10.1101/2023.08.22.554319.

Mahzarnia, Ali, Jacques A. Stout, Robert J. Anderson, Hae Sol Moon, Zay Yar Han, Kate Beck, Jeffrey N. Browndyke, et al. “Identifying vulnerable brain networks associated with Alzheimer's disease risk.” Cereb Cortex 33, no. 9 (April 25, 2023): 5307–22. https://doi.org/10.1093/cercor/bhac419.

Gammon, Seth T., Allison S. Cohen, Adrienne L. Lehnert, Daniel C. Sullivan, Dariya Malyarenko, Henry Charles Manning, David A. Hormuth, et al. “An Online Repository for Pre-Clinical Imaging Protocols (PIPs).” Tomography 9, no. 2 (March 27, 2023): 750–58. https://doi.org/10.3390/tomography9020060.

Allphin, Alex J., Ali Mahzarnia, Darin P. Clark, Yi Qi, Zay Y. Han, Prajwal Bhandari, Ketan B. Ghaghada, Alexandra Badea, and Cristian T. Badea. “Advanced photon counting CT imaging pipeline for cardiac phenotyping of apolipoprotein E mouse models.” PLoS One 18, no. 10 (2023): e0291733. https://doi.org/10.1371/journal.pone.0291733.

Moon, Hae Sol, Lindsay Heffron, Ali Mahzarnia, Barnabas Obeng-Gyasi, Matthew Holbrook, Cristian T. Badea, Wuwei Feng, and Alexandra Badea. “Automated multimodal segmentation of acute ischemic stroke lesions on clinical MR images.” Magn Reson Imaging 92 (October 2022): 45–57. https://doi.org/10.1016/j.mri.2022.06.001.

Stout, Jacques A., Rui Dai, Robert J. Anderson, Scott Cousins, Jie Zhuang, Eleonora M. Lad, Diane Whitaker, et al. “Age-related Macular Degeneration is associated with faster rates of structural brain changes and widespread differences in connectivity.” Cold Spring Harbor Laboratory, July 20, 2022. https://doi.org/10.1101/2022.07.19.500546.

Badea, Alexandra, Didong Li, Andrei R. Niculescu, Robert J. Anderson, Jacques A. Stout, Christina L. Williams, Carol A. Colton, Nobuyo Maeda, and David B. Dunson. “Absolute Winding Number Differentiates Spatial Navigation Strategies with Genetic Risk for Alzheimer's Disease.” Cold Spring Harbor Laboratory, February 8, 2022. https://doi.org/10.1101/2022.02.04.479128.

Badea, Alexandra, Didong Li, Andrei R. Niculescu, Robert J. Anderson, Jacques A. Stout, Christina L. Williams, Carol A. Colton, Nobuyo Maeda, and David B. Dunson. “Corrigendum: Absolute winding number differentiates mouse spatial navigation strategies with genetic risk for Alzheimer's disease.” Front Neurosci 16 (2022): 1070425. https://doi.org/10.3389/fnins.2022.1070425.

Badea, Alexandra, Didong Li, Andrei R. Niculescu, Robert J. Anderson, Jacques A. Stout, Christina L. Williams, Carol A. Colton, Nobuyo Maeda, and David B. Dunson. “Absolute Winding Number Differentiates Mouse Spatial Navigation Strategies With Genetic Risk for Alzheimer's Disease.” Front Neurosci 16 (2022): 848654. https://doi.org/10.3389/fnins.2022.848654.

Allphin, A. J., D. P. Clark, A. Badea, and C. T. Badea. “Anatomical and functional cardiac PCCT imaging pipeline for characterization of Apolipoprotein E mouse models.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 12036, 2022. https://doi.org/10.1117/12.2611806.

Badea, A., J. A. Stout, R. J. Anderson, G. P. Cofer, L. L. Duan, and J. T. Vogelstein. “Imaging Biomarkers for Alzheimer’s Disease Using Magnetic Resonance Microscopy.” In Magnetic Resonance Microscopy: Instrumentation and Applications in Engineering, Life Science, and Energy Research, 283–314, 2022. https://doi.org/10.1002/9783527827244.ch13.

Nair, K Saidas, Chitrangda Srivastava, Robert V. Brown, Swanand Koli, Hélène Choquet, Hong Soon Kang, Yien-Ming Kuo, et al. “GLIS1 regulates trabecular meshwork function and intraocular pressure and is associated with glaucoma in humans.” Nat Commun 12, no. 1 (August 12, 2021): 4877. https://doi.org/10.1038/s41467-021-25181-7.

Bryan, Jordan, Arpita Mandan, Gauri Kamat, W Kirby Gottschalk, Alexandra Badea, Kendra J. Adams, J Will Thompson, et al. “Likelihood ratio statistics for gene set enrichment in Alzheimer's disease pathways.” Alzheimers Dement 17, no. 4 (April 2021): 561–73. https://doi.org/10.1002/alz.12223.

Badea, Alexandra, Robert Schmalzigaug, Woojoo Kim, Pamela Bonner, Umer Ahmed, G Allan Johnson, Gary Cofer, et al. “Microcephaly with altered cortical layering in GIT1 deficiency revealed by quantitative neuroimaging.” Magn Reson Imaging 76 (February 2021): 26–38. https://doi.org/10.1016/j.mri.2020.09.023.

Whitson, Heather, Alexandra Badea, Jacques Stout, Simon Davis, Jie Zhuang, and David Madden. “AGE-RELATED MACULAR DEGENERATION AND THE AGING BRAIN.” In INNOVATION IN AGING, 5:156–156, 2021.

Zhuang, Jie, David J. Madden, Priscila Cunha, Alexandra Badea, Simon W. Davis, Guy G. Potter, Eleonora M. Lad, et al. “Cerebral white matter connectivity, cognition, and age-related macular degeneration.” Neuroimage Clin 30 (2021): 102594. https://doi.org/10.1016/j.nicl.2021.102594.

Slosky, Lauren M., Yushi Bai, Krisztian Toth, Caroline Ray, Lauren K. Rochelle, Alexandra Badea, Rahul Chandrasekhar, et al. “β-Arrestin-Biased Allosteric Modulator of NTSR1 Selectively Attenuates Addictive Behaviors.” Cell 181, no. 6 (June 11, 2020): 1364-1379.e14. https://doi.org/10.1016/j.cell.2020.04.053.

Anderson, Robert J., Christopher M. Long, Evan D. Calabrese, Scott H. Robertson, G Allan Johnson, Gary P. Cofer, Richard J. O’Brien, and Alexandra Badea. “Optimizing Diffusion Imaging Protocols for Structural Connectomics in Mouse Models of Neurological Conditions.” Front Phys 8 (April 2020). https://doi.org/10.3389/fphy.2020.00088.

Holbrook, M. D., S. J. Blocker, Y. M. Mowery, A. Badea, Y. Qi, E. S. Xu, D. G. Kirsch, G. A. Johnson, and C. T. Badea. “MRI-Based Deep Learning Segmentation and Radiomics of Sarcoma in Mice.” Tomography 6, no. 1 (March 2020): 23–33. https://doi.org/10.18383/j.tom.2019.00021.

Holbrook, M. D., S. J. Blocker, Y. Mowery, A. Badea, Y. Qi, D. G. Kirsch, and C. T. Badea. “MRI-based radiomics of sarcomas in the preclinical arm of a Co-clinical trial.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 11317, 2020. https://doi.org/10.1117/12.2549628.

Nair, Saidas, Chitrangda Srivastava, Swanand Koli, Hong Soon Kang, Yien-Ming Kuo, Helene Choquet, Alexandra Badea, Eric Jorgenson, and Anton Jetten. “Kruppel-like zinc finger transcription factor GLIS1 regulates intraocular pressure by maintaining trabecular meshwork function.” In INVESTIGATIVE OPHTHALMOLOGY & VISUAL SCIENCE, Vol. 61, 2020.

Lorenzo, Damaris N., Alexandra Badea, Ruobo Zhou, Peter J. Mohler, Xiaowei Zhuang, and Vann Bennett. “βII-spectrin promotes mouse brain connectivity through stabilizing axonal plasma membranes and enabling axonal organelle transport.” Proc Natl Acad Sci U S A 116, no. 31 (July 30, 2019): 15686–95. https://doi.org/10.1073/pnas.1820649116.

Yang, Rui, Kathryn K. Walder-Christensen, Namsoo Kim, Danwei Wu, Damaris N. Lorenzo, Alexandra Badea, Yong-Hui Jiang, Henry H. Yin, William C. Wetsel, and Vann Bennett. “ANK2 autism mutation targeting giant ankyrin-B promotes axon branching and ectopic connectivity.” Proc Natl Acad Sci U S A 116, no. 30 (July 23, 2019): 15262–71. https://doi.org/10.1073/pnas.1904348116.

Anderson, Robert J., James J. Cook, Natalie Delpratt, John C. Nouls, Bin Gu, James O. McNamara, Brian B. Avants, G Allan Johnson, and Alexandra Badea. “Small Animal Multivariate Brain Analysis (SAMBA) - a High Throughput Pipeline with a Validation Framework.” Neuroinformatics 17, no. 3 (July 2019): 451–72. https://doi.org/10.1007/s12021-018-9410-0.

Badea, Alexandra, Natalie A. Delpratt, R. J. Anderson, Russell Dibb, Yi Qi, Hongjiang Wei, Chunlei Liu, William C. Wetsel, Brian B. Avants, and Carol Colton. “Multivariate MR biomarkers better predict cognitive dysfunction in mouse models of Alzheimer's disease.” Magn Reson Imaging 60 (July 2019): 52–67. https://doi.org/10.1016/j.mri.2019.03.022.

Tange, Runze, Michael Ketcha, Alexandra Badea, Evan D. Calabrese, Daniel S. Margulies, Joshua T. Vogelstein, Carey E. Priebe, and Daniel L. Sussman. “Connectome Smoothing via Low-Rank Approximations.” IEEE Trans Med Imaging 38, no. 6 (June 2019): 1446–56. https://doi.org/10.1109/TMI.2018.2885968.

Nouls, John C., Rohan S. Virgincar, Alexander G. Culbert, Nathann Morand, Dana W. Bobbert, Anne D. Yoder, Robert S. Schopler, et al. “Applications of 3D printing in small animal magnetic resonance imaging.” J Med Imaging (Bellingham) 6, no. 2 (April 2019): 021605. https://doi.org/10.1117/1.JMI.6.2.021605.

Badea, Alexandra, Wenlin Wu, Jordan Shuff, Michele Wang, Robert J. Anderson, Yi Qi, G Allan Johnson, et al. “Identifying Vulnerable Brain Networks in Mouse Models of Genetic Risk Factors for Late Onset Alzheimer's Disease.” Front Neuroinform 13 (2019): 72. https://doi.org/10.3389/fninf.2019.00072.

Badea, Alexandra, Kwan L. Ng, Robert J. Anderson, Jiangyang Zhang, Michael I. Miller, and Richard J. O’Brien. “Magnetic resonance imaging of mouse brain networks plasticity following motor learning.” PLoS One 14, no. 5 (2019): e0216596. https://doi.org/10.1371/journal.pone.0216596.

Wang, Nian, Robert J. Anderson, Alexandra Badea, Gary Cofer, Russell Dibb, Yi Qi, and G Allan Johnson. “Whole mouse brain structural connectomics using magnetic resonance histology.” Brain Struct Funct 223, no. 9 (December 2018): 4323–35. https://doi.org/10.1007/s00429-018-1750-x.

Nouls, John C., Alexandra Badea, Robert B. J. Anderson, Gary P. Cofer, and G. Allan Johnson. “Diffusion tensor imaging using multiple coils for mouse brain connectomics.” NMR Biomed 31, no. 6 (June 2018): e3921. https://doi.org/10.1002/nbm.3921.

Badea, Alexandra, Alaa Kamnaksh, Robert J. Anderson, Evan Calabrese, Joseph B. Long, and Denes V. Agoston. “Repeated mild blast exposure in young adult rats results in dynamic and persistent microstructural changes in the brain.” Neuroimage Clin 18 (2018): 60–73. https://doi.org/10.1016/j.nicl.2018.01.007.

Graña, Gilberto David, Kendall A. Hutson, Alexandra Badea, Andrew Pappa, William Scott, and Douglas C. Fitzpatrick. “The organization of frequency and binaural cues in the gerbil inferior colliculus.” J Comp Neurol 525, no. 9 (June 15, 2017): 2050–74. https://doi.org/10.1002/cne.24155.

Anderson, Robert J., James J. Cook, Natalie A. Delpratt, John C. Nouls, Bin Gu, James O. McNamara, Brian B. Avants, G Allan Johnson, and Alexandra Badea. “An HPC Pipeline with Validation Framework for Small Animal Multivariate Brain Analysis (SAMBA).” CoRR abs/1709.10483 (2017).

Badea, Alexandra, Lauren Kane, Robert J. Anderson, Yi Qi, Mark Foster, Gary P. Cofer, Neil Medvitz, et al. “The fornix provides multiple biomarkers to characterize circuit disruption in a mouse model of Alzheimer's disease.” Neuroimage 142 (November 15, 2016): 498–511. https://doi.org/10.1016/j.neuroimage.2016.08.014.

Bhagat, Srishti L., Sunny Qiu, Zachary F. Caffall, Yehong Wan, Yuanji Pan, Ramona M. Rodriguiz, William C. Wetsel, Alexandra Badea, Ute Hochgeschwender, and Nicole Calakos. “Mouse model of rare TOR1A variant found in sporadic focal dystonia impairs domains affected in DYT1 dystonia patients and animal models.” Neurobiol Dis 93 (September 2016): 137–45. https://doi.org/10.1016/j.nbd.2016.05.003.

Wang, Xiaoming, Alexandra L. Bey, Brittany M. Katz, Alexandra Badea, Namsoo Kim, Lisa K. David, Lara J. Duffney, et al. “Altered mGluR5-Homer scaffolds and corticostriatal connectivity in a Shank3 complete knockout model of autism.” Nat Commun 7 (May 10, 2016): 11459. https://doi.org/10.1038/ncomms11459.

Johnson, G. A., R. J. Anderson, J. J. Cook, C. Long, and A. Badea. “Image-processing pipelines: Applications in magnetic resonance histology.” In Progress in Biomedical Optics and Imaging - Proceedings of SPIE, Vol. 9784, 2016. https://doi.org/10.1117/12.2203525.

Lorenzo, D. N., A. Badea, G. Johnson, and V. Bennett. “An ankyrin-B/beta-2 spectrin-based mechanism regulates axonal organelle transport and axonal growth.” In MOLECULAR BIOLOGY OF THE CELL, Vol. 27. AMER SOC CELL BIOLOGY, 2016.

Calabrese, Evan, Alexandra Badea, Gary Cofer, Yi Qi, and G Allan Johnson. “A Diffusion MRI Tractography Connectome of the Mouse Brain and Comparison with Neuronal Tracer Data.” Cereb Cortex 25, no. 11 (November 2015): 4628–37. https://doi.org/10.1093/cercor/bhv121.

Calabrese, Evan, Alexandra Badea, Christopher L. Coe, Gabriele R. Lubach, Yundi Shi, Martin A. Styner, and G Allan Johnson. “A diffusion tensor MRI atlas of the postmortem rhesus macaque brain.” Neuroimage 117 (August 15, 2015): 408–16. https://doi.org/10.1016/j.neuroimage.2015.05.072.

Borg, Jana Schaich, Mai-Anh Vu, Cristian Badea, Alexandra Badea, G Allan Johnson, and Kafui Dzirasa. “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 (2015). https://doi.org/10.1523/ENEURO.0017-15.2015.

Lorenzo, Damaris Nadia, Alexandra Badea, Jonathan Davis, Janell Hostettler, Jiang He, Guisheng Zhong, Xiaowei Zhuang, and Vann Bennett. “A PIK3C3-ankyrin-B-dynactin pathway promotes axonal growth and multiorganelle transport.” J Cell Biol 207, no. 6 (December 22, 2014): 735–52. https://doi.org/10.1083/jcb.201407063.

Lorenzo, D. N., A. Badea, J. Davis, J. D. Hostettler, J. He, G. Zhong, X. Zhuang, and V. Bennett. “A PIK3C3/Ankyrin-B/Dynactin pathway promotes axonal growth and multi-organelle transport.” In MOLECULAR BIOLOGY OF THE CELL, Vol. 25. AMER SOC CELL BIOLOGY, 2014.

Calabrese, Evan, Alexandra Badea, Christopher L. Coe, Gabriele R. Lubach, Martin A. Styner, and G Allan Johnson. “Investigating the tradeoffs between spatial resolution and diffusion sampling for brain mapping with diffusion tractography: time well spent?” Hum Brain Mapp 35, no. 11 (November 2014): 5667–85. https://doi.org/10.1002/hbm.22578.

Johnson, G Allan, Alexandra Badea, Evan Calabrese, Chunlei Liu, and Luke Xie. “Magnetic resonance histology—Applications in toxicology.” In Toxicology Letters, 229:S31–32. Elsevier BV, 2014. https://doi.org/10.1016/j.toxlet.2014.06.148.

Johnson, G Allan, Evan Calabrese, Peter B. Little, Laurence Hedlund, Yi Qi, and Alexandra Badea. “Quantitative mapping of trimethyltin injury in the rat brain using magnetic resonance histology.” Neurotoxicology 42 (May 2014): 12–23. https://doi.org/10.1016/j.neuro.2014.02.009.

Ashbrook, David G., Anna Delprato, Claudia Grellmann, Marieke Klein, Richard Wetzel, Rupert W. Overall, and Alexandra Badea. “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.” Front Neurosci 8 (2014): 418. https://doi.org/10.3389/fnins.2014.00418.

Clark, D., A. Badea, G. A. Johnson, and C. T. Badea. “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). https://doi.org/10.1117/12.2007043.

Calabrese, Evan, Alexandra Badea, Charles Watson, and G Allan Johnson. “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. https://doi.org/10.1016/j.neuroimage.2013.01.017.

Johnson, G Allan, Alexandra Badea, Evan Calabrese, Chunlei Liu, and Luke Xie. “Magnetic resonance histology: cool images- but who cares?” TOXICOLOGY LETTERS 221 (2013): S50–S50. https://doi.org/10.1016/j.toxlet.2013.06.183.

Badea, Alexandra, and G Allan Johnson. “Magnetic resonance microscopy.” Stud Health Technol Inform 185 (2013): 153–84.

Badea, Alexandra, Sally Gewalt, Brian B. Avants, James J. Cook, and G Allan Johnson. “Quantitative mouse brain phenotyping based on single and multispectral MR protocols.” Neuroimage 63, no. 3 (November 15, 2012): 1633–45. https://doi.org/10.1016/j.neuroimage.2012.07.021.

Clark, Darin, Alexandra Badea, Yilin Liu, G Allan Johnson, and Cristian T. Badea. “Registration-based segmentation of murine 4D cardiac micro-CT data using symmetric normalization.” Phys Med Biol 57, no. 19 (October 7, 2012): 6125–45. https://doi.org/10.1088/0031-9155/57/19/6125.

Driehuys, B., J. Nouls, A. Badea, E. Bucholz, K. Ghaghada, A. Petiet, and L. W. Hedlund. “Small animal imaging with magnetic resonance microscopy.” ILAR Journal 53, no. 1 (September 11, 2012): 35–53.

Johnson, G Allan, Evan Calabrese, Alexandra Badea, George Paxinos, and Charles Watson. “A multidimensional magnetic resonance histology atlas of the Wistar rat brain.” Neuroimage 62, no. 3 (September 2012): 1848–56. https://doi.org/10.1016/j.neuroimage.2012.05.041.

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.

Badea, Alexandra, and G Allan Johnson. “Magnetic resonance microscopy.” Anal Cell Pathol (Amst) 35, no. 4 (2012): 205–27. https://doi.org/10.3233/ACP-2011-0050.

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.

Johnson, Allan G., Alexandra Badea, J. Brandenberg, Pablo Burstein, Carl Gustafson, S. Liu, and Jonathan Nissanov. “Waxholm Space: Target Volumes for a Standard Coordinate System for the Mouse Brain.” Frontiers in Neuroinformatics 3 (2009). https://doi.org/10.3389/conf.neuro.11.2009.08.004.

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.

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.

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.

Bowsher, J. E., H. Yuan, L. W. Hedlund, T. G. Turkington, G. Akabani, A. Badea, W. C. Kurylo, et al. “Utilizing MRI information to estimate F18-FDG distributions in rat flank tumors.” In IEEE Nuclear Science Symposium Conference Record, 4:2488–92, 2004.

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.