Automated segmentation of neuroanatomical structures in multispectral MR microscopy of the mouse brain. - Anjum A. Sharief; Anders M. Dale; Alexandra Badea; G. Allan Johnson (NeuroImage, 2005)

Morphometric analysis of the C57BL/6J mouse brain. - Alexandra Badea; A. A. Ali-Sharief; G. Allan Johnson (NeuroImage, 2007)

Neuroanatomical phenotypes in the Reeler mouse. - Alexandra Badea; Peter Nicholls; G. Allan Johnson; William C. Wetsel (NeuroImage, 2007)

High-throughput morphologic phenotyping of the mouse brain with magnetic resonance histology. - G. Allan Johnson; Anjum Ali-Sharief; Alexandra Badea; Jeffrey Brandenburg; Gary P. Cofer; Boma Fubara; Sally L. Gewalt; Laurence W. Hedlund; Lucy Upchurch (NeuroImage, 2007)

Automated segmentation of the actively stained mouse brain using multi-spectral MR microscopy. - Anjum A. Sharief; Alexandra Badea; Anders M. Dale; G. Allan Johnson (NeuroImage, 2008)

Genetic dissection of the mouse brain using high-field magnetic resonance microscopy. - Alexandra Badea; G. Allan Johnson; Robert W. Williams (NeuroImage, 2009)

Automated segmentation of mouse brain images using extended MRF. - Min Hyeok Bae; Rong Pan; Teresa Wu; Alexandra Badea (NeuroImage, 2009)

Remote sites of structural atrophy predict later amyloid formation in a mouse model of Alzheimer's disease. - Alexandra Badea; G. Allan Johnson; Joanna L. Jankowsky (NeuroImage, 2010)

Waxholm Space: An image-based reference for coordinating mouse brain research. - G. Allan Johnson; Alexandra Badea; Jeffrey Brandenburg; Gary P. Cofer; Boma Fubara; Song Liu; Jonathan Nissanov (NeuroImage, 2010)

Quantitative mouse brain phenotyping based on single and multispectral MR protocols. - Alexandra Badea; Sally L. Gewalt; Brian B. Avants; James J. Cook; G. Allan Johnson (NeuroImage, 2012)

A multidimensional magnetic resonance histology atlas of the Wistar rat brain. - G. Allan Johnson; Evan Calabrese; Alexandra Badea; George Paxinos; Charles Watson (NeuroImage, 2012)

A prior feature SVM-MRF based method for mouse brain segmentation. - Teresa Wu; Min Hyeok Bae; Min Zhang 020; Rong Pan; Alexandra Badea (NeuroImage, 2012)

Constructing a 4D murine cardiac micro-CT atlas for automated segmentation and phenotyping applications. - Darin P. Clark; Alexandra Badea; G. Allan Johnson; Cristian T. Badea (Image Processing, 2013)

A quantitative magnetic resonance histology atlas of postnatal rat brain development with regional estimates of growth and variability. - Evan Calabrese; Alexandra Badea; Charles Watson; G. Allan Johnson (NeuroImage, 2013)

A diffusion tensor MRI atlas of the postmortem rhesus macaque brain. - Evan Calabrese; Alexandra Badea; Christopher L. Coe; Gabriele R. Lubach; Yundi Shi; Martin Andreas Styner; G. Allan Johnson (NeuroImage, 2015)

Image-processing pipelines: applications in magnetic resonance histology. - G. Allan Johnson; Robert J. Anderson; James J. Cook; Christopher Long; Alexandra Badea (Image Processing, 2016)

The fornix provides multiple biomarkers to characterize circuit disruption in a mouse model of Alzheimer's disease. - Alexandra Badea; Lauren Kane; Robert J. Anderson; Yi Qi; Mark Foster; Gary P. Cofer; Neil Medvitz; Anne F. Buckley; Andreas K. Badea; William C. Wetsel; Carol A. Colton (NeuroImage, 2016)

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

Identifying Vulnerable Brain Networks in Mouse Models of Genetic Risk Factors for Late Onset Alzheimer's Disease. - Alexandra Badea; Wenlin Wu; Jordan Shuff; Michele Wang; Robert J. Anderson; Yi Qi; G. Allan Johnson; Joan G. Wilson; Serge Koudoro; Eleftherios Garyfallidis; Carol A. Colton; David B. Dunson (Frontiers Neuroinformatics, 2019)

Small Animal Multivariate Brain Analysis (SAMBA) - a High Throughput Pipeline with a Validation Framework. - Robert J. Anderson; James J. Cook; Natalie A. Delpratt; John C. Nouls; Bin Gu; James O. McNamara; Brian B. Avants; G. Allan Johnson; Alexandra Badea (Neuroinformatics, 2019)

Connectome Smoothing via Low-Rank Approximations. - Runze Tang; Michael D. Ketcha; Alexandra Badea; Evan D. Calabrese; Daniel S. Margulies; Joshua T. Vogelstein; Carey E. Priebe; Daniel L. Sussman (IEEE Trans. Medical Imaging, 2019)

MRI-based radiomics of sarcomas in the preclinical arm of a co-clinical trial. - Matthew D. Holbrook; Stephanie J. Blocker; Yvonne M. Mowery; Alexandra Badea; Yi Qi; David G. Kirsch; Cristian T. Badea (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2020)

Anatomical and functional cardiac PCCT imaging pipeline for characterization of Apolipoprotein E mouse models. - Alex J. Allphin; Darin P. Clark; Alexandra Badea; Cristian T. Badea (Biomedical Applications in Molecular, Structural, and Functional Imaging, 2022)

Learning sources of variability from high-dimensional observational studies. - Eric W. Bridgeford; Jaewon Chung; Brian Gilbert; Sambit Panda; Adam Li; Cencheng Shen; Alexandra Badea; Brian Caffo; Joshua T. Vogelstein (CoRR, 2023)

Discovering the signal subgraph: An iterative screening approach on graphs. - Cencheng Shen; Shangsi Wang; Alexandra Badea; Carey E. Priebe; Joshua T. Vogelstein (Pattern Recognit. Lett., 2024)

Skull stripping with purely synthetic data. - Jong Sung Park; Juhyung Ha; Siddhesh P. Thakur; Alexandra Badea; Spyridon Bakas; Eleftherios Garyfallidis (CoRR, 2025)