A list of our publications:
2024
Winter S, Mahzarnia A, Anderson RJ, Han ZY, Tremblay J, Stout JA, Moon HS, Marcellino D, Dunson DB, Badea A. APOE, Immune Factors, Sex, and Diet Interact to Shape Brain Networks in Mouse Models of Aging. bioRxiv. 2024 Jul 1;2023.10.04.560954. doi:10.1101/2023.10.04.560954. PubMed PMID: 39005377; PMCID: PMC11244909.
https://doi.org/10.1101/2023.10.04.560954
Winter S, Mahzarnia A, Anderson RJ, Han ZY, Tremblay J, Stout JA, Moon HS, Marcellino D, Dunson DB, Badea A. Brain network fingerprints of Alzheimer’s disease risk factors in mouse models with humanized APOE alleles. Magn Reson Imaging. 2024 Dec;114:110251. doi:10.1016/j.mri.2024.110251. PubMed PMID: 39362319.
https://pubmed.ncbi.nlm.nih.gov/39362319
Mahzarnia A, Lutz MW, Badea A. 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. 2024;97(2):635–648. doi:10.3233/JAD-230342. PubMed PMID: 38346613.
https://pubmed.ncbi.nlm.nih.gov/38346613
Blocker SJ, Mowery YM, Everitt JI, Cook J, Cofer GP, Qi Y, Bassil AM, Xu ES, Kirsch DG, Badea CT, Johnson GA. MR histology reveals tissue features beneath heterogeneous MRI signal in genetically engineered mouse models of sarcoma. Front Oncol. 2024;14:1287479. doi:10.3389/fonc.2024.1287479. PubMed PMID: 38951835; PMCID: PMC11077524.
https://doi.org/10.3389/fonc.2024.1287479
Moon HS, Mahzarnia A, Stout JA, Anderson RJ, Strain M, Tremblay JT, Han ZY, Niculescu A, MacFarlane A, King J, Ashley-Koch A, Clark D, Lutz MW, Badea A. 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. 2024 Jan;229(1):231–249. doi:10.1007/s00429-023-02620-x. PubMed PMID: 37994844; PMCID: PMC10829566.
https://pubmed.ncbi.nlm.nih.gov/37994844
2023
Moore SM, Quirk JD, Lassiter AW, Laforest R, Ayers GD, Badea CT, Fedorov AY, Kinahan PE, Holbrook M, Larson PEZ, Sriram R, Chenevert TL, Malyarenko D, Kurhanewicz J, Houghton AM, Ross BD, Pickup S, Gee JC, Zhou R, Gammon ST, Manning HC, Roudi R, Daldrup-Link HE, Lewis MT, Rubin DL, Yankeelov TE, Shoghi KI. Co-Clinical Imaging Metadata Information (CIMI) for Cancer Research to Promote Open Science, Standardization, and Reproducibility in Preclinical Imaging. Tomography. 2023 May 11;9(3):995–1009. doi:10.3390/tomography9030081. PubMed PMID: 37388171; PMCID: PMC10312391.
https://pubmed.ncbi.nlm.nih.gov/37388171
Allphin AJ, Clark DP, Thuering T, Bhandari P, Ghaghada KB, Badea CT. Micro-CT imaging of multiple K-edge elements using GaAs and CdTe photon counting detectors. Phys Med Biol. 2023 Apr 12;68(8):085007. doi:10.1088/1361-6560/accd3c. PubMed PMID: 37041549; PMCID: PMC10208633.
https://pubmed.ncbi.nlm.nih.gov/37041549
Schwartz FR, Clark DP, Rigiroli F, Kalisz K, Wildman-Tobriner B, Thomas S, Wilson J, Badea CT, Marin D. Evaluation of the impact of a novel denoising algorithm on image quality in dual-energy abdominal CT of obese patients. Eur Radiol. 2023 Oct;33(10):7056–7065. doi:10.1007/s00330-023-10155-9. PubMed PMID: 36866751.
https://pubmed.ncbi.nlm.nih.gov/36866751
Gammon ST, Cohen AS, Lehnert AL, Sullivan DC, Malyarenko D, Manning HC, Hormuth DA, Daldrup-Link HE, An H, Quirk JD, Shoghi K, Pagel MD, Kinahan PE, Miyaoka RS, Houghton AM, Lewis MT, Larson P, Sriram R, Blocker SJ, Pickup S, Badea A, Badea CT, Yankeelov TE, Chenevert TL. An Online Repository for Pre-Clinical Imaging Protocols (PIPs). Tomography. 2023 Mar 27;9(2):750–758. doi:10.3390/tomography9020063. PubMed PMID: 37198576; PMCID: PMC10139026.
https://pubmed.ncbi.nlm.nih.gov/37198576
Clark DP, Badea CT. MCR toolkit: A GPU-based toolkit for multi-channel reconstruction of preclinical and clinical x-ray CT data. Med Phys. 2023 Aug;50(8):4775–4796. doi:10.1002/mp.16477. PubMed PMID: 37285215; PMCID: PMC10539992.
https://pubmed.ncbi.nlm.nih.gov/37285215
Peehl DM, Badea CT, Chenevert TL, Daldrup-Link HE, Ding L, Dobrolecki LE, Houghton AM, Kinahan PE, Kurhanewicz J, Lewis MT, Li S, Luker GD, Ma CX, Manning HC, Mowery YM, O’Dwyer PJ, Pautler RG, Rosen MA, Roudi R, Ross BD, Shoghi KI, Sriram R, Talpaz M, Wahl RL, Zhou R. Animal Models and Their Role in Imaging-Assisted Co-Clinical Trials. Tomography. 2023 Mar 16;9(2):657–680. doi:10.3390/tomography9020054. PubMed PMID: 36996429; PMCID: PMC10055538.
https://pubmed.ncbi.nlm.nih.gov/36996429
Patel R, Mowery YM, Qi Y, Bassil AM, Holbrook M, Xu ES, Hong CS, Himes JE, Williams NT, Everitt J, Ma Y, Luo L, Selitsky SR, Modliszewski JL, Gao J, Jung SH, Kirsch DG, Badea CT. Neoadjuvant Radiation Therapy and Surgery Improves Metastasis-Free Survival over Surgery Alone in a Primary Mouse Model of Soft Tissue Sarcoma. Mol Cancer Ther. 2023 Jan 3;22(1):112–122. doi:10.1158/1535-7163.MCT-22-0347. PubMed PMID: 36350764; PMCID: PMC9872379.
https://pubmed.ncbi.nlm.nih.gov/36350764
Moon HS, Mahzarnia A, Stout JA, Anderson RJ, Badea CT, Badea A. Feature attention graph neural network for estimating brain age and identifying important neural connections in mouse models of genetic risk for Alzheimer’s disease. bioRxiv. 2023 Dec 14;2023.12.13.571559. doi:10.1101/2023.12.13.571559. PubMed PMID: 38612686; PMCID: PMC11014035.
https://doi.org/10.1101/2023.12.13.571559
Mahzarnia A, Stout JA, Anderson RJ, Moon HS, Han ZY, Beck K, Browndyke JN, Dunson DB, Johnson KG, O’Brien RJ, Badea A. Identifying vulnerable brain networks associated with Alzheimer’s disease risk. Cereb Cortex. 2023 Apr 25;33(9):5307–5322. doi:10.1093/cercor/bhad134. PubMed PMID: 37092524; PMCID: PMC10411997.
https://pubmed.ncbi.nlm.nih.gov/37092524
Nadkarni R, Clark DP, Allphin AJ, Badea CT. A Deep Learning Approach for Rapid and Generalizable Denoising of Photon-Counting Micro-CT Images. Tomography. 2023 Jul 2;9(4):1286–1302. doi:10.3390/tomography9040102. PubMed PMID: 37563961; PMCID: PMC10410514.
https://pubmed.ncbi.nlm.nih.gov/37563961
2022
Nadkarni R, Allphin AJ, Clark DP, Badea CT. Material decomposition from photon-counting CT using a convolutional neural network and energy-integrating CT training labels. Phys Med Biol. 2022 Jul 18;67(15):155009. doi:10.1088/1361-6560/ac7b79. PubMed PMID: 35849240; PMCID: PMC9395756.
https://pubmed.ncbi.nlm.nih.gov/35849240
Allphin AJ, Mowery YM, Lafata KJ, Clark DP, Bassil AM, Castillo R, Odhiambo D, Holbrook MD, Ghaghada KB, Badea CT. Photon Counting CT and Radiomic Analysis Enables Differentiation of Tumors Based on Lymphocyte Burden. Tomography. 2022 Mar 10;8(2):740–753. doi:10.3390/tomography8020061. PubMed PMID: 35743264; PMCID: PMC9221035.
https://pubmed.ncbi.nlm.nih.gov/35743264
Badea A, Li D, Niculescu AR, Anderson RJ, Stout JA, Williams CL, Colton CA, Maeda N, Dunson DB. Absolute Winding Number Differentiates Mouse Spatial Navigation Strategies With Genetic Risk for Alzheimer’s Disease. Front Neurosci. 2022 Feb 18;16:848654. doi:10.3389/fnins.2022.848654. PubMed PMID: 35250742; PMCID: PMC8893782.
https://pubmed.ncbi.nlm.nih.gov/35250742
Moon HS, Heffron L, Mahzarnia A, Obeng-Gyasi B, Holbrook M, Badea CT, Feng W, Badea A. Automated multimodal segmentation of acute ischemic stroke lesions on clinical MR images. Magn Reson Imaging. 2022 Oct;92:45–57. doi:10.1016/j.mri.2022.05.011. PubMed PMID: 35660223; PMCID: PMC9391765.
https://pubmed.ncbi.nlm.nih.gov/35660223
2021
Holbrook MD, Clark DP, Patel R, Qi Y, Bassil AM, Mowery YM, Badea CT. Detection of Lung Nodules in Micro-CT Imaging Using Deep Learning. Tomography. 2021 Aug 7;7(3):358–372. doi:10.3390/tomography7030032. PubMed PMID: 34484516; PMCID: PMC8417970.
https://pubmed.ncbi.nlm.nih.gov/34484516
Lee CL, Lee JW, Daniel AR, Holbrook M, Hasapis S, Wright AO, Brownstein J, Da Silva Campos L, Ma Y, Mao L, Abraham D, Badea CT, Kirsch DG. Characterization of cardiovascular injury in mice following partial-heart irradiation with clinically relevant dose and fractionation. Radiother Oncol. 2021 Apr;157:155–162. doi:10.1016/j.radonc.2021.01.033. PubMed PMID: 33550049; PMCID: PMC8052857.
https://pubmed.ncbi.nlm.nih.gov/33550049
Clark DP, Badea CT. Advances in micro-CT imaging of small animals. Phys Med. 2021 Aug;88:175–192. doi:10.1016/j.ejmp.2021.06.011. PubMed PMID: 34293647; PMCID: PMC8351391.
https://pubmed.ncbi.nlm.nih.gov/34293647
Blocker SJ, Cook J, Mowery YM, Everitt JI, Qi Y, Hornburg KJ, Cofer GP, Zapata F, Bassil AM, Badea CT, Kirsch DG, Johnson GA. Ex Vivo MR Histology and Cytometric Feature Mapping Connect Three-dimensional in Vivo MR Images to Two-dimensional Histopathologic Images of Murine Sarcomas. Radiol Imaging Cancer. 2021 May;3(3):e200103. doi:10.1148/rycan.2021200103. PubMed PMID: 33980244; PMCID: PMC8102056.
https://pubmed.ncbi.nlm.nih.gov/33980244
Schwartz FR, Clark DP, Ding Y, Ramirez-Giraldo JC, Badea CT, Marin D. Evaluating renal lesions using deep-learning based extension of dual-energy FoV in dual-source CT—A retrospective pilot study. Eur J Radiol. 2021 Jun;139:109734. doi:10.1016/j.ejrad.2021.109734. PubMed PMID: 33933274.
https://pubmed.ncbi.nlm.nih.gov/33933274
Badea A, Schmalzigaug R, Kim W, Bonner P, Ahmed U, Johnson GA, Cofer G, Foster M, Anderson RJ, Badea CT, Premont RT. Microcephaly with altered cortical layering in GIT1 deficiency revealed by quantitative neuroimaging. Magn Reson Imaging. 2021 Feb;76:26–38. doi:10.1016/j.mri.2020.10.005. PubMed PMID: 33086192; PMCID: PMC7850637.
https://pubmed.ncbi.nlm.nih.gov/33086192
2020
Holbrook MD, Blocker SJ, Mowery YM, Badea A, Qi Y, Xu ES, Kirsch DG, Johnson GA, Badea CT. MRI-Based Deep Learning Segmentation and Radiomics of Sarcoma in Mice. Tomography. 2020 Mar;6(1):23–33. doi:10.18383/j.tom.2020.00003. PubMed PMID: 32257938; PMCID: PMC7105842.
https://pubmed.ncbi.nlm.nih.gov/32257938
Holbrook MD, Clark DP, Badea CT. Dual source hybrid spectral micro-CT using an energy-integrating and a photon-counting detector. Phys Med Biol. 2020 Oct 21;65(20):205012. doi:10.1088/1361-6560/abbf23. PubMed PMID: 32947434; PMCID: PMC7776396.
https://pubmed.ncbi.nlm.nih.gov/32947434
Shoghi KI, Badea CT, Blocker SJ, Chenevert TL, Laforest R, Lewis MT, Luker GD, Manning HC, Marcus DS, Mowery YM, Pickup S, Richmond A, Ross BD, Vilgelm AE, Yankeelov TE, Zhou R. Co-Clinical Imaging Resource Program (CIRP): Bridging the Translational Divide to Advance Precision Medicine. Tomography. 2020 Sep;6(3):273–287. doi:10.18383/j.tom.2020.00026. PubMed PMID: 33029179; PMCID: PMC7531330.
https://pubmed.ncbi.nlm.nih.gov/33029179
Clark DP, Schwartz FR, Marin D, Ramirez-Giraldo JC, Badea CT. Deep learning based spectral extrapolation for dual-source, dual-energy x-ray computed tomography. Med Phys. 2020 Sep;47(9):4150–4163. doi:10.1002/mp.14292. PubMed PMID: 32567219; PMCID: PMC7544140.
https://pubmed.ncbi.nlm.nih.gov/32567219
Blocker SJ, Holbrook MD, Mowery YM, Sullivan DC, Badea CT. The impact of respiratory gating on improving volume measurement of murine lung tumors in micro-CT imaging. PLoS One. 2020 Feb 13;15(2):e0225019. doi:10.1371/journal.pone.0225019. PubMed PMID: 32053685; PMCID: PMC7015784.
https://pubmed.ncbi.nlm.nih.gov/32053685
Slosky LM, Bai Y, Toth K, Ray C, Rochelle LK, Badea A, Chandrasekhar R, Pogorelov VM, Abraham DM, Atluri N, Peddibhotla S, Hedrick MP, Hershberger P, Maloney P, Yuan H, Li Z, Wetsel WC, Pinkerton AB, Barak LS, Caron MG. β-Arrestin-Biased Allosteric Modulator of NTSR1 Selectively Attenuates Addictive Behaviors. Cell. 2020 Jun 11;181(6):1364–1379.e14. doi:10.1016/j.cell.2020.04.024. PubMed PMID: 32416068; PMCID: PMC7291539.
https://pubmed.ncbi.nlm.nih.gov/32416068
Wisdom AJ, Mowery YM, Hong CS, Himes JE, Nabet BY, Qin X, Zhang D, Chen L, Fradin H, Patel R, Bassil AM, Muise ES, King DA, Xu ES, Carpenter DJ, Kent CL, Smythe KS, Williams NT, Luo L, Ma Y, Alizadeh AA, Owzar K, Diehn M, Bradley T, Kirsch DG. Single cell analysis reveals distinct immune landscapes in transplant and primary sarcomas that determine response or resistance to immunotherapy. Nat Commun. 2020 Dec 17;11(1):6410. doi:10.1038/s41467-020-20171-3. PubMed PMID: 33335135; PMCID: PMC7747439.
https://pubmed.ncbi.nlm.nih.gov/33335135
Anderson RJ, Long CM, Calabrese ED, Robertson SH, Johnson GA, Cofer GP, O’Brien RJ, Badea A. Optimizing Diffusion Imaging Protocols for Structural Connectomics in Mouse Models of Neurological Conditions. Front Phys. 2020 Apr;8:100. doi:10.3389/fphy.2020.00100. PubMed PMID: 32373492; PMCID: PMC7188524.
https://pubmed.ncbi.nlm.nih.gov/32373492
2019
Badea CT, Clark DP, Holbrook M, Srivastava M, Mowery Y, Ghaghada KB. Functional imaging of tumor vasculature using iodine and gadolinium-based nanoparticle contrast agents: a comparison of spectral micro-CT using energy integrating and photon counting detectors. Phys Med Biol. 2019 Mar 12;64(6):065007. doi:10.1088/1361-6560/ab054b. PubMed PMID: 30767859; PMCID: PMC6446959.
https://pubmed.ncbi.nlm.nih.gov/30767859
Lee CL, Daniel AR, Holbrook M, Brownstein J, Da Silva Campos L, Hasapis S, Ma Y, Borst LB, Badea CT, Kirsch DG. Sensitization of Vascular Endothelial Cells to Ionizing Radiation Promotes the Development of Delayed Intestinal Injury in Mice. Radiat Res. 2019 Sep;192(3):258–266. doi:10.1667/RR15234.1. PubMed PMID: 31335287; PMCID: PMC6884091.
https://pubmed.ncbi.nlm.nih.gov/31335287
Holbrook M, Clark DP, Badea CT. Overcoming detector limitations of x-ray photon counting for preclinical microcomputed tomography. J Med Imaging (Bellingham). 2019 Jan;6(1):011004. doi:10.1117/1.JMI.6.1.011004. PubMed PMID: 30671426; PMCID: PMC6350876.
https://pubmed.ncbi.nlm.nih.gov/30671426
Ma Z, Yu YR, Badea CT, Kovacs JJ, Xiong X, Comhair SA, Piantadosi CA, Rajagopal S. Vascular Endothelial Growth Factor Receptor 3 Regulates Endothelial Function Through β-Arrestin 1. Circulation. 2019 Mar 26;139(13):1629–1642. doi:10.1161/CIRCULATIONAHA.118.037301. PubMed PMID: 30799638; PMCID: PMC6439391.
https://pubmed.ncbi.nlm.nih.gov/30799638
Clark DP, Holbrook M, Lee CL, Badea CT. Photon-counting cine-cardiac CT in the mouse. PLoS One. 2019 Sep 16;14(9):e0218417. doi:10.1371/journal.pone.0218417. PubMed PMID: 31525113; PMCID: PMC6749944.
https://pubmed.ncbi.nlm.nih.gov/31525113
Blocker SJ, Mowery YM, Holbrook MD, Qi Y, Kirsch DG, Johnson GA, Badea CT. Bridging the translational gap: Implementation of multimodal small animal imaging strategies for tumor burden assessment in a co-clinical trial. PLoS One. 2019 Apr 25;14(4):e0207555. doi:10.1371/journal.pone.0207555. PubMed PMID: 31022234; PMCID: PMC6483119.
https://pubmed.ncbi.nlm.nih.gov/31022234
2018
Ashton JR, Gottlin EB, Patz EF Jr, West JL, Badea CT. A comparative analysis of EGFR-targeting antibodies for gold nanoparticle CT imaging of lung cancer. PLoS One. 2018 Nov 12;13(11):e0206950. doi:10.1371/journal.pone.0206950. PubMed PMID: 30419034; PMCID: PMC6231801.
https://pubmed.ncbi.nlm.nih.gov/30419034
Ashton JR, Castle KD, Qi Y, Kirsch DG, West JL, Badea CT. Dual-Energy CT Imaging of Tumor Liposome Delivery After Gold Nanoparticle-Augmented Radiation Therapy. Theranostics. 2018;8(7):1782–1797. doi:10.7150/thno.22757. PubMed PMID: 29556356; PMCID: PMC5858500.
https://pubmed.ncbi.nlm.nih.gov/29556356
Holbrook M, Clark DP, Badea CT. Low-dose 4D cardiac imaging in small animals using dual source micro-CT. Phys Med Biol. 2018 Jan 9;63(2):025009. doi:10.1088/1361-6560/aaa48d. PubMed PMID: 29244132; PMCID: PMC5860024.
https://pubmed.ncbi.nlm.nih.gov/29244132
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