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RSS Recent Publications

Safdar S, Zwick BF, Yu Y, Bourantas GC, Joldes GR, Warfield SK, Hyde DE, Frisken S, Kapur T, Kikinis R, Golby A, Nabavi A, Wittek A, Miller K. SlicerCBM: automatic framework for biomechanical analysis of the brain. Int J Comput Assist Radiol Surg. 2023 Apr 1. PMID: 37004646.

Zheng J, Yang Q, Makris N, Huang K, Liang J, Ye C, Yu X, Tian M, Ma T, Mou T, Guo W, Kikinis R, Gao Y. Three-Dimensional Digital Reconstruction of the Cerebellar Cortex: Lobule Thickness, Surface Area Measurements, and Layer Architecture. Cerebellum. 2023 Apr;22(2):249-260. PMID: 35286708; PMC9470778.

Sadler SJ, Torio EF, Golby AJ. Global cancer surgery in low-resource settings: A strengths, weaknesses, opportunities, and threats analysis. Cancer. 2023 Mar 1;129(5):671-684.  PMID: 36597652; PMC10069626.

Kobayashi S, King F, Hata N. Automatic segmentation of prostate and extracapsular structures in MRI to predict needle deflection in percutaneous prostate intervention. Int J Comput Assist Radiol Surg. 2023 Mar;18(3):449-460. PMID: 36152168; PMC9974805.

Juvekar P, Torio E, Bi WL, Bastos DCA, Golby AJ, Frisken SF. Mapping Resection Progress by Tool-Tip Tracking during Brain Tumor Surgery for Real-Time Estimation of Residual Tumor. Cancers (Basel). 2023 Jan 29;15(3):825. PMID: 36765783; PMC9913508.

Giganti F, Cole AP, Fennessy FM, Clinton T, Moreira PLDF, Bernardes MC, Westin CF, Krishnaswamy D, Fedorov A, Wollin DA, Langbein B, Frego N, Labban M, Badaoui JS, Chang SL, Briggs LG, Tokuda J, Ambrosi A, Kirkham A, Emberton M, Kasivisvanathan V, Moore CM, Allen C, Tempany CM. Promoting the use of the PI-QUAL score for prostate MRI quality: results from the ESOR Nicholas Gourtsoyiannis teaching fellowship. Eur Radiol. 2023 Jan;33(1):461-471. PMID: 35771247; PMC9244244.

Panditharatna E, Marques JG, Wang T, Trissal MC, Liu I, Jiang L, Beck a, Groves a, Dharia NV, Li D, Hoffman SE, Kugener G, Shaw ML, Mire HM, Hack OA, Dempster JM, Lareau C, Dai L, Sigua LH, Quezada MA, Stanton AJ, Wyatt M, Kalani Z, Goodale a, Vazquez F, Piccioni F, Doench JG, Root DE, Anastas JN, Jones KL, Conway as, Stopka S, Regan MS, Liang Y, Seo HS, Song K, Bashyal P, Jerome WP, Mathewson ND, Dhe-Paganon S, Suvà ML, Carcaboso AM, Lavarino C, Mora J, Nguyen QD, Ligon KL, Shi Y, Agnihotri S, Agar NYR, Stegmaier K, Stiles CD, Monje M, Golub TR, Qi J, Filbin MG. BAF Complex Maintains Glioma Stem Cells in Pediatric H3K27M Glioma. Cancer Discov. 2022 Dec 2;12(12):2880-2905. PMID: 36305736; PMC9716260.

Naik S, Burk KS, Budiawan E, Lacson R, Lee LK, Fennessy FM, Tempany C, Cole AP, Trinh QD, Kibel as, Khorasani R. Radiologists’ Contribution to Variation in Detecting Clinically Significant Prostate Cancer in Men With Prostate MRI. J Am Coll Radiol. 2022 Dec;19(12):1312-1321. PMID: 36244674.

Bridge CP, Gorman C, Pieper S, Doyle SW, Lennerz JK, Kalpathy-Cramer J, Clunie DA, Fedorov AY, Herrmann MD. Highdicom: A Python Library for Standardized Encoding of Image Annotations and Machine Learning Model Outputs in Pathology and Radiology. J Digit Imaging. 2022 Dec;35(6):1719-1737. PMID: 35995898; PMC9712874.

Wang S, Zhang F, Huang P, Hong H, Jiaerken Y, Yu X, Zhang R, Zeng Q, Zhang Y, Kikinis R, Rathi Y, Makris N, Lou M, Pasternak O, Zhang M, O’Donnell LJ. Superficial White Matter Microstructure Affects Processing Speed in Cerebral Small Vessel Disease. Hum Brain Mapp. 2022 Dec 1;43(17):5310-5325. PMID: 35822593; PMC9812245.

Spinazzi EF, Argenziano MG, Upadhyayula PS, Banu MA, Neira JA, Higgins DMO, Wu PB, Pereira B, Mahajan a, Humala N, Al-Dalahmah O, Zhao W, Save AV, Gill BJA, Boyett DM, Marie T, Furnari JL, Sudhakar TD, Stopka SA, Regan MS, Catania v, Good L, Zacharoulis S, Behl M, Petridis P, Jambawalikar S, Mintz a, Lignelli a, Agar NYR, Sims PA, Welch MR, Lassman AB, Iwamoto FM, D’Amico RS, Grinband J, Canoll P, Bruce JN. Chronic Convection-Enhanced Delivery of Topotecan for Patients With Recurrent Glioblastoma: A First-in-Patient, Single-Centre, Single- Arm, Phase 1b Trial. Lancet Oncol. 2022 Nov;23(11):1409-1418. PMID: 36243020; PMC9641975.

Sack J, Nitsch J, Meine H, Kikinis R, Halle M, Rutherford a. Quantitative Analysis of Liver Disease Using MRI-Based Radiomic Features of the Liver and Spleen. J Imaging. 2022 Oct 9;8(10):277. PMID: 36286371; PMC9605113.

Lo WC, Bittencourt LK, Panda a, Jiang Y, Tokuda J, Seethamraju R, Tempany- Afdhal C, Obmann v, Wright K, Griswold M, Seiberlich N, Gulani v. Multicenter Repeatability and Reproducibility of MR Fingerprinting in Phantoms and in Prostatic Tissue. Magn Reson Med. 2022 Oct;88(4):1818-1827. PMID: 35713379; PMC9469467.

Notarangelo G, Spinelli JB, Perez EM, Baker GJ, Kurmi K, Elia I, Stopka SA, Baquer G, Lin JR, Golby AJ, Joshi S, Baron HF, Drijvers JM, Georgiev P, Ringel AE, Zaganjor E, McBrayer SK, Sorger PK, Sharpe AH, Wucherpfennig KW, Santagata S, Agar NYR, Suvà ML, Haigis MC. Oncometabolite D-2HG Alters T Cell Metabolism to Impair CD8<Sup>+</Sup> T Cell Function. Science. 2022 Sep 30;377(6614):1519-1529. PMID: 36173860; PMC9629749.

Shi DD, Savani MR, Levitt MM, Wang AC, Endress JE, Bird CE, Buehler J, Stopka SA, Regan MS, Lin YF, Puliyappadamba VT, Gao W, Khanal J, Evans L, Lee JH, Guo L, Xiao Y, Xu M, Huang B, Jennings RB, Bonal DM, Martin-Sandoval MS, Dang T, Gattie LC, Cameron AB, Lee S, Asara JM, Kornblum HI, Mak TW, Looper RE, Nguyen QD, Signoretti S, Gradl S, Sutter a, Jeffers M, Janzer a, Lehrman MA, Zacharias LG, Mathews TP, Losman JA, Richardson TE, Cahill DP, DeBerardinis RJ, Ligon KL, Xu L, Ly P, Agar NYR, Abdullah KG, Harris IS, Kaelin WG Jr, McBrayer SK. De Novo Pyrimidine Synthesis Is a Targetable Vulnerability in IDH Mutant Glioma. Cancer Cell. 2022 Sep 12;40(9):939-956.e16. PMID: 35985343; PMC9515386.

Pal S, Kaplan JP, Nguyen H, Stopka SA, Savani MR, Regan MS, Nguyen QD, Jones KL, Moreau LA, Peng J, Dipiazza MG, Perciaccante AJ, Zhu X, Hunsel BR, Liu KX, Alexandrescu S, Drissi R, Filbin MG, McBrayer SK, Agar NYR, Chowdhury D, Haas- Kogan DA. A Druggable Addiction to De Novo Pyrimidine Biosynthesis in Diffuse Midline Glioma. Cancer Cell. 2022 Sep 12;40(9):957-972.e10. PMID: 35985342; PMC9575661.

Stopka SA, Van Der Reest J, Abdelmoula WM, Ruiz DF, Joshi S, Ringel AE, Haigis MC, Agar NYR. Spatially Resolved Characterization of Tissue Metabolic Compartments in Fasted and High-Fat Diet Livers. PLoS One. 2022 Sep 6;17(9):e0261803. PMID: 36067168; PMC9447892.

Coy S, Wang S, Stopka SA, Lin JR, Yapp C, Ritch CC, Salhi L, Baker GJ, Rashid R, Baquer G, Regan M, Khadka P, Cole KA, Hwang J, Wen PY, Bandopadhayay P, Santi M, De Raedt T, Ligon KL, Agar NYR, Sorger PK, Touat M, Santagata S. Single Cell Spatial Analysis Reveals the Topology of Immunomodulatory Purinergic Signaling in Glioblastoma. Nat Commun. 2022 Aug 16;13(1):4814. PMID: 35973991; PMC9381513.

Ehdaie B, Tempany CM, Holland F, Sjoberg DD, Kibel as, Trinh QD, Durack JC, Akin O, Vickers AJ, Scardino PT, Sperling D, Wong JYC, Yuh B, Woodrum DA, Mynderse LA, Raman SS, Pantuck AJ, Schiffman MH, McClure TD, Sonn GA, Ghanouni P. MRI-Guided Focused Ultrasound Focal Therapy for Patients With Intermediate- Risk Prostate Cancer: A Phase 2b, Multicentre Study. Lancet Oncol. 2022 Jul;23(7):910-918. PMID: 35714666; PMC9400094.

Sefcikova v, Sporrer JK, Juvekar P, Golby a, Samandouras G. Converting Sounds to Meaning With Ventral Semantic Language Networks: Integration of Interdisciplinary Data on Brain Connectivity, Direct Electrical Stimulation and Clinical Disconnection Syndromes. Brain Struct Funct. 2022 Jun;227(5):1545-1564. PMID: 35267079; PMC9098557.

Zhang F, Wells WM, O’Donnell LJ. Deep Diffusion MRI Registration (DDMReg): A Deep Learning Method for Diffusion MRI Registration. IEEE Trans Med Imaging. 2022 Jun;41(6):1454-1467. PMID: 34968177; PMC9273049.

McGarry SD, Brehler M, Bukowy JD, Lowman AK, Bobholz SA, Duenweg SR, Banerjee a, Hurrell SL, Malyarenko D, Chenevert TL, Cao Y, Li Y, You D, Fedorov a, Bell LC, Quarles CC, Prah MA, Schmainda KM, Taouli B, LoCastro E, Mazaheri Y, Shukla-Dave a, Yankeelov TE, Hormuth DA 2nd, Madhuranthakam AJ, Hulsey K, Li K, Huang W, Huang W, Muzi M, Jacobs MA, Solaiyappan M, Hectors S, Antic T, Paner GP, Palangmonthip W, Jacobsohn K, Hohenwalter M, Duvnjak P, Griffin M, See W, Nevalainen MT, Iczkowski KA, LaViolette PS. Multi-Site Concordance of Diffusion- Weighted Imaging Quantification for Assessing Prostate Cancer Aggressiveness. J Magn Reson Imaging. 2022 Jun;55(6):1745-1758. PMID: 34767682; PMC9095769.

Pujol S, Cabeen RP, Yelnik J, François C, Fernandez Vidal S, Karachi C, Bardinet E, Cosgrove GR, Kikinis R. Somatotopic Organization of Hyperdirect Pathway Projections From the Primary Motor Cortex in the Human Brain. Front Neurol. 2022 Apr 25;13:791092. PMID: 35547388; PMC9081715.

Abdelmoula WM, Stopka SA, Randall EC, Regan M, Agar JN, Sarkaria JN, Wells WM, Kapur T, Agar NYR. massNet: Integrated Processing and Classification of Spatially Resolved Mass Spectrometry Data Using Deep Learning for Rapid Tumor Delineation. Bioinformatics. 2022 Mar 28;38(7):2015-2021. PMID: 35040929; PMC8963284.

Sebastian C, Ferrer C, Serra M, Choi JE, Ducano N, Mira a, Shah MS, Stopka SA, Perciaccante AJ, Isella C, Moya-Rull D, Vara-Messler M, Giordano S, Maldi E, Desai N, Capen DE, Medico E, Cetinbas M, Sadreyev RI, Brown D, Rivera MN, Sapino a, Breault DT, Agar NYR, Mostoslavsky R. A Non-Dividing Cell Population With High Pyruvate Dehydrogenase Kinase Activity Regulates Metabolic Heterogeneity and Tumorigenesis in the Intestine. Nat Commun. 2022 Mar 21;13(1):1503. PMID: 35314684; PMC8938512.

Cole AP, Langbein BJ, Giganti F, Fennessy FM, Tempany CM, Emberton M. Is Perfect the Enemy of Good? Weighing the Evidence for Biparametric MRI in Prostate Cancer. Br J Radiol. 2022 Mar 1;95(1131):20210840. PMID: 34826223; PMC8978228.

Maier-Hein L, Eisenmann M, Sarikaya D, März K, Collins T, Malpani a, Fallert J, Feussner H, Giannarou S, Mascagni P, Nakawala H, Park a, Pugh C, Stoyanov D, Vedula SS, Cleary K, Fichtinger G, Forestier G, Gibaud B, Grantcharov T, Hashizume M, Heckmann-Nötzel D, Kenngott HG, Kikinis R, Mündermann L, Navab N, Onogur S, Roß T, Sznitman R, Taylor RH, Tizabi MD, Wagner M, Hager GD, Neumuth T, Padoy N, Collins J, Gockel I, Goedeke J, Hashimoto DA, Joyeux L, Lam K, Leff DR, Madani a, Marcus HJ, Meireles O, Seitel a, Teber D, Ückert F, Müller-Stich BP, Jannin P, Speidel S. Surgical Data Science – From Concepts Toward Clinical Translation. Med Image Anal. 2022 Feb;76:102306. PMID: 34879287; PMC9135051.

Zekelman LR, Zhang F, Makris N, He J, Chen Y, Xue T, Liera D, Drane DL, Rathi Y, Golby AJ, O’Donnell LJ. White Matter Association Tracts Underlying Language and Theory of Mind: An Investigation of 809 Brains From the Human Connectome Project. Neuroimage. 2022 Feb 1;246:118739. PMID: 34856375; PMC8862285.

Robles DJ, Dharani a, Rostowsky KA, Chaudhari NN, Ngo v, Zhang F, O’Donnell LJ, Green L, Sheikh-Bahaei N, Chui HC, Irimia a. Older Age, Male Sex, and Cerebral Microbleeds Predict White Matter Loss After Traumatic Brain Injury. Geroscience. 2022 Feb;44(1):83-102. PMID: 34704219; PMC8811069.

Yu Y, Safdar S, Bourantas G, Zwick B, Joldes G, Kapur T, Frisken S, Kikinis R, Nabavi a, Golby a, Wittek a, Miller K. Automatic Framework for Patient- Specific Modelling of Tumour Resection-Induced Brain Shift. Comput Biol Med. 2022 Jan 30;143:105271. PMID: 35123136; PMC9389918.

Madore B, Belsley G, Cheng CC, Preiswerk F, Kijewski MF, Wu PH, Martell LB, Pluim JPW, Di Carli M, Moore SC. Ultrasound-Based Sensors for Respiratory Motion Assessment in Multimodality PET Imaging. Phys Med Biol. 2022 Jan 19;67(2):10.1088/1361-6560/ac4213. PMID: 34891142; PMC9482332.

Lopez BGC, Kohale in, Du Z, Korsunsky I, Abdelmoula WM, Dai Y, Stopka SA, Gaglia G, Randall EC, Regan MS, Basu SS, Clark AR, Marin BM, Mladek AC, Burgenske DM, Agar JN, Supko JG, Grossman SA, Nabors LB, Raychaudhuri S, Ligon KL, Wen PY, Alexander B, Lee EQ, Santagata S, Sarkaria J, White FM, Agar NYR. Multimodal Platform for Assessing Drug Distribution and Response in Clinical Trials. Neuro Oncol. 2022 Jan 5;24(1):64-77. PMID: 34383057; PMC8730776.

Frisken SF. SurfaceNets for Multi-Label Segmentations With Preservation of Sharp Boundaries. J Comput Graph Tech. 2022 Jan-Mar;11(1):34-54. PMID: 36325473; PMC9623606.

Yu Y, Bourantas G, Zwick B, Joldes G, Kapur T, Frisken S, Kikinis R, Nabavi a, Golby a, Wittek a, Miller K. Computer Simulation of Tumour Resection-Induced Brain Deformation by a Meshless Approach. Int J Numer Method Biomed Eng. 2022 Jan;38(1):e3539. PMID: 34647427; PMC8881972.

Dominas C, Bhagavatula S, Stover E, Deans K, Larocca C, Colson Y, Peruzzi P, Kibel a, Hata N, Tsai L, Hung Y, Packard R, Jonas O. The Translational and Regulatory Development of an Implantable Microdevice for Multiple Drug Sensitivity Measurements in Cancer Patients. IEEE Trans Biomed Eng. 2022 Jan;69(1):412-421. PMID: 34242160; PMC8702455.

Zhou H, Jayender J. EMDQ: Removal of Image Feature Mismatches in Real-Time. IEEE Trans Image Process. 2022;31:706-720. PMID: 34914589; PMC8777235.

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