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View the grants and publications from the Department of Machine Learning.

Grants
  • Combined Radiation Acoustics and Ultrasound Imaging for Real-Time Guidance in Radiotherapy
    Sponsor: Nat Institutes of Health
    PI:El Naqa, I.
  • Optimal Decision Making in Radiotherapy Using Panomics Analytics
    Sponsor: Nat Institutes of Health
    PI:El Naqa, I.
  • Federated Learning for Optimal Decision Making in Radiotherapy Using Panomics Analytics
    Sponsor: Nat Institutes of Health
    PI:El Naqa, I.
  • An Ionizing Radiation Acoustics Imaging (iRAI) Approach for Guided Flash Radiotherapy
    Sponsor: Nat Institutes of Health
    PI:El Naqa, I.
  • Data Science to Improve Treatment Planning for Advanced Prostate Cancer Patients Treated with Radiotherapy
    Sponsor: US Army
    PI:El Naqa, I.
  • Artificial Intelligence for Effective MR-Linac Adaptive Radiotherapy
    Sponsor: ViewRay Technologies
    PI:El Naqa, I.,CO-PI:Rosenberg, S.
Publications
  • Hatt M, Krizsan AK, Rahmim A, Bradshaw TJ, Costa PF, Forgacs A, Seifert R, Zwanenburg A, El Naqa I, Kinahan PE, Tixier F, Jha AK, Visvikis D. Joint EANM/SNMMI guideline on radiomics in nuclear medicine : Jointly supported by the EANM Physics Committee and the SNMMI Physics, Instrumentation and Data Sciences Council. Eur J Nucl Med Mol Imaging. 2022 Nov. Pubmedid: 36326868.
  • Sharma M, Milano MT, Cummings M, Naqa IE. Tumor Control Probability After Radiosurgery of Brain Metastases With and Without Retreatment. Int J Radiat Oncol Biol Phys. 2022 Nov.114(3):537-544. Pubmedid: 35863671.
  • Cui S, Hope A, Dilling TJ, Dawson LA, Ten Haken R, El Naqa I. Artificial Intelligence for Outcome Modeling in Radiotherapy. Semin Radiat Oncol. 2022 Oct.32(4):351-364. Pubmedid: 36202438.
  • Claessens M, Oria CS, Brouwer CL, Ziemer BP, Scholey JE, Lin H, Witztum A, Morin O, Naqa IE, Van Elmpt W, Verellen D. Quality Assurance for AI-Based Applications in Radiation Therapy. Semin Radiat Oncol. 2022 Oct.32(4):421-431. Pubmedid: 36202444.
  • Niraula D, Cui S, Pakela J, Wei L, Luo Y, Ten Haken RK, El Naqa I. Current status and future developments in predicting outcomes in radiation oncology. Br J Radiol. 2022 Oct.95(1139):20220239. Pubmedid: 35867841.
  • Chao M, El Naqa I, Bakst RL, Lo YC, Peñagarícano JA. Cluster model incorporating heterogeneous dose distribution of partial parotid irradiation for radiotherapy induced xerostomia prediction with machine learning methods. Acta Oncol. 2022 Jul.61(7):842-848. Pubmedid: 35527717.
  • Hinton T, Karnak D, Tang M, Jiang R, Luo Y, Boonstra P, Sun Y, Nancarrow DJ, Sandford E, Ray P, Maurino C, Matuszak M, Schipper MJ, Green MD, Yanik GA, Tewari M, Naqa IE, Schonewolf CA, Haken RT, Jolly S, Lawrence TS, Ray D. Improved prediction of radiation pneumonitis by combining biological and radiobiological parameters using a data-driven Bayesian network analysis. Transl Oncol. 2022 Jul.21:101428. Pubmedid: 35460942. Pmcid: PMC9046881.
  • Le TD, Nguyen PD, Korkin D, Thieu T. PHILM2Web: A high-throughput database of macromolecular host-pathogen interactions on the Web. Database (Oxford). 2022 Jun.2022. Pubmedid: 35776535. Pmcid: PMC9248916.
  • Sun W, Niraula D, El Naqa I, Ten Haken RK, Dinov ID, Cuneo K, Jin JJ. Precision radiotherapy via information integration of expert human knowledge and AI recommendation to optimize clinical decision making. Comput Methods Programs Biomed. 2022 Jun.221:106927. Pubmedid: 35675722.
  • Saad M, Lee SJ, Tan AC, El Naqa IM, Hodi FS, Butterfield LH, LaFramboise WA, Storkus W, Karunamurthy AD, Conejo-Garcia J, Hwu P, Streicher H, Sondak VK, Kirkwood JM, Tarhini AA. Enhanced immune activation within the tumor microenvironment and circulation of female high-risk melanoma patients and improved survival with adjuvant CTLA4 blockade compared to males. J Transl Med. 2022 Jun.20(1):253. Pubmedid: 35659704. Pmcid: PMC9164320.
  • Naqa IE, Pogue BW, Zhang R, Oraiqat I, Parodi K. Image guidance for FLASH radiotherapy. Med Phys. 2022 Jun.49(6):4109-4122. Pubmedid: 35396707.
  • McCune JS, Nakamura R, O'Meally D, Randolph TW, Sandmaier BM, Karolak A, Hockenbery D, Navarro SL. Pharmacometabonomic association of cyclophosphamide 4-hydroxylation in hematopoietic cell transplant recipients. Clin Transl Sci. 2022 May.15(5):1215-1224. Pubmedid: 35106927. Pmcid: PMC9099130.
  • Pérez-Morales J, Lu H, Mu W, Tunali I, Kutuk T, Eschrich SA, Balagurunathan Y, Gillies RJ, Schabath MB. Volume doubling time and radiomic features predict tumor behavior of screen-detected lung cancers. Cancer Biomark. 2022 Apr.33(4):489-501. Pubmedid: 35491768. Pmcid: PMC9310661.
  • Keller H, Shek T, Driscoll B, Xu Y, Nghiem B, Nehmeh S, Grkovski M, Schmidtlein CR, Budzevich M, Balagurunathan Y, Sunderland JJ, Beichel RR, Uribe C, Lee TY, Li F, Jaffray DA, Yeung I. Noise-Based Image Harmonization Significantly Increases Repeatability and Reproducibility of Radiomics Features in PET Images: A Phantom Study. Tomography. 2022 Apr.8(2):1113-1128. Pubmedid: 35448725. Pmcid: PMC9025788.
  • Gharzai LA, Pakela J, Jaworski EM, El Naqa I, Shah J, Hawkins PG, Spector ME, Bradford CR, Chinn SB, Malloy K, Kupfer R, Shuman A, Morrison R, Stucken CL, Rosko A, Prince ME, Casper K, Eisbruch A, Wolf G, Swiecicki PL, Worden F, Mierzwa ML. Imaging response assessment for predicting outcomes after bioselection chemotherapy in larynx cancer: A secondary analysis of two prospective trials. Clin Transl Radiat Oncol. 2022 Mar.33:30-36. Pubmedid: 35024462. Pmcid: PMC8728046.
  • Wang S, Budzevich M, Abdalah MA, Balagurunathan Y, Choi JW. In Vivo Imaging of Rat Vascularity with FDG-Labeled Erythrocytes. Pharmaceuticals (Basel). 2022 Feb.15(3). Pubmedid: 35337090. Pmcid: PMC8953049.
  • Chamseddine I, Kim Y, De B, El Naqa I, Duda DG, Wolfgang J, Pursley J, Paganetti H, Wo J, Hong T, Koay EJ, Grassberger C. Predictive Modeling of Survival and Toxicity in Patients With Hepatocellular Carcinoma After Radiotherapy. JCO Clin Cancer Inform. 2022 Feb.6:e2100169. Pubmedid: 35192402. Pmcid: PMC8863122.
  • Turner K, Brownstein NC, Thompson Z, El Naqa I, Luo Y, Jim HSL, Rollison DE, Howard R, Zeng D, Rosenberg SA, Perez B, Saltos A, Oswald LB, Gonzalez BD, Islam JY, Alishahi Tabriz A, Zhang W, Dilling TJ. Longitudinal patient-reported outcomes and survival among early-stage non-small cell lung cancer patients receiving stereotactic body radiotherapy. Radiother Oncol. 2022 Feb.167:116-121. Pubmedid: 34953934. Pmcid: PMC8934278.
  • Tarhini AA, Lee SJ, Tan AC, El Naqa IM, Stephen Hodi F, Butterfield LH, LaFramboise WA, Storkus WJ, Karunamurthy AD, Conejo-Garcia JR, Hwu P, Streicher H, Sondak VK, Kirkwood JM. Improved prognosis and evidence of enhanced immunogenicity in tumor and circulation of high-risk melanoma patients with unknown primary. J Immunother Cancer. 2022 Jan.10(1). Pubmedid: 35074904. Pmcid: PMC8788316.
  • Fuhrman JD, Gorre N, Hu Q, Li H, El Naqa I, Giger ML. A review of explainable and interpretable AI with applications in COVID-19 imaging. Med Phys. 2022 Jan.49(1):1-14. Pubmedid: 34796530. Pmcid: PMC8646613.
  • Karolak A, Levatić J, Supek F. A framework for mutational signature analysis based on DNA shape parameters. PLoS One. 2022 Jan.17(1):e0262495. Pubmedid: 35015788. Pmcid: PMC8752002.
  • Kammer MN, Lakhani DA, Balar AB, Antic SL, Kussrow AK, Webster RL, Mahapatra S, Barad U, Shah C, Atwater T, Diergaarde B, Qian J, Kaizer A, New M, Hirsch E, Feser WJ, Strong J, Rioth M, Miller Y, Balagurunathan Y, Rowe DJ, Helmey S, Chen SC, Bauza J, Deppen SA, Sandler K, Maldonado F, Spira A, Billatos E, Schabath MB, Gillies RJ, Wilson DO, Walker RC, Landman B, Chen H, Grogan EL, Barón AE, Bornhop DJ, Massion PP. Integrated Biomarkers for the Management of Indeterminate Pulmonary Nodules. Am J Respir Crit Care Med. 2021 Dec.204(11):1306-1316. Pubmedid: 34464235. Pmcid: PMC8786067.