Issam El Naqa, PhD

Senior Member Imaging analytics, bioinformatics, and outcoming modelings. Dr. El Naqa is the founding chair of the department of Machine Learning at Moffitt Cancer Center, Tampa, Fl.  He is an internationally recognized authority in the fields of machine learning, data analytics, and oncology outcomes modeling and has published extensively in these areas with more than 220+ peer-reviewed journal publications and 4 edited textbooks. He has been a member and fellow of several academic and professional societies including AAPM and IEEE. His research has been funded by several federal and private grants in Canada and the USA and served on national and international study sections. He acts as a peer-reviewer and editorial board member for several leading international journals in his areas of expertise. 

Associations

• Gastrointestinal Oncology
• Machine Learning
• Radiation Oncology
• Cancer Biology & Evolution Program

Education & Training

Graduate:

• Illinois Institute of Technology, PhD - Electrical & Computer Engineering
• University of Jordan, Amman, Jordan, MS - Electrical Engineering/Telecommunication
• Washington University in St. Louis, MA - Biology

  Bioinformatics and outcome modeling: design and develop large-scale datamining machine/deep learning methods and software tools to identify robust biomarkers of radiotherapy treatment outcomes from clinical and preclinical data using complex systems analysis and machine learning approaches (radiogenomics). Multimodality image-guided targeting and adaptive radiotherapy: design and develop hardware tools and software algorithms for multimodality image analysis and understanding, feature extraction for outcome prediction (radiomics), real-time treatment optimization and targeting. Clinical decision support: develop and design methods and tools for reinforcement machine learning and optimization of decision making for radiotherapy. Medical physics radiation measurement: design and develop new technologies for radiation using optical and acoustics techniques to interrogate radiation response in real time for online targeting and adaptation. Radiobiology: design and develop predictive models of tumor and normal tissue response to radiotherapy (radiogenomics). Investigate the application of these methods to develop therapeutic interventions for protection of normal tissue toxicities.  

• Dudas D, Dilling TJ, El Naqa I. Improved outcome models with denoising diffusion. Phys Med. 2024 Mar.119:103307. Pubmedid: 38325221. Pmcid: PMC10939775.
• Jeong D, Morse B, Polk SL, Chen DT, Li J, Hodul P, Centeno BA, Costello J, Jiang K, Machado S, El Naqa I, Farah PT, Huynh T, Raghunand N, Mok S, Dam A, Malafa M, Qayyum A, Fleming JB, Permuth JB. Pancreatic Cyst Size Measurement on Magnetic Resonance Imaging Compared to Pathology. Cancers (Basel). 2024 Jan.16(1). Pubmedid: 38201633. Pmcid: PMC10778543.
• Wei L, Aryal MP, Cuneo K, Matuszak M, Lawrence TS, Ten Haken RK, Cao Y, Naqa IE. Deep learning prediction of post-SBRT liver function changes and NTCP modeling in hepatocellular carcinoma based on DGAE-MRI. Med Phys. 2023 Sep.50(9):5597-5608. Pubmedid: 36988423.
• El Naqa I, Karolak A, Luo Y, Folio L, Tarhini AA, Rollison D, Parodi K. Translation of AI into oncology clinical practice. Oncogene. 2023 Oct.42(42):3089-3097. Pubmedid: 37684407.
• Amorrortu R, Garcia M, Zhao Y, El Naqa I, Balagurunathan Y, Chen DT, Thieu T, Schabath MB, Rollison DE. Overview of approaches to estimate real-world disease progression in lung cancer. JNCI Cancer Spectr. 2023 Oct.7(6). Pubmedid: 37738580. Pmcid: PMC10637832.
• Eljilany I, Saghand PG, Chen J, Ratan A, McCarter M, Carpten J, Colman H, Ikeguchi AP, Puzanov I, Arnold S, Churchman M, Hwu P, Conejo-Garcia J, Dalton WS, Weiner GJ, El Naqa IM, Tarhini AA. The T Cell Immunoscore as a Reference for Biomarker Development Utilizing Real-World Data from Patients with Advanced Malignancies Treated with Immune Checkpoint Inhibitors. Cancers (Basel). 2023 Oct.15(20). Pubmedid: 37894280. Pmcid: PMC10605389.
• Weygand J, Armstrong T, Bryant JM, Andreozzi JM, Oraiqat IM, Nichols S, Liveringhouse CL, Latifi K, Yamoah K, Costello JR, Frakes JM, Moros EG, El Naqa IM, Naghavi AO, Rosenberg SA, Redler G. Accurate, repeatable, and geometrically precise diffusion-weighted imaging on a 0.35 T magnetic resonance imaging-guided linear accelerator. Phys Imaging Radiat Oncol. 2023 Oct.28:100505. Pubmedid: 38045642. Pmcid: PMC10692914.
• Drabiak K, Kyzer S, Nemov V, El Naqa I. AI and machine learning ethics, law, diversity, and global impact. Br J Radiol. 2023 Oct.96(1150):20220934. Pubmedid: 37191072. Pmcid: PMC10546451.
• Naqa IE, Drukker K. AI in imaging and therapy: innovations, ethics, and impact - introductory editorial. Br J Radiol. 2023 Oct.96(1150):20239004. Pubmedid: 38011226. Pmcid: PMC10546442.
• Wei L, Niraula D, Gates EDH, Fu J, Luo Y, Nyflot MJ, Bowen SR, El Naqa IM, Cui S. Artificial intelligence (AI) and machine learning (ML) in precision oncology: a review on enhancing discoverability through multiomics integration. Br J Radiol. 2023 Oct.96(1150):20230211. Pubmedid: 37660402. Pmcid: PMC10546458.
• Baliga S, Patel S, Naqa IE, Li XA, Cohen LE, Howell RM, Hoppe BS, Constine LS, Palmer JD, Hamstra D, Olch AJ. Testicular Dysfunction in Male Childhood Cancer Survivors Treated With Radiation Therapy: A PENTEC Comprehensive Review. Int J Radiat Oncol Biol Phys. 2023 Oct. Pubmedid: 37791936.
• Cui S, Traverso A, Niraula D, Zou J, Luo Y, Owen D, El Naqa I, Wei L. Interpretable artificial intelligence in radiology and radiation oncology. Br J Radiol. 2023 Oct.96(1150):20230142. Pubmedid: 37493248. Pmcid: PMC10546466.
• Connor M, Salans M, Karunamuni R, Unnikrishnan S, Huynh-Le MP, Tibbs M, Qian A, Reyes A, Stasenko A, McDonald C, Moiseenko V, El-Naqa I, Hattangadi-Gluth J. Fine Motor Skill Decline After Brain Radiation Therapy-A Multivariate Normal Tissue Complication Probability Study of a Prospective Trial. Int J Radiat Oncol Biol Phys. 2023 Nov.117(3):581-593. Pubmedid: 37150258.
• Waqas A, Bui MM, Glassy EF, El Naqa I, Borkowski P, Borkowski AA, Rasool G. Revolutionizing Digital Pathology With the Power of Generative Artificial Intelligence and Foundation Models. Lab Invest. 2023 Nov.103(11):100255. Pubmedid: 37757969.
• Gorre N, Carranza E, Fuhrman J, Li H, Madduri RK, Giger ML, El Naqa I. MIDRC CRP10 AI interface-an integrated tool for exploring, testing and visualization of AI models. Phys Med Biol. 2023 Mar.68(7). Pubmedid: 36716497. Pmcid: PMC10155272.
• Niraula D, Sun W, Jin J, Dinov ID, Cuneo K, Jamaluddin J, Matuszak MM, Luo Y, Lawrence TS, Jolly S, Ten Haken RK, El Naqa I. A clinical decision support system for AI-assisted decision-making in response-adaptive radiotherapy (ARCliDS). Sci Rep. 2023 Mar.13(1):5279. Pubmedid: 37002296. Pmcid: PMC10066294.
• Ger RB, Wei L, Naqa IE, Wang J. The Promise and Future of Radiomics for Personalized Radiotherapy Dosing and Adaptation. Semin Radiat Oncol. 2023 Jul.33(3):252-261. Pubmedid: 37331780.
• 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. 2023 Jan.50(2):352-375. Pubmedid: 36326868. Pmcid: PMC9816255.
• Niraula D, Jamaluddin J, Matuszak MM, Haken RKT, Naqa IE. Author Correction: Quantum deep reinforcement learning for clinical decision support in oncology: application to adaptive radiotherapy. Sci Rep. 2023 Feb.13(1):2318. Pubmedid: 36759642. Pmcid: PMC9911394.
• Dudas D, Saghand PG, Dilling TJ, Perez BA, Rosenberg SA, Naqa IE. Deep Learning-Guided Dosimetry for Mitigating Local Failure of Patients With Non-Small Cell Lung Cancer Receiving Stereotactic Body Radiation Therapy. Int J Radiat Oncol Biol Phys. 2023 Dec. Pubmedid: 38056778.
• Zhang W, Oraiqat I, Litzenberg D, Chang KW, Hadley S, Sunbul NB, Matuszak MM, Tichacek CJ, Moros EG, Carson PL, Cuneo KC, Wang X, El Naqa I. Real-time, volumetric imaging of radiation dose delivery deep into the liver during cancer treatment. Nat Biotechnol. 2023 Aug.41(8):1160-1167. Pubmedid: 36593414. Pmcid: PMC10314963.
• Chamseddine I, Kim Y, De B, Naqa IE, Duda DG, Wolfgang JA, Pursley J, Wo JY, Hong TS, Paganetti H, Koay EJ, Grassberger C. Predictive Model of Liver Toxicity to Aid the Personalized Selection of Proton Versus Photon Therapy in Hepatocellular Carcinoma. Int J Radiat Oncol Biol Phys. 2023 Aug.116(5):1234-1243. Pubmedid: 36739920.
• Akhavanallaf A, Peterson AB, Fitzpatrick K, Roseland M, Wong KK, El-Naqa I, Zaidi H, Dewaraja YK. The predictive value of pretherapy [68Ga]Ga-DOTA-TATE PET and biomarkers in [177Lu]Lu-PRRT tumor dosimetry. Eur J Nucl Med Mol Imaging. 2023 Aug.50(10):2984-2996. Pubmedid: 37171633.
• Mendiratta-Lala M, El Naqa I, Owen D. In silico trials of combination immuno-radiation for unresectable hepatocellular carcinoma. Transl Cancer Res. 2023 Apr.12(4):709-712. Pubmedid: 37180660. Pmcid: PMC10175001.
• 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.
• 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. Pmcid: PMC9793488.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• 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.
• Luo Y, Cuneo KC, Lawrence TS, Matuszak MM, Dawson LA, Niraula D, Ten Haken RK, El Naqa I. A human-in-the-loop based Bayesian network approach to improve imbalanced radiation outcomes prediction for hepatocellular cancer patients with stereotactic body radiotherapy. Front Oncol. 2022 Dec.12:1061024. Pubmedid: 36568208. Pmcid: PMC9782976.
• El Naqa I, Boone JM, Benedict SH, Goodsitt MM, Chan HP, Drukker K, Hadjiiski L, Ruan D, Sahiner B. AI in medical physics: guidelines for publication. Med Phys. 2021 Sep.48(9):4711-4714. Pubmedid: 34545957.
• El Naqa I. Prospective clinical deployment of machine learning in radiation oncology. Nat Rev Clin Oncol. 2021 Oct.18(10):605-606. Pubmedid: 34244694.
• Ba Sunbul NH, Zhang W, Oraiqat I, Litzenberg D, Lam KL, Cuneo K, Moran-Ebm JM, Carson PL, Wang X, Clarke SD, Matuszak MM, Pozzi SA, El Naqa-Ebm I. A simulation study of ionizing radiation acoustic imaging (iRAI) as a real-time dosimetric technique for ultra-high dose rate radiotherapy (UHDR-RT). Med Phys. 2021 Oct.48(10):6137-6151. Pubmedid: 34431520. Pmcid: PMC8943858.
• Pfaehler E, Zhovannik I, Wei L, Boellaard R, Dekker A, Monshouwer R, El Naqa I, Bussink J, Gillies R, Wee L, Traverso A. A systematic review and quality of reporting checklist for repeatability and reproducibility of radiomic features. Phys Imaging Radiat Oncol. 2021 Oct.20:69-75. Pubmedid: 34816024. Pmcid: PMC8591412.
• Avanzo M, Gagliardi V, Stancanello J, Blanck O, Pirrone G, Naqa IE, Revelant A, Sartor G. Combining computed tomography and biologically effective dose in radiomics and deep learning improves prediction of tumor response to robotic lung stereotactic body radiation therapy. Med Phys. 2021 Oct.48(10):6257-6269. Pubmedid: 34415574. Pmcid: PMC9753143.
• Pakela JM, Matuszak MM, Ten Haken RK, McShan DL, El Naqa I. Dynamic stochastic deep learning approaches for predicting geometric changes in head and neck cancer. Phys Med Biol. 2021 Nov.66(22). Pubmedid: 34587597. Pmcid: PMC8637428.
• Royce TJ, Mavroidis P, Wang K, Falchook AD, Sheets NC, Fuller DB, Collins SP, El Naqa I, Song DY, Ding GX, Nahum AE, Jackson A, Grimm J, Yorke E, Chen RC. Tumor Control Probability Modeling and Systematic Review of the Literature of Stereotactic Body Radiation Therapy for Prostate Cancer. Int J Radiat Oncol Biol Phys. 2021 May.110(1):227-236. Pubmedid: 32900561. Pmcid: PMC9445430.
• Hope A, Verduin M, Dilling TJ, Choudhury A, Fijten R, Wee L, Aerts HJ, El Naqa I, Mitchell R, Vooijs M, Dekker A, de Ruysscher D, Traverso A. Artificial Intelligence Applications to Improve the Treatment of Locally Advanced Non-Small Cell Lung Cancers. Cancers (Basel). 2021 May.13(10). Pubmedid: 34069307. Pmcid: PMC8156328.
• Soltys SG, Grimm J, Milano MT, Xue J, Sahgal A, Yorke E, Yamada Y, Ding GX, Li XA, Lovelock DM, Jackson A, Ma L, El Naqa I, Gibbs IC, Marks LB, Benedict S. Stereotactic Body Radiation Therapy for Spinal Metastases: Tumor Control Probability Analyses and Recommended Reporting Standards. Int J Radiat Oncol Biol Phys. 2021 May.110(1):112-123. Pubmedid: 33516580.
• Marciscano AE, Haimovitz-Friedman A, Lee P, Tran PT, Tomé WA, Guha C, Spring Kong FM, Sahgal A, El Naqa I, Rimner A, Marks LB, Formenti SC, DeWeese TL. Immunomodulatory Effects of Stereotactic Body Radiation Therapy: Preclinical Insights and Clinical Opportunities. Int J Radiat Oncol Biol Phys. 2021 May.110(1):35-52. Pubmedid: 30836168.
• Coates JTT, Pirovano G, El Naqa I. Radiomic and radiogenomic modeling for radiotherapy: strategies, pitfalls, and challenges. J Med Imaging (Bellingham). 2021 May.8(3):031902. Pubmedid: 33768134. Pmcid: PMC7985651.
• Stumpf PK, Yorke ED, El Naqa I, Cuneo KC, Grimm J, Goodman KA. Modeling of Tumor Control Probability in Stereotactic Body Radiation Therapy for Adrenal Tumors. Int J Radiat Oncol Biol Phys. 2021 May.110(1):217-226. Pubmedid: 33864824. Pmcid: PMC9446062.
• Soltys SG, Milano MT, Xue J, Tomé WA, Yorke E, Sheehan J, Ding GX, Kirkpatrick JP, Ma L, Sahgal A, Solberg T, Adler J, Grimm J, El Naqa I. Stereotactic Radiosurgery for Vestibular Schwannomas: Tumor Control Probability Analyses and Recommended Reporting Standards. Int J Radiat Oncol Biol Phys. 2021 May.110(1):100-111. Pubmedid: 33375955. Pmcid: PMC9477217.
• Lee P, Loo BW, Biswas T, Ding GX, El Naqa IM, Jackson A, Kong FM, LaCouture T, Miften M, Solberg T, Tome WA, Tai A, Yorke E, Li XA. Local Control After Stereotactic Body Radiation Therapy for Stage I Non-Small Cell Lung Cancer. Int J Radiat Oncol Biol Phys. 2021 May.110(1):160-171. Pubmedid: 30954520. Pmcid: PMC9446070.
• Moiseenko V, Marks LB, Grimm J, Jackson A, Milano MT, Hattangadi-Gluth JA, Huynh-Le MP, Pettersson N, Yorke E, El Naqa I. A Primer on Dose-Response Data Modeling in Radiation Therapy. Int J Radiat Oncol Biol Phys. 2021 May.110(1):11-20. Pubmedid: 33358230. Pmcid: PMC9339232.
• Wang K, Mavroidis P, Royce TJ, Falchook AD, Collins SP, Sapareto S, Sheets NC, Fuller DB, El Naqa I, Yorke E, Grimm J, Jackson A, Chen RC. Prostate Stereotactic Body Radiation Therapy: An Overview of Toxicity and Dose Response. Int J Radiat Oncol Biol Phys. 2021 May.110(1):237-248. Pubmedid: 33358229. Pmcid: PMC8053668.
• Milano MT, Grimm J, Soltys SG, Yorke E, Moiseenko V, Tomé WA, Sahgal A, Xue J, Ma L, Solberg TD, Kirkpatrick JP, Constine LS, Flickinger JC, Marks LB, El Naqa I. Single- and Multi-Fraction Stereotactic Radiosurgery Dose Tolerances of the Optic Pathways. Int J Radiat Oncol Biol Phys. 2021 May.110(1):87-99. Pubmedid: 29534899. Pmcid: PMC9479557.
• Redmond KJ, Gui C, Benedict S, Milano MT, Grimm J, Vargo JA, Soltys SG, Yorke E, Jackson A, El Naqa I, Marks LB, Xue J, Heron DE, Kleinberg LR. Tumor Control Probability of Radiosurgery and Fractionated Stereotactic Radiosurgery for Brain Metastases. Int J Radiat Oncol Biol Phys. 2021 May.110(1):53-67. Pubmedid: 33390244.
• Owen DR, Sun Y, Boonstra PS, McFarlane M, Viglianti BL, Balter JM, El Naqa I, Schipper MJ, Schonewolf CA, Ten Haken RK, Kong FS, Jolly S, Matuszak MM. Investigating the SPECT Dose-Function Metrics Associated With Radiation-Induced Lung Toxicity Risk in Patients With Non-small Cell Lung Cancer Undergoing Radiation Therapy. Adv Radiat Oncol. 2021 May.6(3):100666. Pubmedid: 33817412. Pmcid: PMC8010578.
• Balagurunathan Y, Mitchell R, El Naqa I. Requirements and reliability of AI in the medical context. Phys Med. 2021 Mar.83:72-78. Pubmedid: 33721700. Pmcid: PMC8915137.
• Ba Sunbul N, Oraiqat I, Rosen B, Miller C, Meert C, Matuszak MM, Clarke S, Pozzi S, Moran JM, El Naqa I. Application of radiochromic gel dosimetry to commissioning of a megavoltage research linear accelerator for small-field animal irradiation studies. Med Phys. 2021 Mar.48(3):1404-1416. Pubmedid: 33378092. Pmcid: PMC8917956.
• Wei L, El Naqa I. Artificial Intelligence for Response Evaluation With PET/CT. Semin Nucl Med. 2021 Mar.51(2):157-169. Pubmedid: 33509372. Pmcid: PMC8099153.
• Mahajan A, Stavinoha PL, Rongthong W, Brodin NP, McGovern SL, El Naqa I, Palmer JD, Vennarini S, Indelicato DJ, Aridgides P, Bowers DC, Kremer L, Ronckers C, Constine L, Avanzo M. Neurocognitive Effects and Necrosis in Childhood Cancer Survivors Treated With Radiation Therapy: A PENTEC Comprehensive Review. Int J Radiat Oncol Biol Phys. 2021 Mar. Pubmedid: 33810950.
• Wang LM, Jung S, Serban M, Chatterjee A, Lee S, Jeyaseelan K, El Naqa I, Seuntjens J, Ybarra N. Comparison of quantitative and qualitative scoring approaches for radiation-induced pulmonary fibrosis as applied to a preliminary investigation into the efficacy of mesenchymal stem cell delivery methods in a rat model. BJR Open. 2021 Jul.2(1):20210006. Pubmedid: 34381940. Pmcid: PMC8320116.
• Cui S, Ten Haken RK, El Naqa I. Integrating Multiomics Information in Deep Learning Architectures for Joint Actuarial Outcome Prediction in Non-Small Cell Lung Cancer Patients After Radiation Therapy. Int J Radiat Oncol Biol Phys. 2021 Jul.110(3):893-904. Pubmedid: 33539966. Pmcid: PMC8180510.
• Luo Y, Jolly S, Palma D, Lawrence TS, Tseng HH, Valdes G, McShan D, Ten Haken RK, El Naqa I. A situational awareness Bayesian network approach for accurate and credible personalized adaptive radiotherapy outcomes prediction in lung cancer patients. Phys Med. 2021 Jul.87:11-23. Pubmedid: 34091197. Pmcid: PMC8284560.
• Zaidi H, El Naqa I. Quantitative Molecular Positron Emission Tomography Imaging Using Advanced Deep Learning Techniques. Annu Rev Biomed Eng. 2021 Jul.23:249-276. Pubmedid: 33797938.
• El Naqa I, Li H, Fuhrman J, Hu Q, Gorre N, Chen W, Giger ML. Lessons learned in transitioning to AI in the medical imaging of COVID-19. J Med Imaging (Bellingham). 2021 Jan.8(Suppl 1):010902. Pubmedid: 34646912. Pmcid: PMC8488974.
• Wei L, Owen D, Rosen B, Guo X, Cuneo K, Lawrence TS, Ten Haken R, El Naqa I. A deep survival interpretable radiomics model of hepatocellular carcinoma patients. Phys Med. 2021 Feb.82:295-305. Pubmedid: 33714190. Pmcid: PMC8035300.
• Tomaszewski MR, Latifi K, Boyer E, Palm RF, El Naqa I, Moros EG, Hoffe SE, Rosenberg SA, Frakes JM, Gillies RJ. Delta radiomics analysis of Magnetic Resonance guided radiotherapy imaging data can enable treatment response prediction in pancreatic cancer. Radiat Oncol. 2021 Dec.16(1):237. Pubmedid: 34911546. Pmcid: PMC8672552.
• Niraula D, Jamaluddin J, Matuszak MM, Haken RKT, Naqa IE. Quantum deep reinforcement learning for clinical decision support in oncology: application to adaptive radiotherapy. Sci Rep. 2021 Dec.11(1):23545. Pubmedid: 34876609. Pmcid: PMC8651664.
• Moiseenko V, Hattangadi-Gluth JA, Huynh-Le MP, Marks LB, Grimm J, Milano MT, Jackson A, Yorke E, Pettersson N, Naqa IE. In Reply to Schultheiss. Int J Radiat Oncol Biol Phys. 2021 Aug.110(5):1541-1543. Pubmedid: 34024669.
• Oraiqat I, Zhang W, Litzenberg D, Lam K, Ba Sunbul N, Moran J, Cuneo K, Carson P, Wang X, El Naqa I. An ionizing radiation acoustic imaging (iRAI) technique for real-time dosimetric measurements for FLASH radiotherapy. Med Phys. 2020 Oct.47(10):5090-5101. Pubmedid: 32592212. Pmcid: PMC7722001.
• Thomson DJ, Yom SS, Saeed H, El Naqa I, Ballas L, Bentzen SM, Chao ST, Choudhury A, Coles CE, Dover L, Guadagnolo BA, Guckenberger M, Hoskin P, Jabbour SK, Katz MS, Mukherjee S, Rembielak A, Sebag-Montefiore D, Sher DJ, Terezakis SA, Thomas TV, Vogel J, Estes C. Radiation Fractionation Schedules Published During the COVID-19 Pandemic: A Systematic Review of the Quality of Evidence and Recommendations for Future Development. Int J Radiat Oncol Biol Phys. 2020 Oct.108(2):379-389. Pubmedid: 32798063. Pmcid: PMC7834196.
• Zlateva Y, Muir BR, El Naqa I, Seuntjens J. Step-size effect on calculated photon and electron beam Cherenkov-to-dose conversion factors. Phys Med. 2020 Oct.78:32-37. Pubmedid: 32916557. Pmcid: PMC8957287.
• Farha M, Jairath NK, Lawrence TS, El Naqa I. Characterization of the Tumor Immune Microenvironment Identifies M0 Macrophage-Enriched Cluster as a Poor Prognostic Factor in Hepatocellular Carcinoma. JCO Clin Cancer Inform. 2020 Oct.4:1002-1013. Pubmedid: 33136432. Pmcid: PMC7713549.
• Cui S, Tseng HH, Pakela J, Ten Haken RK, El Naqa I. Introduction to machine and deep learning for medical physicists. Med Phys. 2020 Jun.47(5):e127-e147. Pubmedid: 32418339. Pmcid: PMC7331753.
• El Naqa I, Das S. The role of machine and deep learning in modern medical physics. Med Phys. 2020 Jun.47(5):e125-e126. Pubmedid: 32418342.
• Avanzo M, Wei L, Stancanello J, Vallières M, Rao A, Morin O, Mattonen SA, El Naqa I. Machine and deep learning methods for radiomics. Med Phys. 2020 Jun.47(5):e185-e202. Pubmedid: 32418336. Pmcid: PMC8965689.
• Putora PM, Baudis M, Beadle BM, El Naqa I, Giordano FA, Nicolay NH. Oncology Informatics: Status Quo and Outlook. Oncology-Basel. 2020 Jun.98(6):329-331. Pubmedid: 32408309. Pmcid: PMC8882056.
• Wilkie JR, Mierzwa ML, Casper KA, Mayo CS, Schipper MJ, Eisbruch A, Worden FP, El Naqa I, Viglianti BL, Rosen BS. Predicting late radiation-induced xerostomia with parotid gland PET biomarkers and dose metrics. Radiother Oncol. 2020 Jul.148:30-37. Pubmedid: 32311598. Pmcid: PMC8970466.
• Li H, El Naqa I, Rong Y. Current status of Radiomics for cancer management: Challenges versus opportunities for clinical practice. J Appl Clin Med Phys. 2020 Jul.21(7):7-10. Pubmedid: 32697032. Pmcid: PMC7386181.
• Pakela JM, Tseng HH, Matuszak MM, Ten Haken RK, McShan DL, El Naqa I. Quantum-inspired algorithm for radiotherapy planning optimization. Med Phys. 2020 Jan.47(1):5-18. Pubmedid: 31574176. Pmcid: PMC6980234.
• El Naqa I, Haider MA, Giger ML, Ten Haken RK. Artificial Intelligence: reshaping the practice of radiological sciences in the 21st century. Br J Radiol. 2020 Feb.93(1106):20190855. Pubmedid: 31965813. Pmcid: PMC7055429.
• Wei L, Cui C, Xu J, Kaza R, El Naqa I, Dewaraja YK. Tumor response prediction in 90Y radioembolization with PET-based radiomics features and absorbed dose metrics. EJNMMI Phys. 2020 Dec.7(1):74. Pubmedid: 33296050. Pmcid: PMC7726084.
• Kirby J, Prior F, Petrick N, Hadjiski L, Farahani K, Drukker K, Kalpathy-Cramer J, Glide-Hurst C, El Naqa I. Introduction to special issue on datasets hosted in The Cancer Imaging Archive (TCIA). Med Phys. 2020 Dec.47(12):6026-6028. Pubmedid: 33202038.
• Pursley J, El Naqa I, Sanford NN, Noe B, Wo JY, Eyler CE, Hwang M, Brock KK, Yeap BY, Wolfgang JA, Hong TS, Grassberger C. Dosimetric Analysis and Normal-Tissue Complication Probability Modeling of Child-Pugh Score and Albumin-Bilirubin Grade Increase After Hepatic Irradiation. Int J Radiat Oncol Biol Phys. 2020 Aug.107(5):986-995. Pubmedid: 32353390. Pmcid: PMC7381375.
• Cui S, Luo Y, Tseng HH, Ten Haken RK, El Naqa I. Combining handcrafted features with latent variables in machine learning for prediction of radiation-induced lung damage. Med Phys. 2019 May.46(5):2497-2511. Pubmedid: 30891794. Pmcid: PMC6510637.
• Zlateva Y, Muir BR, El Naqa I, Seuntjens JP. Cherenkov emission-based external radiotherapy dosimetry: I. Formalism and feasibility. Med Phys. 2019 May.46(5):2370-2382. Pubmedid: 31034637.
• Zlateva Y, Muir BR, Seuntjens JP, El Naqa I. Cherenkov emission-based external radiotherapy dosimetry: II. Electron beam quality specification and uncertainties. Med Phys. 2019 May.46(5):2383-2393. Pubmedid: 30706493.
• Luo Y, McShan D, Ray D, Matuszak M, Jolly S, Lawrence T, Ming Kong F, Ten Haken R, El Naqa I. Development of a Fully Cross-Validated Bayesian Network Approach for Local Control Prediction in Lung Cancer. IEEE Trans Radiat Plasma Med Sci. 2019 Mar.3(2):232-241. Pubmedid: 30854500. Pmcid: PMC6404542.
• Cui S, Luo Y, Hsin Tseng H, Ten Haken RK, El Naqa I. Artificial Neural Network with Composite Architectures for Prediction of Local Control in Radiotherapy. IEEE Trans Radiat Plasma Med Sci. 2019 Mar.3(2):242-249. Pubmedid: 30854501. Pmcid: PMC6404537.
• Avanzo M, Pirrone G, Mileto M, Massarut S, Stancanello J, Baradaran-Ghahfarokhi M, Rink A, Barresi L, Vinante L, Piccoli E, Trovo M, El Naqa I, Sartor G. Prediction of skin dose in low-kV intraoperative radiotherapy using machine learning models trained on results of in vivo dosimetry. Med Phys. 2019 Mar.46(3):1447-1454. Pubmedid: 30620412.
• Wei L, Rosen B, Vallières M, Chotchutipan T, Mierzwa M, Eisbruch A, El Naqa I. Automatic recognition and analysis of metal streak artifacts in head and neck computed tomography for radiomics modeling. Phys Imaging Radiat Oncol. 2019 Jun.10:49-54. Pubmedid: 33458268. Pmcid: PMC7807651.
• Nie K, Al-Hallaq H, Li XA, Benedict SH, Sohn JW, Moran JM, Fan Y, Huang M, Knopp MV, Michalski JM, Monroe J, Obcemea C, Tsien CI, Solberg T, Wu J, Xia P, Xiao Y, El Naqa I. NCTN Assessment on Current Applications of Radiomics in Oncology. Int J Radiat Oncol Biol Phys. 2019 Jun.104(2):302-315. Pubmedid: 30711529. Pmcid: PMC6499656.
• Cuneo KC, Devasia T, Sun Y, Schipper MJ, Karnak D, Davis MA, Owen D, Feng M, El Naqa I, Bazzi L, Ten Haken R, Lawrence TS. Serum Levels of Hepatocyte Growth Factor and CD40 Ligand Predict Radiation-Induced Liver Injury. Transl Oncol. 2019 Jul.12(7):889-894. Pubmedid: 31078059. Pmcid: PMC6514276.
• Luo Y, Tseng HH, Cui S, Wei L, Ten Haken RK, El Naqa I. Balancing accuracy and interpretability of machine learning approaches for radiation treatment outcomes modeling. BJR Open. 2019 Jul.1(1):20190021. Pubmedid: 33178948. Pmcid: PMC7592485.
• Chotchutipan T, Rosen BS, Hawkins PG, Lee JY, Saripalli AL, Thakkar D, Eisbruch A, El Naqa I, Mierzwa ML. Volumetric 18 F-FDG-PET parameters as predictors of locoregional failure in low-risk HPV-related oropharyngeal cancer after definitive chemoradiation therapy. Head Neck. 2019 Feb.41(2):366-373. Pubmedid: 30548704. Pmcid: PMC6411288.
• Deist TM, Dankers FJWM, Valdes G, Wijsman R, Hsu IC, Oberije C, Lustberg T, van Soest J, Hoebers F, Jochems A, El Naqa I, Wee L, Morin O, Raleigh DR, Bots W, Kaanders JH, Belderbos J, Kwint M, Solberg T, Monshouwer R, Bussink J, Dekker A, Lambin P. Erratum: "Machine learning algorithms for outcome prediction in (chemo)radiotherapy: An empirical comparison of classifiers" [Med. Phys. 45 (7), 3449-3459 (2018)]. Med Phys. 2019 Feb.46(2):1080-1087. Pubmedid: 30730570.
• Waninger JJ, Green MD, Cheze Le Rest C, Rosen B, El Naqa I. Integrating radiomics into clinical trial design. Q J Nucl Med Mol Imaging. 2019 Dec.63(4):339-346. Pubmedid: 31527581.
• Wei L, Osman S, Hatt M, El Naqa I. Machine learning for radiomics-based multimodality and multiparametric modeling. Q J Nucl Med Mol Imaging. 2019 Dec.63(4):323-338. Pubmedid: 31527580.
• Veit-Haibach P, El Naqa I, Visvikis D. Radiomics in nuclear medicine and hybrid imaging: current standings on clinical applicability. Q J Nucl Med Mol Imaging. 2019 Dec.63(4):321-322. Pubmedid: 31560184.
• Oraiqat I, DeBruin S, Pearce R, Como C, Mikell J, Taylor C, Way J, Suarez M, Rehemtulla A, Clarke R, El Naqa I. Silicon Photomultipliers for Deep Tissue Cerenkov Emission Detection During External Beam Radiotherapy. IEEE Photonics J. 2019 Aug.11(4). Pubmedid: 33747354. Pmcid: PMC7971172.
• El Naqa I, Irrer J, Ritter TA, DeMarco J, Al-Hallaq H, Booth J, Kim G, Alkhatib A, Popple R, Perez M, Farrey K, Moran JM. Machine learning for automated quality assurance in radiotherapy: A proof of principle using EPID data description. Med Phys. 2019 Apr.46(4):1914-1921. Pubmedid: 30734324.
• Deng J, El Naqa I, Xing L. Editorial: Machine Learning With Radiation Oncology Big Data. Front Oncol. 2018 Sep.8:416. Pubmedid: 30319978. Pmcid: PMC6170661.
• El Naqa I, Ten Haken RK. Can radiomics personalise immunotherapy?. Lancet Oncol. 2018 Sep.19(9):1138-1139. Pubmedid: 30120042.
• El Naqa I, Napel S, Zaidi H. Radiogenomics is the future of treatment response assessment in clinical oncology. Med Phys. 2018 Oct.45(10):4325-4328. Pubmedid: 29863785. Pmcid: PMC9560777.
• El Naqa I, Ruan D, Valdes G, Dekker A, McNutt T, Ge Y, Wu QJ, Oh JH, Thor M, Smith W, Rao A, Fuller C, Xiao Y, Manion F, Schipper M, Mayo C, Moran JM, Ten Haken R. Machine learning and modeling: Data, validation, communication challenges. Med Phys. 2018 Oct.45(10):e834-e840. Pubmedid: 30144098. Pmcid: PMC6181755.
• Tseng HH, Wei L, Cui S, Luo Y, Ten Haken RK, El Naqa I. Machine Learning and Imaging Informatics in Oncology. Oncology-Basel. 2018 Nov.98(6):344-362. Pubmedid: 30472716. Pmcid: PMC6533165.
• Owen DR, Boonstra PS, Viglianti BL, Balter JM, Schipper MJ, Jackson WC, El Naqa I, Jolly S, Ten Haken RK, Kong FS, Matuszak MM. Modeling Patient-Specific Dose-Function Response for Enhanced Characterization of Personalized Functional Damage. Int J Radiat Oncol Biol Phys. 2018 Nov.102(4):1265-1275. Pubmedid: 30108006. Pmcid: PMC6202237.
• El Naqa I, Pandey G, Aerts H, Chien JT, Andreassen CN, Niemierko A, Ten Haken RK. Radiation Therapy Outcomes Models in the Era of Radiomics and Radiogenomics: Uncertainties and Validation. Int J Radiat Oncol Biol Phys. 2018 Nov.102(4):1070-1073. Pubmedid: 30353869. Pmcid: PMC7405918.
• Rosen BS, Hawkins PG, Polan DF, Balter JM, Brock KK, Kamp JD, Lockhart CM, Eisbruch A, Mierzwa ML, Ten Haken RK, El Naqa I. Early Changes in Serial CBCT-Measured Parotid Gland Biomarkers Predict Chronic Xerostomia After Head and Neck Radiation Therapy. Int J Radiat Oncol Biol Phys. 2018 Nov.102(4):1319-1329. Pubmedid: 30003997. Pmcid: PMC6411287.
• Milano MT, Sharma M, Soltys SG, Sahgal A, Usuki KY, Saenz JM, Grimm J, El Naqa I. Radiation-Induced Edema After Single-Fraction or Multifraction Stereotactic Radiosurgery for Meningioma: A Critical Review. Int J Radiat Oncol Biol Phys. 2018 Jun.101(2):344-357. Pubmedid: 29726362.
• Lei H, Zhang W, Oraiqat I, Liu Z, Ni J, Wang X, El Naqa I. Toward in vivo dosimetry in external beam radiotherapy using x-ray acoustic computed tomography: A soft-tissue phantom study validation. Med Phys. 2018 Jun. Pubmedid: 29956335.
• Luo Y, McShan DL, Matuszak MM, Ray D, Lawrence TS, Jolly S, Kong FM, Ten Haken RK, El Naqa I. A multiobjective Bayesian networks approach for joint prediction of tumor local control and radiation pneumonitis in nonsmall-cell lung cancer (NSCLC) for response-adapted radiotherapy. Med Phys. 2018 Jun. Pubmedid: 29862533. Pmcid: PMC6279602.
• Deist TM, Dankers FJWM, Valdes G, Wijsman R, Hsu IC, Oberije C, Lustberg T, van Soest J, Hoebers F, Jochems A, El Naqa I, Wee L, Morin O, Raleigh DR, Bots W, Kaanders JH, Belderbos J, Kwint M, Solberg T, Monshouwer R, Bussink J, Dekker A, Lambin P. Machine learning algorithms for outcome prediction in (chemo)radiotherapy: An empirical comparison of classifiers. Med Phys. 2018 Jul.45(7):3449-3459. Pubmedid: 29763967. Pmcid: PMC6095141.
• Tseng HH, Luo Y, Ten Haken RK, El Naqa I. The Role of Machine Learning in Knowledge-Based Response-Adapted Radiotherapy. Front Oncol. 2018 Jul.8:266. Pubmedid: 30101124. Pmcid: PMC6072876.
• Hickling S, Xiang L, Jones KC, Parodi K, Assmann W, Avery S, Hobson M, El Naqa I. Ionizing radiation-induced acoustics for radiotherapy and diagnostic radiology applications. Med Phys. 2018 Jul.45(7):e707-e721. Pubmedid: 29679491.
• El Naqa I, Brock K, Yu Y, Langen K, Klein EE. On the Fuzziness of Machine Learning, Neural Networks, and Artificial Intelligence in Radiation Oncology. Int J Radiat Oncol Biol Phys. 2018 Jan.100(1):1-4. Pubmedid: 29254765.
• El Naqa I, Johansson A, Owen D, Cuneo K, Cao Y, Matuszak M, Bazzi L, Lawrence TS, Ten Haken RK. Modeling of Normal Tissue Complications Using Imaging and Biomarkers After Radiation Therapy for Hepatocellular Carcinoma. Int J Radiat Oncol Biol Phys. 2018 Feb.100(2):335-343. Pubmedid: 29353652. Pmcid: PMC5779633.
• Jochems A, El-Naqa I, Kessler M, Mayo CS, Jolly S, Matuszak M, Faivre-Finn C, Price G, Holloway L, Vinod S, Field M, Barakat MS, Thwaites D, de Ruysscher D, Dekker A, Lambin P. A prediction model for early death in non-small cell lung cancer patients following curative-intent chemoradiotherapy. Acta Oncol. 2018 Feb.57(2):226-230. Pubmedid: 29034756. Pmcid: PMC6108087.
• Vallières M, Serban M, Benzyane I, Ahmed Z, Xing S, El Naqa I, Levesque IR, Seuntjens J, Freeman CR. Investigating the role of functional imaging in the management of soft-tissue sarcomas of the extremities. Phys Imaging Radiat Oncol. 2018 Apr.6:53-60. Pubmedid: 33458389. Pmcid: PMC7807871.
• Jochems A, Deist TM, El Naqa I, Kessler M, Mayo C, Reeves J, Jolly S, Matuszak M, Ten Haken R, van Soest J, Oberije C, Faivre-Finn C, Price G, de Ruysscher D, Lambin P, Dekker A. Developing and Validating a Survival Prediction Model for NSCLC Patients Through Distributed Learning Across 3 Countries. Int J Radiat Oncol Biol Phys. 2017 Oct.99(2):344-352. Pubmedid: 28871984. Pmcid: PMC5575360.
• Vallières M, Laberge S, Diamant A, El Naqa I. Enhancement of multimodality texture-based prediction models via optimization of PET and MR image acquisition protocols: a proof of concept. Phys Med Biol. 2017 Oct.62(22):8536-8565. Pubmedid: 28872054.
• Avanzo M, Stancanello J, El Naqa I. Beyond imaging: The promise of radiomics. Phys Med. 2017 Jun.38:122-139. Pubmedid: 28595812.
• Perez JR, Ybarra N, Chagnon F, Serban M, Lee S, Seuntjens J, Lesur O, El Naqa I. Tracking of Mesenchymal Stem Cells with Fluorescence Endomicroscopy Imaging in Radiotherapy-Induced Lung Injury. Sci Rep. 2017 Jan.7:40748. Pubmedid: 28102237. Pmcid: PMC5244404.
• Hickling S, Lei H, Hobson M, Léger P, Wang X, El Naqa I. Experimental evaluation of x-ray acoustic computed tomography for radiotherapy dosimetry applications. Med Phys. 2017 Feb.44(2):608-617. Pubmedid: 28121381.
• Liu F, Tai A, Lee P, Biswas T, Ding GX, El Naqa I, Grimm J, Jackson A, Kong FS, LaCouture T, Loo B, Miften M, Solberg T, Li XA. Tumor control probability modeling for stereotactic body radiation therapy of early-stage lung cancer using multiple bio-physical models. Radiother Oncol. 2017 Feb.122(2):286-294. Pubmedid: 27871671. Pmcid: PMC5649355.
• Constanzo J, Wei L, Tseng HH, El Naqa I. Radiomics in precision medicine for lung cancer. Transl Lung Cancer Res. 2017 Dec.6(6):635-647. Pubmedid: 29218267. Pmcid: PMC5709132.
• Tseng HH, Luo Y, Cui S, Chien JT, Ten Haken RK, Naqa IE. Deep reinforcement learning for automated radiation adaptation in lung cancer. Med Phys. 2017 Dec.44(12):6690-6705. Pubmedid: 29034482. Pmcid: PMC5734677.
• Berthon B, Spezi E, Galavis P, Shepherd T, Apte A, Hatt M, Fayad H, De Bernardi E, Soffientini CD, Ross Schmidtlein C, El Naqa I, Jeraj R, Lu W, Das S, Zaidi H, Mawlawi OR, Visvikis D, Lee JA, Kirov AS. Toward a standard for the evaluation of PET-Auto-Segmentation methods following the recommendations of AAPM task group No. 211: Requirements and implementation. Med Phys. 2017 Aug.44(8):4098-4111. Pubmedid: 28474819. Pmcid: PMC5575543.
• Vallières M, Kay-Rivest E, Perrin LJ, Liem X, Furstoss C, Aerts HJWL, Khaouam N, Nguyen-Tan PF, Wang CS, Sultanem K, Seuntjens J, El Naqa I. Radiomics strategies for risk assessment of tumour failure in head-and-neck cancer. Sci Rep. 2017 Aug.7(1):10117. Pubmedid: 28860628. Pmcid: PMC5579274.
• El Naqa I, Kerns SL, Coates J, Luo Y, Speers C, West CML, Rosenstein BS, Ten Haken RK. Radiogenomics and radiotherapy response modeling. Phys Med Biol. 2017 Aug.62(16):R179-R206. Pubmedid: 28657906. Pmcid: PMC5557376.
• Luo Y, El Naqa I, McShan DL, Ray D, Lohse I, Matuszak MM, Owen D, Jolly S, Lawrence TS, Kong FS, Ten Haken RK. Unraveling biophysical interactions of radiation pneumonitis in non-small-cell lung cancer via Bayesian network analysis. Radiother Oncol. 2017 Apr.123(1):85-92. Pubmedid: 28237401. Pmcid: PMC5386796.
• Markel D, Levesque I, Larkin J, Léger P, El Naqa I. A 4D biomechanical lung phantom for joint segmentation/registration evaluation. Phys Med Biol. 2016 Oct.61(19):7012-7030. Pubmedid: 27649100.
• Sapir E, Tao Y, Feng F, Samuels S, El Naqa I, Murdoch-Kinch CA, Feng M, Schipper M, Eisbruch A. Predictors of Dysgeusia in Patients With Oropharyngeal Cancer Treated With Chemotherapy and Intensity Modulated Radiation Therapy. Int J Radiat Oncol Biol Phys. 2016 Oct.96(2):354-361. Pubmedid: 27473816.
• Mayo CS, Kessler ML, Eisbruch A, Weyburne G, Feng M, Hayman JA, Jolly S, El Naqa I, Moran JM, Matuszak MM, Anderson CJ, Holevinski LP, McShan DL, Merkel SM, Machnak SL, Lawrence TS, Ten Haken RK. The big data effort in radiation oncology: Data mining or data farming?. Adv Radiat Oncol. 2016 Oct.1(4):260-271. Pubmedid: 28740896. Pmcid: PMC5514231.
• Pater P, Bäckstöm G, Villegas F, Ahnesjö A, Enger SA, Seuntjens J, El Naqa I. Proton and light ion RBE for the induction of direct DNA double strand breaks. Med Phys. 2016 May.43(5):2131. Pubmedid: 27147325.
• Hickling S, Leger P, El Naqa I. On the Detectability of Acoustic Waves Induced Following Irradiation by a Radiotherapy Linear Accelerator. Ieee Trans Ultrason Ferroelectr Freq Control. 2016 May.63(5):683-690. Pubmedid: 26886983.
• Coates J, El Naqa I. Outcome modeling techniques for prostate cancer radiotherapy: Data, models, and validation. Phys Med. 2016 Mar.32(3):512-520. Pubmedid: 27053448.
• Ohri N, Duan F, Snyder BS, Wei B, Machtay M, Alavi A, Siegel BA, Johnson DW, Bradley JD, DeNittis A, Werner-Wasik M, El Naqa I. Pretreatment 18F-FDG PET Textural Features in Locally Advanced Non-Small Cell Lung Cancer: Secondary Analysis of ACRIN 6668/RTOG 0235. J Nucl Med. 2016 Jun.57(6):842-848. Pubmedid: 26912429. Pmcid: PMC4987286.
• Coates J, Souhami L, El Naqa I. Big Data Analytics for Prostate Radiotherapy. Front Oncol. 2016 Jun.6:149. Pubmedid: 27379211. Pmcid: PMC4905980.
• Benedict SH, El Naqa I, Klein EE. Introduction to Big Data in Radiation Oncology: Exploring Opportunities for Research, Quality Assessment, and Clinical Care. Int J Radiat Oncol Biol Phys. 2016 Jul.95(3):871-872. Pubmedid: 27302502.
• Sloan JA, Halyard M, El Naqa I, Mayo C. Lessons From Large-Scale Collection of Patient-Reported Outcomes: Implications for Big Data Aggregation and Analytics. Int J Radiat Oncol Biol Phys. 2016 Jul.95(3):922-929. Pubmedid: 27302508. Pmcid: PMC6544440.
• El Naqa I. Perspectives on making big data analytics work for oncology. Methods. 2016 Dec.111:32-44. Pubmedid: 27586524.
• Maria OM, Maria AM, Ybarra N, Jeyaseelan K, Lee S, Perez J, Shalaby MY, Lehnert S, Faria S, Serban M, Seuntjens J, El Naqa I. Mesenchymal Stem Cells Adopt Lung Cell Phenotype in Normal and Radiation-induced Lung Injury Conditions. Appl Immunohistochem Mol Morphol. 2016 Apr.24(4):283-295. Pubmedid: 26200842.
• Lim K, Erickson B, Jürgenliemk-Schulz IM, Gaffney D, Creutzberg CL, Viswanathan A, Portelance L, Beriwal S, Wolfson A, Bosch W, De Los Santos J, Yashar C, Jhingran A, Varia M, El Naqa I, King B, Fyles A. Variability in clinical target volume delineation for intensity modulated radiation therapy in 3 challenging cervix cancer scenarios. Pract Radiat Oncol. 2015 Nov.5(6):e557-e565. Pubmedid: 26432679. Pmcid: PMC4884648.
• Lee S, Ybarra N, Jeyaseelan K, Faria S, Kopek N, Brisebois P, Bradley JD, Robinson C, Seuntjens J, El Naqa I. Bayesian network ensemble as a multivariate strategy to predict radiation pneumonitis risk. Med Phys. 2015 May.42(5):2421-2430. Pubmedid: 25979036.
• Després P, Beaulieu L, El Naqa I, Seuntjens J. Special section: Selected papers from the Fifth International Workshop on Monte Carlo Techniques in Medical Physics. Phys Med Biol. 2015 Jul.60(13):4947-4950. Pubmedid: 26061970.
• Vallières M, Freeman CR, Skamene SR, El Naqa I. A radiomics model from joint FDG-PET and MRI texture features for the prediction of lung metastases in soft-tissue sarcomas of the extremities. Phys Med Biol. 2015 Jul.60(14):5471-5496. Pubmedid: 26119045.
• Hatt M, Majdoub M, Vallières M, Tixier F, Le Rest CC, Groheux D, Hindié E, Martineau A, Pradier O, Hustinx R, Perdrisot R, Guillevin R, El Naqa I, Visvikis D. 18F-FDG PET uptake characterization through texture analysis: investigating the complementary nature of heterogeneity and functional tumor volume in a multi-cancer site patient cohort. J Nucl Med. 2015 Jan.56(1):38-44. Pubmedid: 25500829.
• Klein EE, El Naqa I, Langen K, Dogan N. Physics: The Use of Magnetic Resonance Imaging for Radiation Therapy is Accelerating in Utility and Novelty. Int J Radiat Oncol Biol Phys. 2015 Dec.93(5):953-956. Pubmedid: 26581131.
• Coates J, Jeyaseelan AK, Ybarra N, David M, Faria S, Souhami L, Cury F, Duclos M, El Naqa I. Contrasting analytical and data-driven frameworks for radiogenomic modeling of normal tissue toxicities in prostate cancer. Radiother Oncol. 2015 Apr.115(1):107-113. Pubmedid: 25818395.
• Coates J, Ybarra N, El Naqa I. Non-invasive whole-body plethysmograph for assessment and prediction of radiation-induced lung injury using simultaneously acquired nitric oxide and lung volume measurements. Physiol Meas. 2014 Sep.35(9):1737-1750. Pubmedid: 25119582.
• Johnson ME, Pereira GC, El Naqa IM, Goddu SM, Al-Lozi R, Apte A, Mansur DB. Determination of planning target volume for whole stomach irradiation using daily megavoltage computed tomographic images. Pract Radiat Oncol. 2014 Mar.2(4):e85-e88. Pubmedid: 24674190.
• Pater P, Seuntjens J, El Naqa I, Bernal MA. On the consistency of Monte Carlo track structure DNA damage simulations. Med Phys. 2014 Dec.41(12):121708. Pubmedid: 25471955.
• Robinson CG, DeWees TA, El Naqa IM, Creach KM, Olsen JR, Crabtree TD, Meyers BF, Puri V, Bell JM, Parikh PJ, Bradley JD. Patterns of failure after stereotactic body radiation therapy or lobar resection for clinical stage I non-small-cell lung cancer. J Thorac Oncol. 2013 Feb.8(2):192-201. Pubmedid: 23287852.
• Markel D, Zaidi H, El Naqa I. Novel multimodality segmentation using level sets and Jensen-Rényi divergence. Med Phys. 2013 Dec.40(12):121908. Pubmedid: 24320519.
• White B, Zhao T, Lamb J, Wuenschel S, Bradley J, El Naqa I, Low D. Distribution of lung tissue hysteresis during free breathing. Med Phys. 2013 Apr.40(4):043501. Pubmedid: 23556925. Pmcid: PMC3612117.
• Kidd EA, El Naqa I, Siegel BA, Dehdashti F, Grigsby PW. FDG-PET-based prognostic nomograms for locally advanced cervical cancer. Gynecol Oncol. 2012 Oct.127(1):136-140. Pubmedid: 22735785. Pmcid: PMC3991305.
• Zaidi H, Abdoli M, Fuentes CL, El Naqa IM. Comparative methods for PET image segmentation in pharyngolaryngeal squamous cell carcinoma. Eur J Nucl Med Mol Imaging. 2012 May.39(5):881-891. Pubmedid: 22289958. Pmcid: PMC3326239.
• Pater P, Bernal M, Naqa IE, Seuntjens J. SU-E-T-05: Comparing DNA Strand Break Yields for Photons under Different Irradiation Conditions with Geant4-DNA. Med Phys. 2012 Jun.39(6Part9):3703. Pubmedid: 28519038.
• Seuntjens J, Beaulieu L, El Naqa I, Després P. Special section: Selected papers from the Fourth International Workshop on Recent Advances in Monte Carlo Techniques for Radiation Therapy. Phys Med Biol. 2012 Jun.57(11). Pubmedid: 22764369.
• Lee S, Stroian G, Kopek N, AlBahhar M, Seuntjens J, El Naqa I. Analytical modelling of regional radiotherapy dose response of lung. Phys Med Biol. 2012 Jun.57(11):3309-3321. Pubmedid: 22572393.
• Markel D, Naqa IE, Freeman C, Vallières M. SU-E-J-110: A Novel Level Set Active Contour Algorithm for Multimodality Joint Segmentation/Registration Using the Jensen-Rényi Divergence. Med Phys. 2012 Jun.39(6Part7):3678. Pubmedid: 28519785.
• Vallières M, Freeman CR, Skamene SR, Naqa IE. SU-D-BRB-03: Prediction of Tumor Outcomes Through Wavelet Image Fusion and Texture Analysis of PET/MR Imaging. Med Phys. 2012 Jun.39(6Part3):3615. Pubmedid: 28517427.
• Watson P, Mainegra-Hing E, Soisson E, Naqa IE, Seuntjens J. SU-E-I-04: Implementation of a Fast Monte Carlo Scatter Correction for Cone- Beam Computed Tomography. Med Phys. 2012 Jun.39(6Part4):3625. Pubmedid: 28519491.
• El Naqa I, Pater P, Seuntjens J. Monte Carlo role in radiobiological modelling of radiotherapy outcomes. Phys Med Biol. 2012 Jun.57(11):R75-R97. Pubmedid: 22571871.
• Markel D, Naqa IE. WE-E-213CD-08: A Novel Level Set Active Contour Algorithm Using the Jensen-Renyi Divergence for Tumor Segmentation in PET. Med Phys. 2012 Jun.39(6Part27):3961. Pubmedid: 28519993.
• Creach KM, El Naqa I, Bradley JD, Olsen JR, Parikh PJ, Drzymala RE, Bloch C, Robinson CG. Dosimetric predictors of chest wall pain after lung stereotactic body radiotherapy. Radiother Oncol. 2012 Jul.104(1):23-27. Pubmedid: 22385795.
• Gay HA, Barthold HJ, O'Meara E, Bosch WR, El Naqa I, Al-Lozi R, Rosenthal SA, Lawton C, Lee WR, Sandler H, Zietman A, Myerson R, Dawson LA, Willett C, Kachnic LA, Jhingran A, Portelance L, Ryu J, Small W, Gaffney D, Viswanathan AN, Michalski JM. Pelvic normal tissue contouring guidelines for radiation therapy: a Radiation Therapy Oncology Group consensus panel atlas. Int J Radiat Oncol Biol Phys. 2012 Jul.83(3):e353-e362. Pubmedid: 22483697. Pmcid: PMC3904368.
• Watson P, Mainegra-Hing E, Soisson E, Naqa IE, Seuntjens J. Sci-Fri PM: Delivery - 12: Scatter-B-Gon: Implementing a fast Monte Carlo cone-beam computed tomography scatter correction on real data. Med Phys. 2012 Jul.39(7Part4):4644. Pubmedid: 28516651.
• Vaidya M, Creach KM, Frye J, Dehdashti F, Bradley JD, El Naqa I. Combined PET/CT image characteristics for radiotherapy tumor response in lung cancer. Radiother Oncol. 2012 Feb.102(2):239-245. Pubmedid: 22098794.
• Huang EX, Bradley JD, El Naqa I, Hope AJ, Lindsay PE, Bosch WR, Matthews JW, Sause WT, Graham MV, Deasy JO. Modeling the risk of radiation-induced acute esophagitis for combined Washington University and RTOG trial 93-11 lung cancer patients. Int J Radiat Oncol Biol Phys. 2012 Apr.82(5):1674-1679. Pubmedid: 21658856. Pmcid: PMC3783997.
• Olsen JR, Robinson CG, El Naqa I, Creach KM, Drzymala RE, Bloch C, Parikh PJ, Bradley JD. Dose-response for stereotactic body radiotherapy in early-stage non-small-cell lung cancer. Int J Radiat Oncol Biol Phys. 2011 Nov.81(4):e299-e303. Pubmedid: 21477948.
• White BM, Low DA, Zhao T, Wuenschel S, Lu W, Lamb JM, Mutic S, Bradley JD, El Naqa I. Investigation of a breathing surrogate prediction algorithm for prospective pulmonary gating. Med Phys. 2011 Mar.38(3):1587-1595. Pubmedid: 21520870. Pmcid: PMC3060936.
• Oh JH, Craft JM, Townsend R, Deasy JO, Bradley JD, El Naqa I. A bioinformatics approach for biomarker identification in radiation-induced lung inflammation from limited proteomics data. J Proteome Res. 2011 Mar.10(3):1406-1415. Pubmedid: 21226504. Pmcid: PMC3127583.
• Oh JH, Craft J, Al Lozi R, Vaidya M, Meng Y, Deasy JO, Bradley JD, El Naqa I. A Bayesian network approach for modeling local failure in lung cancer. Phys Med Biol. 2011 Mar.56(6):1635-1651. Pubmedid: 21335651. Pmcid: PMC4646092.
• Perkins SM, Rubin JB, Leonard JR, Smyth MD, El Naqa I, Michalski JM, Simpson JR, Limbrick DL, Park TS, Mansur DB. Glioblastoma in children: a single-institution experience. Int J Radiat Oncol Biol Phys. 2011 Jul.80(4):1117-1121. Pubmedid: 21220190.
• Yang D, Brame S, El Naqa I, Aditya A, Wu Y, Goddu SM, Mutic S, Deasy JO, Low DA. Technical note: DIRART--A software suite for deformable image registration and adaptive radiotherapy research. Med Phys. 2011 Jan.38(1):67-77. Pubmedid: 21361176. Pmcid: PMC3017581.
• Huang EX, Hope AJ, Lindsay PE, Trovo M, El Naqa I, Deasy JO, Bradley JD. Heart irradiation as a risk factor for radiation pneumonitis. Acta Oncol. 2011 Jan.50(1):51-60. Pubmedid: 20874426. Pmcid: PMC4041523.
• Lim K, Small W, Portelance L, Creutzberg C, Jürgenliemk-Schulz IM, Mundt A, Mell LK, Mayr N, Viswanathan A, Jhingran A, Erickson B, De los Santos J, Gaffney D, Yashar C, Beriwal S, Wolfson A, Taylor A, Bosch W, El Naqa I, Fyles A. Consensus guidelines for delineation of clinical target volume for intensity-modulated pelvic radiotherapy for the definitive treatment of cervix cancer. Int J Radiat Oncol Biol Phys. 2011 Feb.79(2):348-355. Pubmedid: 20472347.
• Wang D, Bosch W, Kirsch DG, Al Lozi R, El Naqa I, Roberge D, Finkelstein SE, Petersen I, Haddock M, Chen YL, Saito NG, Hitchcock YJ, Wolfson AH, DeLaney TF. Variation in the gross tumor volume and clinical target volume for preoperative radiotherapy of primary large high-grade soft tissue sarcoma of the extremity among RTOG sarcoma radiation oncologists. Int J Radiat Oncol Biol Phys. 2011 Dec.81(5):e775-e780. Pubmedid: 21277104. Pmcid: PMC3099246.
• Mutic S, Brame RS, Oddiraju S, Parikh P, Westfall MA, Hopkins ML, Medina AD, Danieley JC, Michalski JM, El Naqa IM, Low DA, Wu B. Event (error and near-miss) reporting and learning system for process improvement in radiation oncology. Med Phys. 2010 Sep.37(9):5027-5036. Pubmedid: 20964222.
• Chen R, Parry JJ, Akers WJ, Berezin MY, El Naqa IM, Achilefu S, Edwards WB, Rogers BE. Multimodality imaging of gene transfer with a receptor-based reporter gene. J Nucl Med. 2010 Sep.51(9):1456-1463. Pubmedid: 20720053. Pmcid: PMC2981350.
• Zaidi H, El Naqa I. PET-guided delineation of radiation therapy treatment volumes: a survey of image segmentation techniques. Eur J Nucl Med Mol Imaging. 2010 Nov.37(11):2165-2187. Pubmedid: 20336455.
• Lawrence YR, Li XA, El Naqa I, Hahn CA, Marks LB, Merchant TE, Dicker AP. Radiation dose-volume effects in the brain. Int J Radiat Oncol Biol Phys. 2010 Mar.76(3 Suppl):S20-S27. Pubmedid: 20171513. Pmcid: PMC3554255.
• Roach M, Nam J, Gagliardi G, El Naqa I, Deasy JO, Marks LB. Radiation dose-volume effects and the penile bulb. Int J Radiat Oncol Biol Phys. 2010 Mar.76(3 Suppl):S130-S134. Pubmedid: 20171507. Pmcid: PMC4786051.
• Marks LB, Bentzen SM, Deasy JO, Kong FM, Bradley JD, Vogelius IS, El Naqa I, Hubbs JL, Lebesque JV, Timmerman RD, Martel MK, Jackson A. Radiation dose-volume effects in the lung. Int J Radiat Oncol Biol Phys. 2010 Mar.76(3 Suppl):S70-S76. Pubmedid: 20171521. Pmcid: PMC3576042.
• Bradley JD, El Naqa I, Drzymala RE, Trovo M, Jones G, Denning MD. Stereotactic body radiation therapy for early-stage non-small-cell lung cancer: the pattern of failure is distant. Int J Radiat Oncol Biol Phys. 2010 Jul.77(4):1146-1150. Pubmedid: 19800181.
• Trovo M, Linda A, El Naqa I, Javidan-Nejad C, Bradley J. Early and late lung radiographic injury following stereotactic body radiation therapy (SBRT). Lung Cancer. 2010 Jul.69(1):77-85. Pubmedid: 19910075.
• Yang D, Goddu SM, Lu W, Pechenaya OL, Wu Y, Deasy JO, El Naqa I, Low DA. Technical note: deformable image registration on partially matched images for radiotherapy applications. Med Phys. 2010 Jan.37(1):141-145. Pubmedid: 20175475. Pmcid: PMC4108644.
• Michalski JM, Lawton C, El Naqa I, Ritter M, O'Meara E, Seider MJ, Lee WR, Rosenthal SA, Pisansky T, Catton C, Valicenti RK, Zietman AL, Bosch WR, Sandler H, Buyyounouski MK, Ménard C. Development of RTOG consensus guidelines for the definition of the clinical target volume for postoperative conformal radiation therapy for prostate cancer. Int J Radiat Oncol Biol Phys. 2010 Feb.76(2):361-368. Pubmedid: 19394158. Pmcid: PMC2847420.
• Allozi R, Li XA, White J, Apte A, Tai A, Michalski JM, Bosch WR, El Naqa I. Tools for consensus analysis of experts' contours for radiotherapy structure definitions. Radiother Oncol. 2010 Dec.97(3):572-578. Pubmedid: 20708285. Pmcid: PMC3116271.
• Dehing-Oberije C, De Ruysscher D, Petit S, Van Meerbeeck J, Vandecasteele K, De Neve W, Dingemans AM, El Naqa I, Deasy J, Bradley J, Huang E, Lambin P. Development, external validation and clinical usefulness of a practical prediction model for radiation-induced dysphagia in lung cancer patients. Radiother Oncol. 2010 Dec.97(3):455-461. Pubmedid: 21084125.
• Crabtree TD, Denlinger CE, Meyers BF, El Naqa I, Zoole J, Krupnick AS, Kreisel D, Patterson GA, Bradley JD. Stereotactic body radiation therapy versus surgical resection for stage I non-small cell lung cancer. J Thorac Cardiovasc Surg. 2010 Aug.140(2):377-386. Pubmedid: 20400121.
• Oh JH, Yang Y, El Naqa I. Adaptive learning for relevance feedback: application to digital mammography. Med Phys. 2010 Aug.37(8):4432-4444. Pubmedid: 20879602. Pmcid: PMC2927692.
• El Naqa I, Bradley JD, Lindsay PE, Hope AJ, Deasy JO. Predicting radiotherapy outcomes using statistical learning techniques. Phys Med Biol. 2009 Sep.54(18):S9-S30. Pubmedid: 19687564. Pmcid: PMC4041524.
• Hu X, Macdonald DM, Huettner PC, Feng Z, El Naqa IM, Schwarz JK, Mutch DG, Grigsby PW, Powell SN, Wang X. A miR-200 microRNA cluster as prognostic marker in advanced ovarian cancer. Gynecol Oncol. 2009 Sep.114(3):457-464. Pubmedid: 19501389.
• Spencer SJ, Bonnin DA, Deasy JO, Bradley JD, El Naqa I. Bioinformatics methods for learning radiation-induced lung inflammation from heterogeneous retrospective and prospective data. J Biomed Biotechnol. 2009 Oct.2009:892863. Pubmedid: 19704920. Pmcid: PMC2688763.
• Goddu SM, Yaddanapudi S, Pechenaya OL, Chaudhari SR, Klein EE, Khullar D, El Naqa I, Mutic S, Wahab S, Santanam L, Zoberi I, Low DA. Dosimetric consequences of uncorrected setup errors in helical Tomotherapy treatments of breast-cancer patients. Radiother Oncol. 2009 Oct.93(1):64-70. Pubmedid: 19733408.
• Tang J, Rangayyan RM, Xu J, El Naqa I, Yang Y. Computer-aided detection and diagnosis of breast cancer with mammography: recent advances. Ieee Trans Inf Technol Biomed. 2009 Mar.13(2):236-251. Pubmedid: 19171527.
• Lawton CA, Michalski J, El-Naqa I, Buyyounouski MK, Lee WR, Menard C, O'Meara E, Rosenthal SA, Ritter M, Seider M. RTOG GU Radiation oncology specialists reach consensus on pelvic lymph node volumes for high-risk prostate cancer. Int J Radiat Oncol Biol Phys. 2009 Jun.74(2):383-387. Pubmedid: 18947938. Pmcid: PMC2905150.
• Lawton CA, Michalski J, El-Naqa I, Kuban D, Lee WR, Rosenthal SA, Zietman A, Sandler H, Shipley W, Ritter M, Valicenti R, Catton C, Roach M, Pisansky TM, Seider M. Variation in the definition of clinical target volumes for pelvic nodal conformal radiation therapy for prostate cancer. Int J Radiat Oncol Biol Phys. 2009 Jun.74(2):377-382. Pubmedid: 18947941. Pmcid: PMC2905162.
• El Naqa I, Grigsby P, Apte A, Kidd E, Donnelly E, Khullar D, Chaudhari S, Yang D, Schmitt M, Laforest R, Thorstad W, Deasy JO. Exploring feature-based approaches in PET images for predicting cancer treatment outcomes. Pattern Recognit. 2009 Jun.42(6):1162-1171. Pubmedid: 20161266. Pmcid: PMC2701316.
• Brankov JG, Yang Y, Wei L, El Naqa I, Wernick MN. Learning a channelized observer for image quality assessment. Ieee T Med Imaging. 2009 Jul.28(7):991-999. Pubmedid: 19211351. Pmcid: PMC2826509.
• Myerson RJ, Garofalo MC, El Naqa I, Abrams RA, Apte A, Bosch WR, Das P, Gunderson LL, Hong TS, Kim JJ, Willett CG, Kachnic LA. Elective clinical target volumes for conformal therapy in anorectal cancer: a radiation therapy oncology group consensus panel contouring atlas. Int J Radiat Oncol Biol Phys. 2009 Jul.74(3):824-830. Pubmedid: 19117696. Pmcid: PMC2709288.
• Yang D, Chaudhari SR, Goddu SM, Pratt D, Khullar D, Deasy JO, El Naqa I. Deformable registration of abdominal kilovoltage treatment planning CT and tomotherapy daily megavoltage CT for treatment adaptation. Med Phys. 2009 Feb.36(2):329-338. Pubmedid: 19291972. Pmcid: PMC5148039.
• Yang D, Lu W, Low DA, Deasy JO, Hope AJ, El Naqa I. 4D-CT motion estimation using deformable image registration and 5D respiratory motion modeling. Med Phys. 2008 Oct.35(10):4577-4590. Pubmedid: 18975704. Pmcid: PMC2673589.
• Yang D, Li H, Low DA, Deasy JO, El Naqa I. A fast inverse consistent deformable image registration method based on symmetric optical flow computation. Phys Med Biol. 2008 Nov.53(21):6143-6165. Pubmedid: 18854610. Pmcid: PMC3915046.
• Trovo M, Bradley J, El Naqa I, Foster E, Meyers B, Govindan R, Patterson A. Esophageal carcinoma with celiac nodal metastases; curative or palliative?. J Thorac Oncol. 2008 Jul.3(7):751-755. Pubmedid: 18594321.
• Zheng J, Ochoa E, Misselwitz B, Yang D, El Naqa I, Woodard PK, Abendschein D. Targeted contrast agent helps to monitor advanced plaque during progression: a magnetic resonance imaging study in rabbits. Invest Radiol. 2008 Jan.43(1):49-55. Pubmedid: 18097277.
• Wang X, El Naqa IM. Prediction of both conserved and nonconserved microRNA targets in animals. Bioinformatics. 2008 Feb.24(3):325-332. Pubmedid: 18048393.
• Lin LL, El Naqa I, Leonard JR, Park TS, Hollander AS, Michalski JM, Mansur DB. Long-term outcome in children treated for craniopharyngioma with and without radiotherapy. J Neurosurg Pediatr. 2008 Feb.1(2):126-130. Pubmedid: 18352781.
• Santanam L, Esthappan J, Mutic S, Klein EE, Goddu SM, Chaudhari S, Wahab S, El Naqa IM, Low DA, Grigsby PW. Estimation of setup uncertainty using planar and MVCT imaging for gynecologic malignancies. Int J Radiat Oncol Biol Phys. 2008 Aug.71(5):1511-1517. Pubmedid: 18538499.
• Deasy JO, El Naqa I. Image-based modeling of normal tissue complication probability for radiation therapy. Cancer Treat Res. 2008.139:215-256. Pubmedid: 18236719.
• El Naqa I, Cui J, Lindsay P, Olivera G, Deasy JO. The denoising of Monte Carlo dose distributions using convolution superposition calculations. Phys Med Biol. 2007 Sep.52(17):N375-N385. Pubmedid: 17762073.
• Bradley JD, Hope A, El Naqa I, Apte A, Lindsay PE, Bosch W, Matthews J, Sause W, Graham MV, Deasy JO. A nomogram to predict radiation pneumonitis, derived from a combined analysis of RTOG 9311 and institutional data. Int J Radiat Oncol Biol Phys. 2007 Nov.69(4):985-992. Pubmedid: 17689035. Pmcid: PMC2196217.
• Christensen GE, Song JH, Lu W, El Naqa I, Low DA. Tracking lung tissue motion and expansion/compression with inverse consistent image registration and spirometry. Med Phys. 2007 Jun.34(6):2155-2163. Pubmedid: 17654918.
• Lindsay PE, El Naqa I, Hope AJ, Vicic M, Cui J, Bradley JD, Deasy JO. Retrospective monte carlo dose calculations with limited beam weight information. Med Phys. 2007 Jan.34(1):334-346. Pubmedid: 17278519.
• El Naqa I, Yang D, Apte A, Khullar D, Mutic S, Zheng J, Bradley JD, Grigsby P, Deasy JO. Concurrent multimodality image segmentation by active contours for radiotherapy treatment planning. Med Phys. 2007 Dec.34(12):4738-4749. Pubmedid: 18196801.
• El Naqa I, Low DA, Bradley JD, Vicic M, Deasy JO. Deblurring of breathing motion artifacts in thoracic PET images by deconvolution methods. Med Phys. 2006 Oct.33(10):3587-3600. Pubmedid: 17089825.
• El Naqa I, Suneja G, Lindsay PE, Hope AJ, Alaly JR, Vicic M, Bradley JD, Apte A, Deasy JO. Dose response explorer: an integrated open-source tool for exploring and modelling radiotherapy dose-volume outcome relationships. Phys Med Biol. 2006 Nov.51(22):5719-5735. Pubmedid: 17068361.
• Biehl KJ, Kong FM, Dehdashti F, Jin JY, Mutic S, El Naqa I, Siegel BA, Bradley JD. 18F-FDG PET definition of gross tumor volume for radiotherapy of non-small cell lung cancer: is a single standardized uptake value threshold approach appropriate?. J Nucl Med. 2006 Nov.47(11):1808-1812. Pubmedid: 17079814.
• Hope AJ, Lindsay PE, El Naqa I, Alaly JR, Vicic M, Bradley JD, Deasy JO. Modeling radiation pneumonitis risk with clinical, dosimetric, and spatial parameters. Int J Radiat Oncol Biol Phys. 2006 May.65(1):112-124. Pubmedid: 16618575.
• El Naqa I, Bradley J, Blanco AI, Lindsay PE, Vicic M, Hope A, Deasy JO. Multivariable modeling of radiotherapy outcomes, including dose-volume and clinical factors. Int J Radiat Oncol Biol Phys. 2006 Mar.64(4):1275-1286. Pubmedid: 16504765.
• Bradley JD, Nofal AN, El Naqa IM, Lu W, Liu J, Hubenschmidt J, Low DA, Drzymala RE, Khullar D. Comparison of helical, maximum intensity projection (MIP), and averaged intensity (AI) 4D CT imaging for stereotactic body radiation therapy (SBRT) planning in lung cancer. Radiother Oncol. 2006 Dec.81(3):264-268. Pubmedid: 17113668.
• Mansur DB, Kong FM, El Naqa I, Taylor ME, Zoberi I, Bradley JD, Perez CA, Klein EE. CT localization of axillary lymph nodes in relation to the humeral head: significance of arm position for radiation therapy planning. Radiother Oncol. 2005 Nov.77(2):191-193. Pubmedid: 16271409.
• El Naqa I, Kawrakow I, Fippel M, Siebers JV, Lindsay PE, Wickerhauser MV, Vicic M, Zakarian K, Kauffmann N, Deasy JO. A comparison of Monte Carlo dose calculation denoising techniques. Phys Med Biol. 2005 Mar.50(5):909-922. Pubmedid: 15798264.
• Lu W, Low DA, Parikh PJ, Nystrom MM, El Naqa IM, Wahab SH, Handoko M, Fooshee D, Bradley JD. Comparison of spirometry and abdominal height as four-dimensional computed tomography metrics in lung. Med Phys. 2005 Jul.32(7Part1):2351-2357. Pubmedid: 28493581.
• Lu W, Low DA, Parikh PJ, Nystrom MM, El Naqa IM, Wahab SH, Handoko M, Fooshee D, Bradley JD. Comparison of spirometry and abdominal height as four-dimensional computed tomography metrics in lung. Med Phys. 2005 Jul.32(7):2351-2357. Pubmedid: 16121592.
• Blanco AI, Chao KS, El Naqa I, Franklin GE, Zakarian K, Vicic M, Deasy JO. Dose-volume modeling of salivary function in patients with head-and-neck cancer receiving radiotherapy. Int J Radiat Oncol Biol Phys. 2005 Jul.62(4):1055-1069. Pubmedid: 15990009.
• Zheng J, El Naqa I, Rowold FE, Pilgram TK, Woodard PK, Saffitz JE, Tang D. Quantitative assessment of coronary artery plaque vulnerability by high-resolution magnetic resonance imaging and computational biomechanics: a pilot study ex vivo. Magn Reson Med. 2005 Dec.54(6):1360-1368. Pubmedid: 16265643. Pmcid: PMC1474004.
• Lu W, Parikh PJ, El Naqa IM, Nystrom MM, Hubenschmidt JP, Wahab SH, Mutic S, Singh AK, Christensen GE, Bradley JD, Low DA. Quantitation of the reconstruction quality of a four-dimensional computed tomography process for lung cancer patients. Med Phys. 2005 Apr.32(4):890-901. Pubmedid: 15895571.
• El-Naqa I, Yang Y, Galatsanos NP, Nishikawa RM, Wernick MN. A similarity learning approach to content-based image retrieval: application to digital mammography. Ieee T Med Imaging. 2004 Oct.23(10):1233-1244. Pubmedid: 15493691.
• Bradley J, Deasy JO, Bentzen S, El-Naqa I. Dosimetric correlates for acute esophagitis in patients treated with radiotherapy for lung carcinoma. Int J Radiat Oncol Biol Phys. 2004 Mar.58(4):1106-1113. Pubmedid: 15001251.
• Mansur DB, El Naqa I, Kong F, Klein EE, Taylor ME, Zoberi I, Bradley JD, Perez CA. Localization of internal mammary lymph nodes by CT simulation: implications for breast radiation therapy planning. Radiother Oncol. 2004 Dec.73(3):355-357. Pubmedid: 15588882.
• El-Naqa I, Yang Y, Wernick MN, Galatsanos NP, Nishikawa RM. A support vector machine approach for detection of microcalcifications. Ieee T Med Imaging. 2002 Dec.21(12):1552-1563. Pubmedid: 12588039.

• Title: Artificial Intelligence for Effective MR-Linac Adaptive Radiotherapy
  Sponsor: ViewRay Technologies
  PI: El Naqa, I., CO-PI: Rosenberg, S.
• Title: Use Machine Learning to Identify Novel Image-Based Markers That Can Distinguish Between ICUS, CCUS, and MDS and Aid in the Prediction of Disease Evolution, Survival, and Genetic Evolution in Patients with Pre-MDS Condition and MDS
  Sponsor: Evans Fdtn.
  PI: El Naqa, I., CO-PI: Komrokji, R.
• Title: Federated Learning for Optimal Decision Making in Radiotherapy Using Panomics Analytics
  Sponsor: Nat Institutes of Health
  PI: El Naqa, I.
• Title: An Ionizing Radiation Acoustics Imaging (iRAI) Approach for Guided Flash Radiotherapy
  Sponsor: Nat Institutes of Health
  PI: El Naqa, I.
• Title: Data Science to Improve Treatment Planning for Advanced Prostate Cancer Patients Treated with Radiotherapy
  Sponsor: US Army
  PI: El Naqa, I.
• Title: Medical Imaging and Data Resource Center (MIDRC) for Rapid Response to COVID-19 Pandemic
  Sponsor: Nat Institutes of Health
  PI: El Naqa, I.
• Title: Optimal Decision Making in Radiotherapy Using Panomics Analytics
  Sponsor: Nat Institutes of Health
  PI: El Naqa, I.
• Title: Combined Radiation Acoustics and Ultrasound Imaging for Real-Time Guidance in Radiotherapy
  Sponsor: Nat Institutes of Health
  PI: El Naqa, I.