Department Metrics

• An Ionizing Radiation Acoustics Imaging (iRAI) Approach for Guided Flash Radiotherapy
  Award Number:
  Sponsor: Nat Institutes of Health
  PI (MPI):El Naqa, I.
• 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
  Award Number:
  Sponsor: Evans Fdtn.
  PI:El Naqa, I.,CO-PI:Komrokji, R.

CLINICAL TRIAL 23565
LUNAR-2: Pivotal, Randomized, Open-Label Study of Tumor Treating Fields (TTFields, 150 kHz) Concomitant with Pembrolizumab and Platinum Based Chemotherapy for the Treatment of Metastatic Non-Small Cell Lung Cancer
Condition: Thoracic
Intervention: Alimta (Pemetrexed); Nab-paclitaxel (Abraxane); Paraplatin (carboplatin); Pembrolizumab (Keytruda); Pemetrexed (); Taxol (paclitaxel); carboplatin (); cisplatin (); paclitaxel ()

CLINICAL TRIAL 23952
Treatment Effect vs. Tumor Progression - Quantitative Analysis Using Machine Learning
Condition: Neurologic Oncology
Intervention:

• Tripathi A, Waqas A, Venkatesan K, Ullah E, Khan A, Khalil F, Chen WS, Ozturk ZG, Saeed-Vafa D, Bui MM, Schabath MB, Rasool G. Using Consensus-Based Reasoning and Large Language Models to Extract Structured Data From Surgical Pathology Reports. Lab Invest. 2026 Feb.106(2):104272. Pubmedid: 41412350.
• Hartsock I, Araujo C, Folio L, Rasool G. Improving Radiology Report Conciseness and Structure via Local Large Language Models. J Imaging Inform Med. 2026 Feb.39(1):1005-1016. Pubmedid: 40259201.
• Moassefi M, Houshmand S, Faghani S, Chang PD, Sun SH, Khosravi B, Triphati AG, Rasool G, Bhatia NK, Folio L, Andriole KP, Gichoya JW, Erickson BJ. Cross-Institutional Evaluation of Large Language Models for Radiology Diagnosis Extraction: A Prompt-Engineering Perspective. J Imaging Inform Med. 2026 Feb.39(1):989-994. Pubmedid: 40341981.
• Abudalou S, Choi J, Gage K, Pow-Sang J, Yilmaz Y, Balagurunathan Y. Challenges in Using Deep Neural Networks Across Multiple Readers in Delineating Prostate Gland Anatomy. J Imaging Inform Med. 2026 Feb.39(1):532-547. Pubmedid: 40392414.
• Rockne RC, Andersen M, Anderson ARA, Basanta D, Bentivegna A, Benzekry S, Branciamore S, Brüningk SC, Conte M, Farahpour F, Karolak A, Köhn-Luque A, Lorenzo G, Manookian B, Rodin AS, Schmalenstroer L, Soler J, Tomasetti C, Urbaniak K. The future of mathematical oncology in the age of AI. NPJ Syst Biol Appl. 2026 Jan.12(1):22. Pubmedid: 41588010. Pmcid: PMC12890909.
• Chow R, Zheng A, Gao C, Vermeulen M, Yu F, Yacoub I, Chhabra AM, Choi JI, Lin H, Valdes G, Simone CB. ChatGPT Versus DeepSeek: Assessing Artificial Intelligence Performance on Radiation Oncology Examination Questions. Adv Radiat Oncol. 2026 Jan.11(1):101929. Pubmedid: 41404490. Pmcid: PMC12703953.
• Altinok O, Rasool G, Waqas A, Schabath MB, Guvenis A. Habitat Radiomics Predict HPV Status in Oropharyngeal Cancer. Cancer Med. 2025 Dec.14(24):e71481. Pubmedid: 41422495. Pmcid: PMC12718549.
• Olumoyin K, El Naqa L, Rejniak K. Learning Model Parameter Dynamics in a Combination Therapy for Bladder Cancer from Sparse Biological Data. ArXiv. 2025 Dec. Pubmedid: 41445818. Pmcid: PMC12723788.
• Cuneo KC, Zhang W, Litzenberg D, Huang Y, Hadley S, Oraiqat I, Chang KW, Gonzalez G, Dykstra S, Zhang M, Moros EG, Carson PL, Naqa IE, Wang X. Clinical Pilot Study of Ionizing Radiation Acoustic Imaging for Real-Time Visualization of Radiation Therapy Dose Delivery in Cancer Patients. Int J Radiat Oncol Biol Phys. 2025 Dec. Pubmedid: 41397468.
• Park MA, Davis EW, Alhassan S, Arnoletti JP, Basinski TL, McKee AB, Bloomston M, Carson TL, Biachi de Castria T, Chen DT, Cortizas EM, Crowder SL, Delgado MG, Douglas WG, Fleming JB, Hodul P, Huguet KL, Jiang K, Kim DW, Koomen J, Luthra AK, Malafa M, Menon AA, Morales R, Merchant NB, Meredith K, Mo Q, Molina-Vega MA, Moreno-Urazan L, Olumoyin KD, Parker N, Pimiento JM, Rasool G, Rejniak KA, Sansil S, Sparks LM, Stewart P, Tassielli AF, Teer JK, Tran DV, Trevino JG, Velanovich V, Whelan CJ, Jeong D, Judge SM, Judge AR, Permuth JB. Race-based differences in serum biomarkers for cancer-associated cachexia in a diverse cohort of patients with pancreatic ductal adenocarcinoma. Commun Med (Lond). 2025 Dec.6(1):19. Pubmedid: 41413302. Pmcid: PMC12789063.
• Cruz-Chamorro R, Bryant JM, Henning J, Robinson LA, Lee DH, Fontaine J, Toloza E, Rosenberg SA, Kim J, Naqa IE, Dilling TJ. Factors impacting cardiac dose and overall survival in post-operative non-small cell lung cancer patients. Radiother Oncol. 2025 Nov.212:111117. Pubmedid: 40854381.
• Nguyen T, Karolak A. Transformer graph variational autoencoder for generative molecular design. Biophys J. 2025 Nov.124(22):3867-3875. Pubmedid: 39885689. Pmcid: PMC12709429.
• Niraula D, Shotande MO, El Naqa I. Human-machine Interaction in the Age of Generative AI. Cancer J. 2025 Nov.31(6). Pubmedid: 41252128.
• Abdelrahman A, El Naqa I. The Role of PET Image Quantification in Modern Radiation Therapy. PET Clin. 2025 Oct.20(4):525-534. Pubmedid: 40816963.
• Tripathi A, Waqas A, Schabath MB, Yilmaz Y, Rasool G. HONeYBEE: enabling scalable multimodal AI in oncology through foundation model-driven embeddings. NPJ Digit Med. 2025 Oct.8(1):622. Pubmedid: 41131352. Pmcid: PMC12549884.
• Davis EW, Park MA, Basinski TL, Arnoletti JP, Bloomston M, Carson TL, Biachi De Castria T, Chen DT, Cortizas EM, Crowder SL, Genilo-Delgado M, Douglas WG, Huguet KL, Jiang K, Hodul PJ, Karolak A, Kim DW, Koomen JM, Menon AA, Mo Q, Mok SR, Molina-Vega MA, Moreno-Urazan L, Ahmed S, Parker NH, Pimiento JM, Rasool G, Sparks LM, Stewart PA, Tassielli AF, Teer JK, Trevino JG, Velanovich V, Wang X, Whelan CJ, Judge SM, Judge AR, Fleming JB, Malafa MP, Jeong D, Permuth JB. The Impact of Edema on Skeletal Muscle Changes among Patients with Pancreatic Ductal Adenocarcinoma. Cancer Epidemiol Biomarkers Prev. 2025 Sep.34(9):1609-1617. Pubmedid: 40553455.
• Huang Y, Wei L, Litzenberg D, Li B, Ma C, Kim H, Liu Y, Zhang C, Carson PL, Naqa IE, Zhang W, Wang X. Towards quantitative ionizing radiation acoustic imaging (iRAI) for radiation dose measurement: Validation from simulations to experiments. Med Phys. 2025 Sep.52(9):e18091. Pubmedid: 40891090. Pmcid: PMC12402745.
• Gonzalez BD, Li X, Gudenkauf LM, Pullukkara JJ, Oswald LB, Hoogland AI, Le T, El Naqa I, Saltos AN, Haura EB, Luo Y. Using Bayesian Networks to Predict Urgent Care Visits in Patients Receiving Systemic Therapy for Non-Small Cell Lung Cancer. JCO Clin Cancer Inform. 2025 Sep.9:e2400315. Pubmedid: 40939115. Pmcid: PMC12483286.
• Ahmed S, Parker N, Park M, Davis EW, Jeong D, Permuth JB, Schabath MB, Yilmaz Y, Rasool G. Multimodal AI-driven Biomarker for Early Detection of Cancer Cachexia. medRxiv. 2025 Sep. Pubmedid: 41001462. Pmcid: PMC12458964.
• Flack D, Tripathi A, Waqas A, Rasool G, Dera D. Robust Multimodal Fusion for Survival Prediction in Cancer Patients. Cancer Inform. 2025 Sep.24. Pubmedid: 41024938. Pmcid: PMC12476512.
• Tarhini AA, El Naqa I. Artificial Intelligence for Multiscale Spatial Analysis in Oncology: Current Applications and Future Implications. Int J Mol Sci. 2025 Aug.26(16). Pubmedid: 40869323. Pmcid: PMC12387104.
• Murphy A, Bowen K, Naqa IME, Yoga B, Green BL. Bridging Health Disparities in the Data-Driven World of Artificial Intelligence: A Narrative Review. J Racial Ethn Health Disparities. 2025 Aug.12(4):2367-2379. Pubmedid: 38955956.
• Tarhini AA, Obermayer A, Lee SJ, LaFramboise WA, Hodi FS, Karunamurthy AD, Eljilany I, Chen DT, Hwu P, El Naqa IM, Streicher H, Sondak VK, Storkus WJ, Butterfield LH, Shaw TI, Kirkwood JM. Integrative Immune Signature of Complementary Circulating and Tumoral Biomarkers Maximizes the Predictive Power of Adjuvant Immunotherapeutic Benefits in High-risk Melanoma. Clin Cancer Res. 2025 Aug.31(15):3249-3258. Pubmedid: 40392969. Pmcid: PMC12316551.
• Huang Y, Oraiqat I, Litzenberg D, Karthikesh MS, Tichacek C, Gonzalez G, Xu Z, Dykstra S, Li B, Hadley S, Moros EG, Zhang M, Carson PL, Cuneo KC, Wang X, El Naqa I, Zhang W. Ionizing radiation acoustic and ultrasound dual-modality imaging for visualization of dose on anatomical structures during radiotherapy. Photoacoustics. 2025 Aug.44:100742. Pubmedid: 40600002. Pmcid: PMC12209899.
• Hoogland CE, Sutton SK, Fennell BS, Simmons VN, Vinci C, Naqa IE, Salloum RG, Shete SS, Hembree T, Vidrine DJ, Vidrine JI. Early Treatment Engagement and Long-Term Smoking Abstinence Among Women With Cervical Intraepithelial Neoplasia or Cervical Cancer. AJPM Focus. 2025 Aug.4(4):100361. Pubmedid: 40673008. Pmcid: PMC12264617.
• Tripathi A, Nielsen IE, Umer M, Ramachandran RP, Rasool G. Explainable AI in Genomics: Transcription Factor Binding Site Prediction with Mixture of Experts. ArXiv. 2025 Jul. Pubmedid: 40709306. Pmcid: PMC12288655.
• Waqas A, Tripathi A, Ahmed S, Mukund A, Farooq H, Johnson JO, Stewart PA, Naeini M, Schabath MB, Rasool G. Self-Normalizing Multi-Omics Neural Network for Pan-Cancer Prognostication. Int J Mol Sci. 2025 Jul.26(15). Pubmedid: 40806487. Pmcid: PMC12347193.
• El Naqa I. The Biophysics of Flash Radiotherapy: Tools for Measuring Tumor and Normal Tissues Microenvironment. Antioxidants (Basel). 2025 Jul.14(8). Pubmedid: 40867798. Pmcid: PMC12383113.
• Keall PJ, El Naqa I, Fast MF, Hewson EA, Hindley N, Poulsen P, Sengupta C, Tyagi N, Waddington DEJ. Real-Time Dose-Guided Radiation Therapy. Int J Radiat Oncol Biol Phys. 2025 Jul.122(4):787-801. Pubmedid: 40327027.
• Koutsoubis N, Waqas A, Yilmaz Y, Ramachandran RP, Schabath MB, Rasool G. Privacy-preserving Federated Learning and Uncertainty Quantification in Medical Imaging. Radiol Artif Intell. 2025 Jul.7(4):e240637. Pubmedid: 40366260. Pmcid: PMC12319697.
• Song WY, Roumeliotis M, Lee J, Fenster A, Rodgers J, Trumpour T, Glicksman R, Berlin A, Carlsson Tedgren Å, Vijande J, Beaulieu L, Morén B, Meyers SM, Rink A, Gao Y, Fahimian B, China D, Ding K, Podder T, Carver E, Rivard MJ, Richardson S, Grkovski M, Meftahi M, Gardner U, Kumar R, Scanderbeg D, Yashar C, El Naqa I, Viswanathan AN, Jia X. Roadmap: medical physics technologies in brachytherapy. Phys Med Biol. 2025 Jul.70(14). Pubmedid: 40480262.
• Veith T, Beck R, Tagal V, Li T, Alahmari S, Cole J, Hannaby D, Kyei J, Yu X, Maksin K, Schultz A, Lee H, El Naqa I, Eschrich S, Ji HP, Diaz A, Andor N. CLONEID: A Framework for Longitudinal Integration of Phenotypic and Genotypic Data to Monitor and Steer Subclonal Dynamics. bioRxiv. 2025 Jul. Pubmedid: 40631300. Pmcid: PMC12236826.
• Sharma M, Naqa IE, Sneed PK. Does Time to Retreatment Matter? A Normal Tissue Complication Probability Model to Predict Radionecrosis After Repeat Stereotactic Radiosurgery for Recurrent Brain Metastases Incorporating Time-dependent Discounted Dose. Int J Radiat Oncol Biol Phys. 2025 Jun.122(2):467-475. Pubmedid: 39900228.
• Balagurunathan Y, Choi JW, Thompson Z, Jain M, Locke FL. Radiomic Features Prognosticate Treatment Response in CAR-T Cell Therapy. Cancers (Basel). 2025 May.17(11). Pubmedid: 40507312. Pmcid: PMC12153729.
• Matrosic CK, Andrzejewski P, Bergman A, Chng N, Naqa IE, Freislederer P, Hoffmann L, Hope A, Jacqmin D, Kelly C, Kuo L, Lin H, Mayo C, Murrell DH, Ödén J, Svensson S, Thompson S, Osorio EV, West N, Wicha R, Yorke E, Appelt AL, Paradis KC. Software Support Tools for Reirradiation: A Report From Reirradiation Collaborative Group (ReCOG) 2024. Int J Radiat Oncol Biol Phys. 2025 May.122(1):181-185. Pubmedid: 40240108.
• Waqas A, Khan A, Ozturk ZG, Saeed-Vafa D, Chen W, Dhillon J, Bychkov A, Bui MM, Ullah E, Khalil F, Chumbalkar V, Jameel Z, Bittar HT, Singh RS, Parwani AV, Schabath MB, Rasool G. REASONING BEYOND ACCURACY: EXPERT EVALUATION OF LARGE LANGUAGE MODELS IN DIAGNOSTIC PATHOLOGY. medRxiv. 2025 Apr. Pubmedid: 40297448. Pmcid: PMC12036407.
• Ullah E, Baig MM, Waqas A, Rasool G, Singh R, Shandilya A, GholamHossieni H, Parwani AV. Multimodal Generative AI for Anatomic Pathology-A Review of Current Applications to Envisage the Future Direction. Adv Anat Pathol. 2025 Apr. Pubmedid: 40298358.
• Ahmed S, Parker N, Park M, Jeong D, Peres L, Davis EW, Permuth JB, Siegel E, Schabath MB, Yilmaz Y, Rasool G. Reliable Radiologic Skeletal Muscle Area Assessment - A Biomarker for Cancer Cachexia Diagnosis. medRxiv. 2025 Apr. Pubmedid: 40313262. Pmcid: PMC12045449.
• Benyahia S, Avila M, Coughlin E, Mahil A, Riveron A, Luo Y, Wenham R, Huang J. Impact of Intraoperative Blood Transfusions on Survival Rates in Ovarian Cancer Patients. Cancer Control. 2025 Jan.32. Pubmedid: 40294239. Pmcid: PMC12038196.
• Tripathi A, Waqas A, Venkatesan K, Ullah E, Khan A, Khalil F, Chen WS, Ozturk ZG, Saeed-Vafa D, Bui MM, Schabath MB, Rasool G. Employing Consensus-Based Reasoning with Locally Deployed LLMs for Enabling Structured Data Extraction from Surgical Pathology Reports. medRxiv. 2025 Apr. Pubmedid: 40343037. Pmcid: PMC12060942.
• Freeman CL, Noble J, Menges M, Villanueva R, Nakashima JY, Figura NB, Tonseth RP, Idiaquez DW, Skelson L, Smith EC, Abraham-Miranda J, Corallo S, De Avila G, Castaneda Puglianini O, Liu HD, Alsina M, Nishihori T, Shain KH, Baz RC, Blue BJ, Grajales-Cruz A, Koomen JM, Atkins RM, Hansen DK, Siqueira Silva A, Kim J, Balagurunathan Y, Locke FL. Tumor burden quantified by soluble B-cell maturation antigen and metabolic tumor volume determines myeloma CAR-T outcomes. Blood. 2025 Apr.145(15):1645-1657. Pubmedid: 39652773.
• Brodsky V, Ullah E, Bychkov A, Song AH, Walk EE, Louis P, Rasool G, Singh RS, Mahmood F, Bui MM, Parwani AV. Generative Artificial Intelligence in Anatomic Pathology. Arch Pathol Lab Med. 2025 Apr.149(4):298-318. Pubmedid: 39836377.
• Conahan P, Robinson LA, Le T, Valdes G, Schabath MB, Byrne MM, Green L, El Naqa I, Luo Y. Easy ensemble classifier-group and intersectional fairness and threshold (EEC-GIFT): a fairness-aware machine learning framework for lung cancer screening eligibility using real-world data. JNCI Cancer Spectr. 2025 Mar.9(2). Pubmedid: 40111867. Pmcid: PMC11986816.
• Park MA, Whelan CJ, Ahmed S, Boeringer T, Brown J, Carson TL, Crowder SL, Gage K, Gregg C, Jeong DK, Jim HSL, Judge AR, Mason TM, Parker N, Pillai S, Qayyum A, Rajasekhara S, Rasool G, Tinsley SM, Schabath MB, Stewart P, West J, McDonald P, Permuth JB. Correction: Park et al. Defining and Addressing Research Priorities in Cancer Cachexia through Transdisciplinary Collaboration. Cancers 2024, 16, 2364. Cancers (Basel). 2025 Mar.17(6). Pubmedid: 40149388. Pmcid: PMC11941415.
• Permuth J, Park M, Davis E, Alhassan S, Arnoletti J, Basinski T, McKee A, Bloomston M, Carson T, de Castria TB, Chen DT, Cortizas E, Crowder S, Delgado MG, Douglas W, Fleming J, Hodul P, Huguet K, Jiang K, Kim DW, Koomen J, Luthra A, Malafa M, Menon A, Morales R, Merchant N, Meredith K, Mo Q, Molina-Vega M, Moreno-Urazan L, Olumoyin K, Parker N, Pimiento J, Rasool G, Rejniak K, Sansil S, Sparks L, Stewart P, Tassielli A, Teer J, Tran DV, Trevino J, Velanovich V, Whelan C, Jeong D, Judge S, Judge A. Race-based differences in serum biomarkers for cancer-associated cachexia in a diverse cohort of patients with pancreatic ductal adenocarcinoma. Res Sq. 2025 Feb. Pubmedid: 39989973. Pmcid: PMC11844656.
• Avasthi KK, Choi JW, Glushko T, Manley BJ, Yu A, Park JY, Brown JS, Pow-Sang J, Gatenby R, Wang L, Balagurunathan Y. Extracellular Microvesicle MicroRNAs and Imaging Metrics Improve the Detection of Aggressive Prostate Cancer: A Pilot Study. Cancers (Basel). 2025 Feb.17(5). Pubmedid: 40075682. Pmcid: PMC11898942.