Peer-Reviewed Publications

Refereed Journal Papers

J-1.      Stauder MC, Macdonald OK, Olivier KR, Call JA, Lafata KJ, Mayo CS, Miller RC, Brown PD, Bauer HJ, Garces YI. Early pulmonary toxicity following lung stereotactic body radiation therapy delivered in consecutive daily fractions. Radiother Oncol. 2011 May;99(2):166-71. doi: 10.1016/j.radonc.2011.04.002. PMID: 21571384.


J-2.      Lafata KJ, Bushe H, Aronowitz JN. A simple technique for the generation of institution-specific nomograms for permanent prostate cancer brachytherapy. J Contemp Brachytherapy. 2014 Oct;6(3):293-6. doi: 10.5114/jcb.2014.45582. PMID: 25337132; PMCID: PMC4200185.


J-3.      Ackerson BG, Tong BC, Hong JC, Gu L, Chino J, Trotter JW, D'Amico TA, Torok JA, Lafata KJ, Chang C, Kelsey CR. Stereotactic body radiation therapy versus sublobar resection for stage I NSCLC. Lung Cancer. 2018 Nov;125:185-191. doi: 10.1016/j.lungcan.2018.09.020. PMID: 30429018.


J-4.      Lafata KJ, Cai J, Wang C, Hong J, Kelsey CR, Yin FF. Spatial-temporal variability of radiomic features and its effect on the classification of lung cancer histology. Phys Med Biol. 2018 Nov 8;63(22):225003. doi: 10.1088/1361-6560/aae56a. PMID: 30272571.


J-5.      Lafata KJ, Hong JC, Geng R, Ackerson BG, Liu JG, Zhou Z, Torok J, Kelsey CR, Yin FF. Association of pre-treatment radiomic features with lung cancer recurrence following stereotactic body radiation therapy. Phys Med Biol. 2019 Jan 8;64(2):025007. doi: 10.1088/1361-6560/aaf5a5. PMID: 30524018.


J-6.      Corradetti MN, Torok JA, Hatch AJ, Xanthopoulos EP, Lafata KJ, Jacobs C, Rushing C, Calaway J, Jones G, Kelsey CR, Nixon AB. Dynamic Changes in Circulating Tumor DNA During Chemoradiation for Locally Advanced Lung Cancer. Adv Radiat Oncol. 2019 May 22;4(4):748-752. doi: 10.1016/j.adro.2019.05.004. PMID: 31673668; PMCID: PMC6817521.


J-7.      Lafata KJ, Zhou Z, Liu JG, Hong J, Kelsey CR, Yin FF. An exploratory radiomics approach to quantifying pulmonary function in CT images. Sci Rep. 2019 Aug 8;9(1):11509. doi: 10.1038/s41598-019-48023-5. PMID: 31395937; PMCID: PMC6687824.


J-8.      Lafata KJ, Zhou Z, Liu JG, Yin FF. Data clustering based on Langevin annealing with a self-consistent potential. Quarterly of Applied Mathematics. 2019 Sep;77(3):591-613. 


J-9.      Chang Y, Lafata KJ, Sun W, Wang C, Chang Z, Kirkpatrick JP, Yin FF. An investigation of machine learning methods in delta-radiomics feature analysis. PLoS One. 2019 Dec 13;14(12):e0226348. doi: 10.1371/journal.pone.0226348. PMID: 31834910; PMCID: PMC6910670.


J-10.   Chang Y, Lafata KJ, Wang C, Duan X, Geng R, Yang Z, Yin FF. Digital phantoms for characterizing inconsistencies among radiomics extraction toolboxes. Biomed Phys Eng Express. 2020 Mar 2;6(2):025016. doi: 10.1088/2057-1976/ab779c. PMID: 33438642.


J-11.   Chang Y, Lafata KJ, Segars WP, Yin FF, Ren L. Development of realistic multi-contrast textured XCAT (MT-XCAT) phantoms using a dual-discriminator conditional-generative adversarial network (D-CGAN). Phys Med Biol. 2020 Mar 19;65(6):065009. doi: 10.1088/1361-6560/ab7309. PMID: 32023555; PMCID: PMC7252912.


J-12.   Wang C, Liu C, Chang Y, Lafata KJ, Cui Y, Zhang J, Sheng Y, Mowery Y, Brizel D, Yin FF. Dose-Distribution-Driven PET Image-Based Outcome Prediction (DDD-PIOP): A Deep Learning Study for Oropharyngeal Cancer IMRT Application. Front Oncol. 2020 Aug 18;10:1592. doi: 10.3389/fonc.2020.01592. PMID: 33014811; PMCID: PMC7461989.


J-13.   Liu C, Hu SC, Wang C, Lafata KJ, Yin FF. Automatic detection of pulmonary nodules on CT images with YOLOv3: development and evaluation using simulated and patient data. Quant Imaging Med Surg. 2020 Oct;10(10):1917-1929. doi: 10.21037/qims-19-883. PMID: 33014725; PMCID: PMC7495314.


J-14.   Barisoni L, Lafata KJ, Hewitt SM, Madabhushi A, Balis UGJ. Digital pathology and computational image analysis in nephropathology. Nat Rev Nephrol. 2020 Nov;16(11):669-685. doi: 10.1038/s41581-020-0321-6. PMID: 32848206; PMCID: PMC7447970.


J-15.   Lafata KJ, Corradetti MN, Gao J, Jacobs CD, Weng J, Chang Y, Wang C, Hatch A, Xanthopoulos E, Jones G, Kelsey CR, Yin FF. Radiogenomic Analysis of Locally Advanced Lung Cancer Based on CT Imaging and Intratreatment Changes in Cell-Free DNA. Radiol Imaging Cancer. 2021 Apr;3(4):e200157. doi: 10.1148/rycan.2021200157. PMID: 34114913; PMCID: PMC8344351.


J-16.   Chang Y, Jiang Z, Segars WP, Zhang Z, Lafata KJ, Cai J, Yin FF, Ren L. A generative adversarial network (GAN)-based technique for synthesizing realistic respiratory motion in the extended cardiac-torso (XCAT) phantoms. Phys Med Biol. 2021 May 31;66(11):10.1088/1361-6560/ac01b4. doi: 10.1088/1361-6560/ac01b4. PMID: 34061044; PMCID: PMC9139421.


J-17.   Lafata KJ, Chang Y, Wang C, Mowery YM, Vergalasova I, Niedzwiecki D, Yoo DS, Liu JG, Brizel DM, Yin FF. Intrinsic radiomic expression patterns after 20 Gy demonstrate early metabolic response of oropharyngeal cancers. Med Phys. 2021 Jul;48(7):3767-3777. doi: 10.1002/mp.14926. PMID: 33959972; PMCID: PMC9113754.


J-18.   Jiang H, Chen HC, Lafata KJ, Bashir MR. Week 4 Liver Fat Reduction on MRI as an Early Predictor of Treatment Response in Participants with Nonalcoholic Steatohepatitis. Radiology. 2021 Aug;300(2):361-368. doi: 10.1148/radiol.2021204325. PMID: 34060937.


J-19.   Li X, Davis RC, Xu Y, Wang Z, Souma N, Sotolongo G, Bell J, Ellis M, Howell D, Shen X, Lafata KJ, Barisoni L. Deep learning segmentation of glomeruli on kidney donor frozen sections. J Med Imaging(Bellingham). 2021 Nov;8(6):067501. doi: 10.1117/1.JMI.8.6.067501. PMID: 34950750; PMCID: PMC8685284.


J-20.   Rigiroli F, Hoye J, Lerebours R, Lafata KJ, Li C, Meyer M, Lyu P, Ding Y, Schwartz FR, Mettu NB, Zani S Jr, Luo S, Morgan DE, Samei E, Marin D. CT Radiomic Features of Superior Mesenteric Artery Involvement in Pancreatic Ductal Adenocarcinoma: A Pilot Study. Radiology. 2021 Dec;301(3):610-622. doi: 10.1148/radiol.2021210699. PMID: 34491129.

J-21.   Glass C, Lafata KJ, Jeck W, Horstmeyer R, Cooke C, Everitt J, Glass M, Dov D, Seidman MA. The Role of Machine Learning in Cardiovascular Pathology. Can J Cardiol. 2022 Feb;38(2):234-245. doi: 10.1016/j.cjca.2021.11.008. PMID: 34813876.


J-22.   Jiang H, Song B, Qin Y, Wei Y, Konanur M, Wu Y, Zaki IH, McInnes MDF, Lafata KJ, Bashir MR. Data-Driven Modification of the LI-RADS Major Feature System on Gadoxetate Disodium-Enhanced MRI: Toward Better Sensitivity and Simplicity. J Magn Reson Imaging. 2022 Feb;55(2):493-506. doi: 10.1002/jmri.27824. PMID: 34236120.


J-23.   Allphin AJ, Mowery YM, Lafata KJ, Clark DP, Bassil AM, Castillo R, Odhiambo D, Holbrook MD, Ghaghada KB, Badea CT. Photon Counting CT and Radiomic Analysis Enables Differentiation of Tumors Based on Lymphocyte Burden. Tomography. 2022 Mar 10;8(2):740-753. doi: 10.3390/tomography8020061. PMID: 35314638; PMCID: PMC8938796.


J-24.   Ji H, Lafata KJ, Mowery Y, Brizel D, Bertozzi AL, Yin FF, Wang C. Post-Radiotherapy PET Image Outcome Prediction by Deep Learning Under Biological Model Guidance: A Feasibility Study of Oropharyngeal Cancer Application. Front Oncol. 2022 May 13;12:895544. doi: 10.3389/fonc.2022.895544. PMID: 35646643; PMCID: PMC9135979.


J-25.   Kierans AS, Lafata KJ, Ludwig DR, Burke LMB, Chernyak V, Fowler KJ, Fraum TJ, McGinty KA, McInnes MDF, Mendiratta-Lala M, Cunha GM, Allen BC, Hecht EM, Jaffe TA, Kalisz KR, Ranathunga DS, Wildman-Tobriner B, Cardona DM, Aslam A, Gaur S, Bashir MR. Comparing Survival Outcomes of Patients With LI-RADS-M Hepatocellular Carcinomas and Intrahepatic Cholangiocarcinomas. J Magn Reson Imaging. 2022 May 5. doi: 10.1002/jmri.28218. Epub ahead of print. PMID: 35512243.


J-26.   Hu Z, Yang Z, Lafata KJ, Yin FF, Wang C. A radiomics-boosted deep-learning model for COVID-19 and non-COVID-19 pneumonia classification using chest x-ray images. Med Phys. 2022 May;49(5):3213-3222. doi: 10.1002/mp.15582. PMID: 35263458; PMCID: PMC9088469.


J-27.   Ding Y, Meyer M, Lyu P, Rigiroli F, Ramirez-Giraldo JC, Lafata KJ, Yang S, Marin D. Can radiomic analysis of a single-phase dual-energy CT improve the diagnostic accuracy of differentiating enhancing from non-enhancing small renal lesions? Acta Radiol. 2022 Jun;63(6):828-838. doi: 10.1177/02841851211010396. PMID: 33878931.


J-28.   Yang Z, Lafata KJ, Chen X, Bowsher J, Chang Y, Wang C, Yin FF. Quantification of lung function on CT images based on pulmonary radiomic filtering. Med Phys. 2022 Jun 30. doi: 10.1002/mp.15837. Epub ahead of print. PMID: 35770964.


J-29.   Jiang H, Song B, Qin Y, Konanur M, Wu Y, McInnes MDF, Lafata KJ, Bashir MR. Modifying LI-RADS on Gadoxetate Disodium-Enhanced MRI: A Secondary Analysis of a Prospective Observational Study. J Magn Reson Imaging. 2022 Aug;56(2):399-412. doi: 10.1002/jmri.28056. PMID: 34994029.


J-30.   Lafata KJ, Wang Y, Konkel B, Yin FF, Bashir MR. Radiomics: a primer on high-throughput image phenotyping. Abdom Radiol (NY). 2022 Sep;47(9):2986-3002. doi: 10.1007/s00261-021-03254-x. PMID: 34435228.


J-31.   DeFreitas MR, Toronka A, Nedrud MA, Cubberley S, Zaki IH, Konkel B, Uronis HE, Palta M, Blazer DG, Lafata KJ, Bashir MR. CT-derived body composition measurements as predictors for neoadjuvant treatment tolerance and survival in gastroesophageal adenocarcinoma. Abdom Radiol (NY). 2022 Oct 9. doi: 10.1007/s00261-022-03695-y. Epub ahead of print. PMID: 36209446.


J-32.   Carpenter DJ, Natarajan B, Arshad M, Natesan D, Schultz O, Moravan MJ, Read C, Lafata KJ, Giles W, Fecci P, Mullikin TC, Reitman ZJ, Kirkpatrick JP, Floyd SR, Chmura SJ, Hong JC, Salama JK. Prognostic Model for Intracranial Progression after Stereotactic Radiosurgery: A Multicenter Validation Study. Cancers (Basel). 2022 Oct 22;14(21):5186. doi: 10.3390/cancers14215186. PMID: 36358606.


J-33.   Wang Y, Li X, Konanur M, Konkel B, Seyferth E, Brajer N, Liu JG, Bashir MR, Lafata KJ. Towards optimal deep fusion of imaging and clinical data via a model-based description of fusion quality. Med Phys. 2022 Dec 22. doi: 10.1002/mp.16181. Epub ahead of print. PMID: 36548913.


J-34.   Kelleher CB, Macdonald J, Jaffe TA, Allen BC, Kalisz KR, Kauffman TH, Smith JD, Maurer KR, Thomas SP, Coleman AD, Zaki IH, Kannengiesser S, Lafata KJ, Gupta RT, Bashir MR. A Faster Prostate MRI: Comparing a Novel Denoised, Single-Average T2 Sequence to the Conventional Multiaverage T2 Sequence Regarding Lesion Detection and PI-RADS Score Assessment. J Magn Reson Imaging. 2023 Jan 6. doi: 10.1002/jmri.28577. Epub ahead of print. PMID: 36607254.


J-35.   Konkel B, Macdonald J, Lafata KJ, Zaki IH, Bozdogan E, Chaudhry M, Wang Y, Janas G, Wiggins WF, Bashir MR. Systematic Analysis of Common Factors Impacting Deep Learning Model Generalizability in Liver Segmentation. Radiol Artif Intell. 2023 Feb 22;5(3):e220080. doi: 10.1148/ryai.220080. PMID: 37293348; PMCID: PMC10245179.


J-36.   Chen Y, Zee J, Janowczyk AR, Rubin J, Toro P, Lafata KJ, Mariani LH, Holzman LB, Hodgin JB, Madabhushi A, Barisoni L. Clinical Relevance of Computationally Derived Attributes of Peritubular Capillaries from Kidney Biopsies. Kidney360. 2023 May 1;4(5):648-658. doi: 10.34067/KID.0000000000000116. Epub 2023 Apr 5. PMID: 37016482; PMCID: PMC10278770.


J-37.   Yang Z, Yang Z, Hu Z, Ji H, Lafata KJ, Vaios E, Floyd S, Yin FF, Wang C. A neural ordinary differential equation model for visualizing deep neural network behaviors in multi-parametric MRI-based glioma segmentation. Med Phys. 2023 Aug;50(8):4825-4838. doi: 10.1002/mp.16286. Epub 2023 Mar 2. PMID: 36840621; PMCID: PMC10440249.


J-38.   Rigiroli F, Hoye J, Lerebours R, Lyu P, Lafata KJ, Zhang AR, Erkanli A, Mettu NB, Morgan DE, Samei E, Marin D. Exploratory analysis of mesenteric-portal axis CT radiomic features for survival prediction of patients with pancreatic ductal adenocarcinoma. Eur Radiol. 2023 Aug;33(8):5779-5791. doi: 10.1007/s00330-023-09532-0. Epub 2023 Mar 10. PMID: 36894753.


J-39.   Yang Z, Lafata KJ, Vaios E, Hu Z, Mullikin T, Fang Yin F, Wang C. Quantifying U-Net uncertainty in multi-parametric MRI-based glioma segmentation by spherical image projection. Med Phys. 2023 Sep 11. doi: 10.1002/mp.16695. Epub ahead of print. PMID: 37696029.


J-40.   Lafata KJ, Read C. Tong B, Akinyemiju T, Wang C, Cerullo M, Tailor TD. Lung cancer screening in clinical practice: A five-year review of frequency and predictors of lung cancer in the screened population. J. Am. Coll. Radiol. 2023. Accepted.


J-41.   Yang Z, Wang C, Wang Y, Lafata KJ, Zhang H, Ackerson B, Kelsey C, Tong C, Yin FF. Development of a multi-feature-combined model: Proof-of-concept with application to local failure prediction of post-SBRT or surgery early-stage NSCLC patients. Front Oncol. 2023. Accepted.


J-42.   Kreiss L, Jiang S, Li X, Xu S, Zhou KC, Lee KC, Mühlberg A, Kim K, Chaware A, Ando M, Barisoni L, Lee SA, Zheng G, 

Lafata KJ, Friedrich O, Horstmeyer R. Digital staining in optical microscopy using deep learning - a review. PhotoniX. 2023. Accepted.


J-43.   Stevens JB, Riley B, Je J, Gao Y, Wang C, Mowery YM, Brizel DM, Yin FF, Liu JG, Lafata KJ. Radiomics on spatial-temporal manifolds via Fokker-Planck dynamics. Med Phys. 2023. Accepted. 

Refereed Conference Papers


C-1.    Allphin AJ, Mowery Y, Lafata KJ, Clark DP, Basil A, Castillo R, Holbrook MD, Ghaghada KB, Badea CT. Spectral micro-CT and radiomic analysis for classification of tumors based on lymphocytic burden in cancer therapy studies. Proc. SPIE 12036, Medical Imaging 2022: Biomedical Applications in Molecular, Structural, and Functional Imaging, 120361H (4 April 2022).


C-2.    Ray A, Li X, Barisoni L, Chakrabarty K, Lafata KJ. Decoding the encoder. 2023 IEEE SoutheastCon.


C-3.    Ray A, Lafata KJ, Zhang Z, Xiong Y, Chakrabarty K. Privacy-preserving job scheduler for GPU sharing. 2023 IEEE International Symposium on Cluster Computing and the Grid. 


C-4.    Dahal L, Wang, Y Tushar FI, Montero I, Lafata KJ, Abadi E, Samei E, Segars WP, Lo JY. Automatic quality control in computed tomography volumes segmentation using a small set of XCAT as reference images. SPIE Medical Imaging 2023: Physics of Medical Imaging. 2023/4/7. 857-861.  


C-5.    Domanski P, Ray A, Firouzi F, Lafata KJ, Chakrabarty K, Pfluger D. Blood glucose prediction for type-1 diabetics using deep reinforcement learning. 2023 IEEE International Conference on Digital Health (ICDH). 2023/7/2. 339-347.


C-6.    Ray A, Lafata KJ, Zhang Z, Xiong Y, Chakrabarty K. Job recommendation service for GPU sharing in Kubernetes. 2023 IEEE Cloud Summit. 2023/7/6. 7-14. 

Published Academic Documents

Kyle Jon Lafata. Novel identification of radiomic biomarkers with Langevin annealing (PhD Dissertation), Duke University, 2018.