Peer-Reviewed Publications

Refereed Journal Papers

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. Radiotherapy and Oncology. 2011 May;99(2):166-71. doi: 10.1016/j.radonc.2011.04.002. PMID: 21571384.

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

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.

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. Physics in Medicine and Biology. 2018 Nov 8;63(22):225003. doi: 10.1088/1361-6560/aae56a. PMID: 30272571.

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. Physics in Medicine and Biology. 2019 Jan 8;64(2):025007. doi: 10.1088/1361-6560/aaf5a5. PMID: 30524018.

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. Advances in Radiation Oncology. 2019 May 22;4(4):748-752. doi: 10.1016/j.adro.2019.05.004. PMID: 31673668; PMCID: PMC6817521.

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

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. 

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.

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

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). Physics in Medicine and Biology. 2020 Mar 19;65(6):065009. doi: 10.1088/1361-6560/ab7309. PMID: 32023555; PMCID: PMC7252912.

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. Frontiers in Oncology. 2020 Aug 18;10:1592. doi: 10.3389/fonc.2020.01592. PMID: 33014811; PMCID: PMC7461989.

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. Quantitative Imaging in Medicine and Surgery. 2020 Oct;10(10):1917-1929. doi: 10.21037/qims-19-883. PMID: 33014725; PMCID: PMC7495314.

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

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. Radiology: Imaging Cancer. 2021 Apr;3(4):e200157. doi: 10.1148/rycan.2021200157. PMID: 34114913; PMCID: PMC8344351.

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. Physics in Medicine and Biology. 2021 May 31;66(11):10.1088/1361-6560/ac01b4. doi: 10.1088/1361-6560/ac01b4. PMID: 34061044; PMCID: PMC9139421.

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. Medical Physics. 2021 Jul;48(7):3767-3777. doi: 10.1002/mp.14926. PMID: 33959972; PMCID: PMC9113754.

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.

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. Journal of Medical Imaging. 2021 Nov;8(6):067501. doi: 10.1117/1.JMI.8.6.067501. PMID: 34950750; PMCID: PMC8685284.

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.

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. Canadian Journal of Cardiology. 2022 Feb;38(2):234-245. doi: 10.1016/j.cjca.2021.11.008. PMID: 34813876.

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. Journal of Magnetic Resonance Imaging. 2022 Feb;55(2):493-506. doi: 10.1002/jmri.27824. PMID: 34236120.

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.

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. Frontiers in Oncology. 2022 May 13;12:895544. doi: 10.3389/fonc.2022.895544. PMID: 35646643; PMCID: PMC9135979.

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. Journal of Magnetic Resonance Imaging. 2022 May 5. doi: 10.1002/jmri.28218. PMID: 35512243.

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. Medical Physics. 2022 May;49(5):3213-3222. doi: 10.1002/mp.15582. PMID: 35263458; PMCID: PMC9088469.

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 Radiologica. 2022 Jun;63(6):828-838. doi: 10.1177/02841851211010396. PMID: 33878931. 

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. Medical Physics. 2022 Jun 30. doi: 10.1002/mp.15837. PMID: 35770964.

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. Journal of Magnetic Resonance Imaging. 2022 Aug;56(2):399-412. doi: 10.1002/jmri.28056. PMID: 34994029.

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

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. Abdominal Radiology. 2022 Oct 9. doi: 10.1007/s00261-022-03695-y. PMID: 36209446.

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. 2022 Oct 22;14(21):5186. doi: 10.3390/cancers14215186. PMID: 36358606.

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. Medical Physics. 2022 Dec 22. doi: 10.1002/mp.16181. PMID: 36548913.

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. Journal of Magnetic Resonance Imaging. 2023 Jan 6. doi: 10.1002/jmri.28577. PMID: 36607254.

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. Radiology: Artificial Intelligence. 2023 Feb 22;5(3):e220080. doi: 10.1148/ryai.220080. PMID: 37293348; PMCID: PMC10245179.

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. PMID: 37016482; PMCID: PMC10278770.

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. Medical Physics. 2023 Aug;50(8):4825-4838. doi: 10.1002/mp.16286. PMID: 36840621; PMCID: PMC10440249.

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. European Radiology. 2023 Aug;33(8):5779-5791. doi: 10.1007/s00330-023-09532-0. PMID: 36894753.

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. Medical Physics. 2023 Sep 11. doi: 10.1002/mp.16695. PMID: 37696029.

40. Lafata KJ, Read C, Tong BC, Akinyemiju T, Wang C, Cerullo M, Tailor TD. Lung Cancer Screening in Clinical Practice: A 5-Year Review of Frequency and Predictors of Lung Cancer in the Screened Population. Journal of the American College of Radiology. 2024 May;21(5):767-777. doi: 10.1016/j.jacr.2023.05.027. PMID: 37952807.

41. Yang Z, Wang C, Wang Y, Lafata KJ, Zhang H, Ackerson BG, Kelsey C, Tong B, 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. Frontiers in Oncology. 2023 Sep 13;13:1185771. doi: 10.3389/fonc.2023.1185771. PMID: 37781201; PMCID: PMC10534017.

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. In Press.

43. Stevens JB, Riley BA, 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. Medical Physics. 2024 May;51(5):3334-3347. doi: 10.1002/mp.16905. PMID: 38190505.

44. Kang J, Lafata KJ, Kim E, Yao C, Lin F, Rattay T, Nori H, Katsoulakis E, Lee C. Artificial intelligence across oncology specialties: current applications and emerging tools. BMJ Oncology. 2024. In Press.

45. Riley BA, Stevens JB, Li X, Yang Z, Wang C, Mowery YM, Brizel DM, Yin FF, Lafata KJ. Prognostic value of different discretization parameters in 18fluorodeoxyglucose positron emission tomography radiomics of oropharyngeal squamous cell carcinoma. Journal of Medical Imaging. 2024 Mar;11(2):024007. doi: 10.1117/1.JMI.11.2.024007. PMID: 38549835; PMCID: PMC10966359.

46. Zhao J, Vaios E, Wang Y, Yang Z, Cui Y, Reitman ZJ, Lafata KJ, Fecci P, Kirkpatrick J, Fang Yin F, Floyd S, Wang C. Dose-Incorporated Deep Ensemble Learning for Improving Brain Metastasis Stereotactic Radiosurgery Outcome Prediction. International Journal of Radiation Oncology Biology and Physics. 2024 Apr 12:S0360-3016(24)00505-4. doi: 10.1016/j.ijrobp.2024.04.006. PMID: 38615888.

47. Domanski P, Ray A, Firouzi F, Lafata KJ, Chakrabarty K, Pfluger D. Advancing blood glucose prediction with neural architecture search and deep reinforcement learning for Type 1 diabetics. Biocybernetics and Biomedical Engineering. 2024. In Press.

48. Zhou J, Li X, Demeke D, Dinh TA, Yang Y, Janowczyk AR, Zee J, Holzman L, Mariani L, Chakrabarty K, Barisoni L, Hodgin JB, Lafata KJ. Characterization of arteriosclerosis based on computer-aided measurements of intra-arterial thickness. Journal of Medical Imaging. 2024. In Press. Featured on Journal Cover.

49. Zhou J, Luo Y, Darcy JW, Lafata KJ, Ruiz JR, Grego S. Long-term, automated stool monitoring using a novel smart toilet: a feasibility study. Neurogastroenterology and Motility. 2024. In Press.

50. Li X, Heirman CC, Rickard AG, Sotolongo G, Castillo R, Adanlawo T, Everitt JI, Hodgin JB, Watts TL, Janowczyk A, Mowery YM, Barisoni L, Lafata KJ. Computational staining of CD3/CD20 positive lymphocytes in human tissues with experimental confirmation in a genetically engineered mouse model. Frontiers in Immunology. 2024. In Press.

51. Chen Y, Wang B, Demeke D, Fan F, Berthier C, Mariani LH, Lafata KJ, Holzman LB, Hodgin JB, Janowczyk AR, Barisoni L, Madabhushi A. Clinical relevance of computational pathology analysis of interplay between kidney microvasculature and interstitial microenvironment. Clinical Journal of the American Society of Nephrology. 2024. In Press.

Full Length Conference Papers

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).

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

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.

4. Dahal L, Wang Y, 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.

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.

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.

7. Ray A, Saha S, Chakrabarty K, Collins L, Lafata KJ, Emami-Naeini P. Exploring the impact of ethnicity on susceptibility to voice phishing. USENIX-SOUPS. 2023.

8. Ray A, Dannull L, Firouzi F, Lafata KJ, Chakrabarty K. Inference serving system for stable diffusion as a service. 2024 IEEE Cloud Summit. 2024 best paper award.

9. Liardo A, Ray A, Firouzi F, Lafata KJ, Chakrabarty K. Neural architecture search for blood glucose prediction in type-1 diabetics. IEEE Body Sensor Networks. 2024.

10. Ray A, Firouzi F, Lafata KJ, Chakrabarty K. Preserving accuracy while stealing watermarked deep neural networks. IEEE International Conference on Machine Learning and Applications. 2024. 

Published Academic Documents

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

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