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[18F] FDG Positron Emission Tomography (PET) Tumor and Penumbra Imaging Features Predict Recurrence in Non-Small Cell Lung Cancer.

Mattonen SA, Davidzon GA, Bakr S, Echegaray S, Leung ANC, Vasanawala M, Horng G, Napel S, Nair VS.

Tomography. 2019 Mar;5(1):145-153. doi: 10.18383/j.tom.2018.00026.


Quantitative imaging of cancer in the postgenomic era: Radio(geno)mics, deep learning, and habitats.

Napel S, Mu W, Jardim-Perassi BV, Aerts HJWL, Gillies RJ.

Cancer. 2018 Dec 15;124(24):4633-4649. doi: 10.1002/cncr.31630. Epub 2018 Nov 1. Review.


A radiogenomic dataset of non-small cell lung cancer.

Bakr S, Gevaert O, Echegaray S, Ayers K, Zhou M, Shafiq M, Zheng H, Benson JA, Zhang W, Leung ANC, Kadoch M, Hoang CD, Shrager J, Quon A, Rubin DL, Plevritis SK, Napel S.

Sci Data. 2018 Oct 16;5:180202. doi: 10.1038/sdata.2018.202.


Magnetic resonance imaging and molecular features associated with tumor-infiltrating lymphocytes in breast cancer.

Wu J, Li X, Teng X, Rubin DL, Napel S, Daniel BL, Li R.

Breast Cancer Res. 2018 Sep 3;20(1):101. doi: 10.1186/s13058-018-1039-2.


Community Health Centers in the Dakotas, 2018.

Vogt HB, Tinguely J, Franken J, Ten Napel S.

S D Med. 2018 Aug;71(8):355-360.


Deep Learning Techniques for Automatic MRI Cardiac Multi-Structures Segmentation and Diagnosis: Is the Problem Solved?

Bernard O, Lalande A, Zotti C, Cervenansky F, Yang X, Heng PA, Cetin I, Lekadir K, Camara O, Gonzalez Ballester MA, Sanroma G, Napel S, Petersen S, Tziritas G, Grinias E, Khened M, Kollerathu VA, Krishnamurthi G, Rohe MM, Pennec X, Sermesant M, Isensee F, Jager P, Maier-Hein KH, Full PM, Wolf I, Engelhardt S, Baumgartner CF, Koch LM, Wolterink JM, Isgum I, Jang Y, Hong Y, Patravali J, Jain S, Humbert O, Jodoin PM.

IEEE Trans Med Imaging. 2018 Nov;37(11):2514-2525. doi: 10.1109/TMI.2018.2837502. Epub 2018 May 17.


Erratum: Semi-automated pulmonary nodule interval segmentation using the NLST data.

Balagurunathan Y, Beers A, Kalpathy-Cramer J, McNitt-Gray M, Hadjiiski L, Zhao B, Zhu J, Yang H, Yip SSF, Aerts HJWL, Napel S, Cherezov D, Cha K, Chan HP, Flores C, Garcia A, Gillies R, Goldgof D.

Med Phys. 2018 Jun;45(6):2689-2690. doi: 10.1002/mp.12905. Epub 2018 Apr 24. No abstract available.


Radiogenomics is the future of treatment response assessment in clinical oncology.

El Naqa I, Napel S, Zaidi H.

Med Phys. 2018 Oct;45(10):4325-4328. doi: 10.1002/mp.13035. Epub 2018 Jun 21. No abstract available.


GFPT2-Expressing Cancer-Associated Fibroblasts Mediate Metabolic Reprogramming in Human Lung Adenocarcinoma.

Zhang W, Bouchard G, Yu A, Shafiq M, Jamali M, Shrager JB, Ayers K, Bakr S, Gentles AJ, Diehn M, Quon A, West RB, Nair V, van de Rijn M, Napel S, Plevritis SK.

Cancer Res. 2018 Jul 1;78(13):3445-3457. doi: 10.1158/0008-5472.CAN-17-2928. Epub 2018 May 14.


Intratumoral Spatial Heterogeneity at Perfusion MR Imaging Predicts Recurrence-free Survival in Locally Advanced Breast Cancer Treated with Neoadjuvant Chemotherapy.

Wu J, Cao G, Sun X, Lee J, Rubin DL, Napel S, Kurian AW, Daniel BL, Li R.

Radiology. 2018 Jul;288(1):26-35. doi: 10.1148/radiol.2018172462. Epub 2018 May 1.


Semi-automated pulmonary nodule interval segmentation using the NLST data.

Balagurunathan Y, Beers A, Kalpathy-Cramer J, McNitt-Gray M, Hadjiiski L, Zhao B, Zhu J, Yang H, Yip SSF, Aerts HJWL, Napel S, Cherezov D, Cha K, Chan HP, Flores C, Garcia A, Gillies R, Goldgof D.

Med Phys. 2018 Mar;45(3):1093-1107. doi: 10.1002/mp.12766. Epub 2018 Feb 19. Erratum in: Med Phys. 2018 Jun;45(6):2689-2690.


Quantitative Image Feature Engine (QIFE): an Open-Source, Modular Engine for 3D Quantitative Feature Extraction from Volumetric Medical Images.

Echegaray S, Bakr S, Rubin DL, Napel S.

J Digit Imaging. 2018 Aug;31(4):403-414. doi: 10.1007/s10278-017-0019-x.


Radiomics in Brain Tumor: Image Assessment, Quantitative Feature Descriptors, and Machine-Learning Approaches.

Zhou M, Scott J, Chaudhury B, Hall L, Goldgof D, Yeom KW, Iv M, Ou Y, Kalpathy-Cramer J, Napel S, Gillies R, Gevaert O, Gatenby R.

AJNR Am J Neuroradiol. 2018 Feb;39(2):208-216. doi: 10.3174/ajnr.A5391. Epub 2017 Oct 5. Review.


Prediction of EGFR and KRAS mutation in non-small cell lung cancer using quantitative 18F FDG-PET/CT metrics.

Minamimoto R, Jamali M, Gevaert O, Echegaray S, Khuong A, Hoang CD, Shrager JB, Plevritis SK, Rubin DL, Leung AN, Napel S, Quon A.

Oncotarget. 2017 May 10;8(32):52792-52801. doi: 10.18632/oncotarget.17782. eCollection 2017 Aug 8.


Noninvasive radiomics signature based on quantitative analysis of computed tomography images as a surrogate for microvascular invasion in hepatocellular carcinoma: a pilot study.

Bakr S, Echegaray S, Shah R, Kamaya A, Louie J, Napel S, Kothary N, Gevaert O.

J Med Imaging (Bellingham). 2017 Oct;4(4):041303. doi: 10.1117/1.JMI.4.4.041303. Epub 2017 Aug 21.


Non-Small Cell Lung Cancer Radiogenomics Map Identifies Relationships between Molecular and Imaging Phenotypes with Prognostic Implications.

Zhou M, Leung A, Echegaray S, Gentles A, Shrager JB, Jensen KC, Berry GJ, Plevritis SK, Rubin DL, Napel S, Gevaert O.

Radiology. 2018 Jan;286(1):307-315. doi: 10.1148/radiol.2017161845. Epub 2017 Jul 20.


Heterogeneous Enhancement Patterns of Tumor-adjacent Parenchyma at MR Imaging Are Associated with Dysregulated Signaling Pathways and Poor Survival in Breast Cancer.

Wu J, Li B, Sun X, Cao G, Rubin DL, Napel S, Ikeda DM, Kurian AW, Li R.

Radiology. 2017 Nov;285(2):401-413. doi: 10.1148/radiol.2017162823. Epub 2017 Jul 14.


A Rapid Segmentation-Insensitive "Digital Biopsy" Method for Radiomic Feature Extraction: Method and Pilot Study Using CT Images of Non-Small Cell Lung Cancer.

Echegaray S, Nair V, Kadoch M, Leung A, Rubin D, Gevaert O, Napel S.

Tomography. 2016 Dec;2(4):283-294. doi: 10.18383/j.tom.2016.00163.


Variations in the functional visual field for detection of lung nodules on chest computed tomography: Impact of nodule size, distance, and local lung complexity.

Ebner L, Tall M, Choudhury KR, Ly DL, Roos JE, Napel S, Rubin GD.

Med Phys. 2017 Jul;44(7):3483-3490. doi: 10.1002/mp.12277. Epub 2017 May 23.


Adaptive local window for level set segmentation of CT and MRI liver lesions.

Hoogi A, Beaulieu CF, Cunha GM, Heba E, Sirlin CB, Napel S, Rubin DL.

Med Image Anal. 2017 Apr;37:46-55. doi: 10.1016/ Epub 2017 Jan 13.


Radiomics of Lung Nodules: A Multi-Institutional Study of Robustness and Agreement of Quantitative Imaging Features.

Kalpathy-Cramer J, Mamomov A, Zhao B, Lu L, Cherezov D, Napel S, Echegaray S, Rubin D, McNitt-Gray M, Lo P, Sieren JC, Uthoff J, Dilger SK, Driscoll B, Yeung I, Hadjiiski L, Cha K, Balagurunathan Y, Gillies R, Goldgof D.

Tomography. 2016 Dec;2(4):430-437. doi: 10.18383/j.tom.2016.00235.


Predictive radiogenomics modeling of EGFR mutation status in lung cancer.

Gevaert O, Echegaray S, Khuong A, Hoang CD, Shrager JB, Jensen KC, Berry GJ, Guo HH, Lau C, Plevritis SK, Rubin DL, Napel S, Leung AN.

Sci Rep. 2017 Jan 31;7:41674. doi: 10.1038/srep41674.


A Convolutional Neural Network for Automatic Characterization of Plaque Composition in Carotid Ultrasound.

Lekadir K, Galimzianova A, Betriu A, Del Mar Vila M, Igual L, Rubin DL, Fernandez E, Radeva P, Napel S.

IEEE J Biomed Health Inform. 2017 Jan;21(1):48-55. doi: 10.1109/JBHI.2016.2631401. Epub 2016 Nov 22.


Robust Intratumor Partitioning to Identify High-Risk Subregions in Lung Cancer: A Pilot Study.

Wu J, Gensheimer MF, Dong X, Rubin DL, Napel S, Diehn M, Loo BW Jr, Li R.

Int J Radiat Oncol Biol Phys. 2016 Aug 1;95(5):1504-1512. doi: 10.1016/j.ijrobp.2016.03.018. Epub 2016 Mar 24.


A Comparison of Lung Nodule Segmentation Algorithms: Methods and Results from a Multi-institutional Study.

Kalpathy-Cramer J, Zhao B, Goldgof D, Gu Y, Wang X, Yang H, Tan Y, Gillies R, Napel S.

J Digit Imaging. 2016 Aug;29(4):476-87. doi: 10.1007/s10278-016-9859-z.


Special Section Guest Editorial:Radiomics and Imaging Genomics: Quantitative Imaging for Precision Medicine.

Napel S, Giger M.

J Med Imaging (Bellingham). 2015 Oct;2(4):041001. doi: 10.1117/1.JMI.2.4.041001. Epub 2015 Dec 11. No abstract available.


Core samples for radiomics features that are insensitive to tumor segmentation: method and pilot study using CT images of hepatocellular carcinoma.

Echegaray S, Gevaert O, Shah R, Kamaya A, Louie J, Kothary N, Napel S.

J Med Imaging (Bellingham). 2015 Oct;2(4):041011. doi: 10.1117/1.JMI.2.4.041011. Epub 2015 Nov 18.


Magnetic resonance image features identify glioblastoma phenotypic subtypes with distinct molecular pathway activities.

Itakura H, Achrol AS, Mitchell LA, Loya JJ, Liu T, Westbroek EM, Feroze AH, Rodriguez S, Echegaray S, Azad TD, Yeom KW, Napel S, Rubin DL, Chang SD, Harsh GR 4th, Gevaert O.

Sci Transl Med. 2015 Sep 2;7(303):303ra138. doi: 10.1126/scitranslmed.aaa7582.


Content-based image retrieval in radiology: analysis of variability in human perception of similarity.

Faruque J, Beaulieu CF, Rosenberg J, Rubin DL, Yao D, Napel S.

J Med Imaging (Bellingham). 2015 Apr;2(2):025501. doi: 10.1117/1.JMI.2.2.025501. Epub 2015 Apr 3.


Glioblastoma Multiforme: Exploratory Radiogenomic Analysis by Using Quantitative Image Features.

Gevaert O, Mitchell LA, Achrol AS, Xu J, Echegaray S, Steinberg GK, Cheshier SH, Napel S, Zaharchuk G, Plevritis SK.

Radiology. 2015 Jul;276(1):313. doi: 10.1148/radiol.2015154019. No abstract available.


NCI Workshop Report: Clinical and Computational Requirements for Correlating Imaging Phenotypes with Genomics Signatures.

Colen R, Foster I, Gatenby R, Giger ME, Gillies R, Gutman D, Heller M, Jain R, Madabhushi A, Madhavan S, Napel S, Rao A, Saltz J, Tatum J, Verhaak R, Whitman G.

Transl Oncol. 2014 Oct 24;7(5):556-69. doi: 10.1016/j.tranon.2014.07.007. eCollection 2014 Oct.


Characterizing search, recognition, and decision in the detection of lung nodules on CT scans: elucidation with eye tracking.

Rubin GD, Roos JE, Tall M, Harrawood B, Bag S, Ly DL, Seaman DM, Hurwitz LM, Napel S, Roy Choudhury K.

Radiology. 2015 Jan;274(1):276-86. doi: 10.1148/radiol.14132918. Epub 2014 Oct 16.


On combining image-based and ontological semantic dissimilarities for medical image retrieval applications.

Kurtz C, Depeursinge A, Napel S, Beaulieu CF, Rubin DL.

Med Image Anal. 2014 Oct;18(7):1082-100. doi: 10.1016/ Epub 2014 Jul 2.


CT angiography after 20 years: a transformation in cardiovascular disease characterization continues to advance.

Rubin GD, Leipsic J, Joseph Schoepf U, Fleischmann D, Napel S.

Radiology. 2014 Jun;271(3):633-52. doi: 10.1148/radiol.14132232. Review.


Glioblastoma multiforme: exploratory radiogenomic analysis by using quantitative image features.

Gevaert O, Mitchell LA, Achrol AS, Xu J, Echegaray S, Steinberg GK, Cheshier SH, Napel S, Zaharchuk G, Plevritis SK.

Radiology. 2014 Oct;273(1):168-74. doi: 10.1148/radiol.14131731. Epub 2014 May 12. Erratum in: Radiology. 2015 Jul;276(1):313.


Predicting visual semantic descriptive terms from radiological image data: preliminary results with liver lesions in CT.

Depeursinge A, Kurtz C, Beaulieu C, Napel S, Rubin D.

IEEE Trans Med Imaging. 2014 Aug;33(8):1669-76. doi: 10.1109/TMI.2014.2321347. Epub 2014 May 1.


A hierarchical knowledge-based approach for retrieving similar medical images described with semantic annotations.

Kurtz C, Beaulieu CF, Napel S, Rubin DL.

J Biomed Inform. 2014 Jun;49:227-44. doi: 10.1016/j.jbi.2014.02.018. Epub 2014 Mar 12.


Automatic annotation of radiological observations in liver CT images.

Gimenez F, Xu J, Liu Y, Liu T, Beaulieu C, Rubin D, Napel S.

AMIA Annu Symp Proc. 2012;2012:257-63. Epub 2012 Nov 3.


Modeling perceptual similarity measures in CT images of focal liver lesions.

Faruque J, Rubin DL, Beaulieu CF, Napel S.

J Digit Imaging. 2013 Aug;26(4):714-20. doi: 10.1007/s10278-012-9557-4.


Quantifying the margin sharpness of lesions on radiological images for content-based image retrieval.

Xu J, Napel S, Greenspan H, Beaulieu CF, Agrawal N, Rubin D.

Med Phys. 2012 Sep;39(9):5405-18. doi: 10.1118/1.4739507.


Non-small cell lung cancer: identifying prognostic imaging biomarkers by leveraging public gene expression microarray data--methods and preliminary results.

Gevaert O, Xu J, Hoang CD, Leung AN, Xu Y, Quon A, Rubin DL, Napel S, Plevritis SK.

Radiology. 2012 Aug;264(2):387-96. doi: 10.1148/radiol.12111607. Epub 2012 Jun 21.


Prognostic PET 18F-FDG uptake imaging features are associated with major oncogenomic alterations in patients with resected non-small cell lung cancer.

Nair VS, Gevaert O, Davidzon G, Napel S, Graves EE, Hoang CD, Shrager JB, Quon A, Rubin DL, Plevritis SK.

Cancer Res. 2012 Aug 1;72(15):3725-34. doi: 10.1158/0008-5472.CAN-11-3943. Epub 2012 Jun 18. Erratum in: Cancer Res. 2012 Sep 15;72(18):4870-1.


Uncluttered Single-Image Visualization of Vascular Structures Using GPU and Integer Programming.

Won JH, Jeon Y, Rosenberg JK, Yoon S, Rubin GD, Napel S.

IEEE Trans Vis Comput Graph. 2013 Jan;19(1):81-93. doi: 10.1109/TVCG.2012.25. Epub 2012 Jan 31.


Accuracy of a remote eye tracker for radiologic observer studies: effects of calibration and recording environment.

Tall M, Choudhury KR, Napel S, Roos JE, Rubin GD.

Acad Radiol. 2012 Feb;19(2):196-202. doi: 10.1016/j.acra.2011.10.011.


Automated temporal tracking and segmentation of lymphoma on serial CT examinations.

Xu J, Greenspan H, Napel S, Rubin DL.

Med Phys. 2011 Nov;38(11):5879-86. doi: 10.1118/1.3643027.


A comprehensive descriptor of shape: method and application to content-based retrieval of similar appearing lesions in medical images.

Xu J, Faruque J, Beaulieu CF, Rubin D, Napel S.

J Digit Imaging. 2012 Feb;25(1):121-8. doi: 10.1007/s10278-011-9388-8.


Automated quantification of aortoaortic and aortoiliac angulation for computed tomographic angiography of abdominal aortic aneurysms before endovascular repair: preliminary study.

Raman B, Raman R, Napel S, Rubin GD.

J Vasc Interv Radiol. 2010 Nov;21(11):1746-50. doi: 10.1016/j.jvir.2010.07.025. Epub 2010 Oct 8.


Managing biomedical image metadata for search and retrieval of similar images.

Korenblum D, Rubin D, Napel S, Rodriguez C, Beaulieu C.

J Digit Imaging. 2011 Aug;24(4):739-48. doi: 10.1007/s10278-010-9328-z.

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