Publications

Book chapter:

“Devices for Evaluating Imaging Systems”, in Nuclear Medicine Physics, A Handbook for Teachers and Students, will be published by IAEA.

Journal Papers:

• 1. Turning EGFP into a highly sensitive, rapid and a-large-dynamic-range method using Markov Random Field based image segmentation (in preparation)

  2. "Quantification of Bone Metastasis in Whole-body PETCT Images”, Omer Demirkaya, Mohei Abuzied, Tarek Munshi, Ayman Rifai (in preparation)

  3. L. Al-Haj, W. Al-Ahmadi, M. Al-Saif, O. Demirkaya, and K. Khabar, "Cloning-free regulated monitoring of reporter and gene expression," BMC Molecular Biology, vol. 10, p. 20, 2009.

  4. Omer Demirkaya and Refaat Al Mazrou, "Acceptance Testing on Gamma Camera Systems", (under revision) Nuclear Medicine Communications

  5. Omer Demirkaya and Refaat Al Mazrou, "Performance Test Data Analysis of Gamma Cameras", IEEE Transaction on Nuclear Science, 5:1506-1515, 2007

  6. Al-Zoghaibi, Fahad; Abuleef, Hana; Demirkaya, Omer; Khabar, Khalid, "Bioinformatics and experimental derivation of an efficient 3' untranslated region and use in translationally active linear DNA with minimum Poly(A) region", Gene. 2007 Apr 15;391(1-2):130-9

  7. A. S. Alzahrani, G. E. Mohamed, A. A. Rifai, A. Al-Sugair, S. A. Salam, O. M.Sulaiman, and O. Demirkaya, "Role of [(18)f fluorodeoxyglucose positron emission tomography in follow-up of differentiated thyroid cancer," Endocr Pract, vol. 12, pp. 152-8, 2006.

  8. Musa H. Asyali, Dilek Kaya, Omer Demirkaya, Mehmet S. Inan, “Gene Expression Profile Classification: A Review”, Current Bioinformatics, Vol 1, No 1, 2006.

  9. Omer Demirkaya, Musa H. Asyali and Mohamed Shoukri, Segmentation of Microarray cDNA Spots Using Markov Random Field Modeling, Bioinformatics, 21 (13): 2994. (2005)

  10. Omer Demirkaya, “Post-Reconstruction Filtering of PET Whole-body Emission Images and Attenuation Maps Using Nonlinear Diffusion Filtering”, Academic Radiology, vol. 11, Issue 10, October 2004, pp. 1105-1114

  11. Omer Demirkaya and Musa Asyali “Determination of image bimodality thresholds for different intensity distributions”, Signal Processing: Image Communication, vol. 19, no. 6, pp.507-516, 2004

  12. Omer Demirkaya, “Smoothing Impulsive Noise Using Nonlinear Diffusion Filtering”, Sonka, Milan; Kakadiaris, Ioannis A.; Kybic, Jan (Eds.), CVAMIA-MMBIA 2004, Lecture Notes in Computer Science, 3117, 438 pp. 111-122, Springer-Verlag Berlin Heidelberg 2004.

  13. Musa Asyali, Mohammed Shoukri, Omer Demirkaya, Khalid Khabar, “Assessment of Reliability of Microarray Data and Estimation of Signal Thresholds Using Mixture Modeling”, Nucleic Acids Res., April 27, 2004; 32(8): 2323 - 2335.

  14. Omer Demirkaya, “Anisotropic Diffusion Filtering of PET Attenuation Data to Improve Emission Images”, Physics in Medicine and Biology. 47 No 20 (21 October 2002) N271-N278

  15. Mohamed Shoukri and Omer Demirkaya, “Sample size requirement to compare rater’ s precision”, Journal of Applied Statistics, Vol. 27, No 4, pp. 483-494,2000

  16. Steven M. Jorgensen, Omer Demirkaya, and Eric L. Ritman, "Three dimensional imaging of vasculature and parencyhyma in intact rodent organs with x-ray Micro-CT", Am J Physiol 275(Heart Circ Physiol 44): H1103-H1114, 1998

  17. Omer Demirkaya, Robert M. Cothren, Geoffrey Vince, Fredrick Cornhill, "Automated identification of stained cells in tissue sections using digital image analysis" Analyt Quant Cytol Histol, 1999; 21(2):93-102

  18. Omer Demirkaya, Fatih Yalcin and Yelda Ozsunar, "Peculiarities of Coronary Atheromateus Plaque and Importance of Intravascular Ultrasound Imaging”, Medical Network: Cardiology, 4(3): 1-5, June 1997

  19. D. Geoffrey Vince, Omer Demirkaya, Robert M. Cothren, and J. Fredrick Cornhill, “Quantitative Analysis of Inflammatory Cells in Aortic Atherosclerosis of Young Adults”, Cardiovascular Pathology, 5(1): 3-10, 1996

Conference Proceedings:

• 1. Omer Demirkaya and Musa H. Asyali, “Segmentation of cDNA microarray Spots using MRF-based method” Proc of IEEE EMBS, 2003.

  2. Omer Demirkaya, “Lesion segmentation in wholebody images of PET”,Proc. of IEEE NSS/MIC, 2003.

  3. Sharok Kimiaei, Refaat Mazrou and Omer Demirkaya, “Resolution recovery in PET using "local convolution" deconvolution: a novel approach” Medical Imaging 2003: Physics of Medical Imaging, Vol. 5030, 2003.

  4. Omer Demirkaya,”Improving SNR in PET images by using anisotropic diffusion filtration”, Proc. of IEEE EMBS, vol.1, pp. 501 –503, 2000.

  5. Omer Demirkaya and Erik L Ritman, “Noise Reduction in X-ray Microtomographic Images by Anisotropic Diffusion Filtration of the Scanner Projection”, Proc. SPIE, vol. 3661, pp. 690-697,1999.

  6. Omer Demirkaya, "Between-class variance as a measure of image sharpness and bimodality", Proc of IEEE EMBS, vol.2, pp. 590 –593, 1997