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Journals

  1. G. Olgun, C. Sokmensuer, and C. Gunduz-Demir, "Local object patterns for tissue image representation and cancer classification," 2013 (submitted).

  2. S. Arslan, T. Ersahin, R. Cetin-Atalay, and C. Gunduz-Demir, "Attributed relational graphs for cell nucleus segmentation in fluorescence microscopy images," IEEE Transactions on Medical Imaging, 2013 (in press).

  3. E. Ozdemir and C. Gunduz-Demir, "A hybrid classification model for digital pathology using structural and statistical pattern recognition," IEEE Transactions on Medical Imaging, 32(2):474-483, 2013. [pdf]

  4. C.F. Koyuncu, S. Arslan, I. Durmaz, R. Cetin-Atalay, and C. Gunduz-Demir, "Smart markers for watershed-based cell segmentation," PLoS ONE, 7(11):e48664, 2012. [pdf]

  5. E. Ozdemir, C. Sokmensuer, and C. Gunduz-Demir, "A resampling-based Markovian model for automated colon cancer diagnosis," IEEE Transactions on Biomedical Engineering, 59(1):281-289, 2012. [pdf]

  6. A.C. Simsek, A.B. Tosun, C. Aykanat, C. Sokmensuer, and C. Gunduz-Demir, "Multilevel segmentation of histopathological images using cooccurrence of tissue objects," IEEE Transactions on Biomedical Engineering, 59(6):1681-1690, 2012. [pdf]

  7. A.B. Tosun and C. Gunduz-Demir, "Graph run-length matrices for histopathological image segmentation," IEEE Transactions on Medical Imaging, 30(3):721-732, 2011. [pdf]

  8. C. Gunduz-Demir, M. Kandemir, A.B. Tosun, and C. Sokmensuer, "Automatic segmentation of colon glands using object-graphs," Medical Image Analysis, 14(1):1-12, 2010. [pdf]

  9. D. Altunbay, C. Cigir, C. Sokmensuer, and C. Gunduz-Demir, "Color graphs for automated cancer diagnosis and grading," IEEE Transactions on Biomedical Engineering, 57(3):665-674, 2010. [pdf]

  10. M. Cebe and C. Gunduz-Demir, "Qualitative test-cost sensitive classification," Pattern Recognition Letters, 31(13):2043-2051, 2010. [pdf]

  11. A.B. Tosun, M. Kandemir, C. Sokmensuer, and C. Gunduz-Demir, "Object-oriented texture analysis for the unsupervised segmentation of biopsy images for cancer detection," Pattern Recognition, 42(6):1104-1112, 2009. [pdf]

  12. C. Gunduz-Demir, "Mathematical modeling of the malignancy of cancer using graph evolution," Mathematical Biosciences, 209(2):514-527, 2007. [pdf]

  13. C. Demir, S.H. Gultekin, and B. Yener, "Learning the topological properties of brain tumors," IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2(3):262-270, 2005.

  14. C. Demir, S.H. Gultekin, and B. Yener, "Augmented cell-graphs for automated cancer diagnosis," Bioinformatics, 21(Suppl 2):ii7-ii12, 2005.

  15. C. Demir and E. Alpaydin, "Cost-conscious classifier ensembles," Pattern Recognition Letters, 26(14):2206-2214, 2005.

  16. C. Gunduz, B. Yener, and S.H. Gultekin, "The cell-graphs of cancer," Bioinformatics, 20(Suppl 1):i145-i151, 2004.

Conferences

  1. A.B. Tosun, C. Sokmensuer, and C. Gunduz-Demir, "Unsupervised tissue image segmentation through object-oriented texture," 20th International Conference on Pattern Recognition, Istanbul, Turkey, August 2010.

  2. M. Cebe and C. Gunduz-Demir, "Test-cost sensitive classification based on conditioned loss functions," 18th European Conference on Machine Learning, Warsaw, Poland, September 2007 (published in LNAI 4701, Springer-Verlag).

  3. C.C.Bilgin, C. Demir, C. Nagi, and B. Yener, "Cell-graph mining for breast tissue modeling and classification," 29th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, Lyon, France, August 2007.

  4. C. Demir, S.H. Gultekin, and B. Yener, "Augmented cell-graphs for automated cancer diagnosis," 4th European Conference on Computational Biology, Madrid, Spain, September 2005.

  5. C. Demir, S.H. Gultekin, and B. Yener, "Spectral analysis of cell-graphs for automated cancer diagnosis," 4th Conference on Modeling and Simulation in Biology, Medicine and Biomedical Engineering, Linkoping, Sweden, May 2005.

  6. C. Demir, S.H. Gultekin, and B. Yener, "Rule-based automated cancer diagnosis," 2nd Annual Rocky Mountain Regional Bioinformatics Conference, Aspen, Colorado, December 2004.

  7. C. Gunduz, B. Yener, and S.H. Gultekin, "The cell-graphs of cancer," 12th International Conference on Intelligent Systems for Molecular Biology (ISMB), Glasgow, Scotland, August 2004.

  8. C. Gunduz, O.T. Yildiz, E. Alpaydin, and T. Bilgic, "An algorithm to learn the structure of a Bayesian network," 10th Turkish Symposium on Artificial Intelligence and Neural Networks, June 2001.

National Conferences

  1. S. Arslan, I. Durmaz, R. Cetin-Atalay, and C. Gunduz-Demir, "Unsupervised segmentation of live cell images using Gaussian modeling," IEEE 19th Signal Processing, Communication, and Applications Conference, Antalya, Turkey, April 2011.

  2. E.B. Ozgul, C. Sokmensuer, and C. Gunduz-Demir, "Detection of colon glands using subgraph modeling," IEEE 19th Signal Processing, Communication, and Applications Conference, Antalya, Turkey, April 2011.

  3. E. Ozdemir, C. Sokmensuer, and C. Gunduz-Demir, "Histopathological Image Classification with the Bag of Words Model," IEEE 19th Signal Processing, Communication, and Applications Conference, Antalya, Turkey, April 2011.

  4. C. Cigir, C. Sokmensuer, and C. Gunduz-Demir, "Mathematical analysis of colon glands for cancer diagnosis," IEEE 17th Signal Processing, Communication, and Applications Conference, Antalya, Turkey, April 2009.

Invited Talks

  1. C. Gunduz-Demir, "Tissue image analysis for automated cancer diagnosis and grading," Nanyang Technological University, School of Electrical and Electronic Engineering, Singapore (April 3, 2009).

  2. C. Gunduz-Demir, "Tissue representation and analysis for automated cancer diagnosis and grading," Bilkent University, Department of Molecular Biology and Genetics, Ankara (December 20, 2006).

  3. C. Gunduz-Demir, "Automated cancer diagnosis and grading on biopsies," Middle East Technical University, Department of Computer Engineering, Ankara (November 24, 2006).

  4. C. Gunduz-Demir, "The cell-graphs of cancer," University of Texas, MD Anderson Cancer Center, Houston, TX (November 9, 2005).

  5. C. Gunduz-Demir, "The cell-graphs of cancer," Bilkent University, Department of Computer Engineering, Ankara (June 13, 2005).

Others

Technical reports

  1. C. Demir and B.Yener, "Automated cancer diagnosis based on histopathological images: a systematic survey," Technical report, Rensselaer Polytechnic Institute, Department of Computer Science, TR-05-09, March 2005.

  2. C. Demir, S.H. Gultekin, and B.Yener, "Spectral analysis of cell-graphs of cancer," Technical report, Rensselaer Polytechnic Institute, Department of Computer Science, TR-04-17, November 2004.

  3. C. Demir, S.H. Gultekin, and B.Yener, "Learning the topological properties of brain tumors," Technical report, Rensselaer Polytechnic Institute, Department of Computer Science, TR-04-14, November 2004.

  4. C. Gunduz, B. Yener, and S.H. Gultekin, "Learning the cell-graphs: Macroscopic modeling of brain tumors," Technical report, Rensselaer Polytechnic Institute, Department of Computer Science, TR-03-12, October 2003.

  5. C. Gunduz and B. Yener, "Accuracy and sampling trade-offs for inferring Internet router graph," Technical report, Rensselaer Polytechnic Institute, Department of Computer Science, TR-03-9, July 2003.

  6. C. Gunduz, M. Balman, and B. Yener, "Evasiveness of Internet topology," Technical report, Rensselaer Polytechnic Institute, Department of Computer Science, TR-03-2, March 2003.

Theses

  1. C. Gunduz, "The cell-graphs of brain cancer," Ph.D. thesis, Rensselaer Polytechnic Institute, Troy, NY, December 2005.

  2. C. Gunduz, "Value of representation in pattern recognition," M.S. thesis, Bogazici University, Istanbul, Turkey, June 2001.