GRADUATE SCHOOL OF INFORMATICS


Ünal Erkan Mumcuoğlu

Picture of the person
Prof. Dr. Ünal Erkan Mumcuoğlu
Medical Informatics
Room No: 
A-218
Tel No: 
+90 (312) 210-3753
E-mail: 
merkan@metu.edu.tr
Personal Web Page: 
Education: 

1990-94 Ph.D, EE, University of Southern Californica(USC), USA
1987-90 M.Sc., EE, Bilkent University, Turkey
1983-87 B.Sc., EE, Middle East Technical University, Turkey

Research Interests: 

Dr. Erkan Mumcuoğlu is involved in research activities in an array of 2D and 3D Medical and Biological Image Analysis applications. The main areas of his research focus in recent years are: Automatic and Semi-Automatic Image Segmentation, Computer-Aided Diagnosis, Rigid/Non-rigid Image Alignment (Registration), Content-Based Image Retrieval, PACS, Medical Informatics and Bioinformatics

 

Some of his recent research projects:

» Computer-assisted airway wall and vessel measurements from lung CT images

» Computer-aided diagnosis systems on renal scintigraphy, mammography and chest radiography images

» Fusion of MR andCT images for 3D human head modeling

» Mitocondria detection and segmentation on Electron Microscopy images

 

Part of his research activities are in collaboration with the National Center for Microscopy and Imaging Research (NCMIR) at the University of California San Diego and the Department of Biomedical Informatics of Ohio State University College of Medicine on some research projects.

 

 

He is also one of the founders of the Health Informatics Department in the Informatics Institute, Middle East Technical University.

Courses / Laboratories: 

» MIN 524 Fundamentals of Medical Imaging: Acquisition and Reconstruction

» MIN 528 Fundamentals of Mathematics for Information Systems

» MIN 530 Medical Image Analysis

» MIN 711 Advanced Topics in Medical Image Analysis

» IS 566 Image Processing Algorithms

» IS 503 Database

» ION 523 Data Mining

» ION 574 Medical Imaging Technology

Thesis / Research Information: 
 

Honors, Scholarships and Awards


» 2009 Fulbright Scholar, for supporting research in USA, 6-months (at Biomedical Informatics Department, Ohio State University)

» 2009 Academic Performance Award, METU

» 2008 Best paper award finalist, Tıp Bilişimi Kongresi

» 2007 Thesis of the Year Award, METU: (Thesis Supervisor of Hasan Oğul)

» 2007 Serhat Özyar Young Investigator Award: (Thesis Supervisor of Hasan Oğul)

» 2005 Academic Performance Award, METU

» 2004 Dr. Suphi Artunkal Award winner, 6th International Congress of Nuclear Oncology and 17th National Congress of Turkish Nuclear Medicine jointly with eight authors

» 1994 1st prize in the Young Investigator Award competition in Computer and Instrumentation from the Society of Nuclear Medicine

» 1990-91 Turkish Education Ministry PhD scholarship to study abroad

» 1983-87 Undergraduate Scholarship, TÜBİTAK

Professional Experience


» 2013 –        Full Professor, Health Informatics Department, Informatics institute, METU, Ankara, Turkey

» 2006 – 2012 Associate Professor, Health Informatics Department, Informatics Institute, METU, Ankara, Turkey

» 2001 - 2006  Assistant Professor, Information Systems Department, Informatics institute, METU, Ankara, Turkey

» 1999 – 2001  System Design Engineer, on Ultrasound Imaging Acuson Inc., Mountain View, CA, USA

» 1997 – 1998 Systems Software Engineer, Teradyne Inc., CA, USA

» 1997 Research Associate, Biomedical Engineering Department, USC, USA

» 1995 - 1996 Post-Doctoral Research Fellow, Crump Institute for Biological Imaging, UCLA, USA

» 1991 – 1994 Research Assistant, Signal & Image Processing Institute, Electrical Engineering Department, University

of Southern California(USC), USA

» 1987 – 1990 Research Assistant, Electrical Engineering Department, Bilkent University, Ankara, Turkey

» 1985 – 1987 Part-time Engineer, R&D center, ASELSAN Electronics Inc, Ankara, Turkey

 

Administrative Duties

 

» 2004 –2008 Department Chair, Health Informatics Department, METU

» 2006 - 2008 Member of Board of Directors of “Turkish Medical Informatics Association”

» 2003 - 2007 Director of ION Graduate Program, METU

» 2003 - 2007 Director of MIN Master and PhD program, METU

 

Industrial Consulting

 

» 2010-2011 Metasoft Bilgisayar,  

» 2012- Akgün Yazılım,          

» 2012- Asya Yazılım, 

 

Theses Supervised

Past:       

» Emre Şener (PhD, 2012), Automatic Bayesian Segmentation of Human Facial Tissue Using 3D MR-CT Fusion by Inporporating models of Image Blurring, Noise and Partial Volume

» Ayşegül Kutlay (MSc, 2012 Analysis of factors affecting acceptance of homecare technologies by patients with chronic care

» Emre Kale (MSc, 2011) Human head tissue segmentation by fusion of MR and CT imaging modalities using Level Set and Bayesian methods

» Umut Kocak (MSc, 2007), Haptic Rendering in Dental Education Simulation

» Hasan Oğul (PhD, 2006), Computational Representation of Protein Sequences for Homology Detection and Classification

» Emre Kösen (MSc, 2004), Design and implementation ofa mobile patient data collection and transmission system for an emergency ambulance

» Koray Orhun (MSc, 2004), Interactive Volume Rendering for Medical Images

» Erhan Ergüt (MSc, 2003), Analysis of microarray images using FCM and k-means clustering algorithms (co-supervised with Yasamin Yardimcı)

» Birsen Gülden (MSc, 2003), GIS application for Ambulance Routing Services: A Prototype (co-supervised with Nazife Baykal)

 

Ongoing:

» Serdar Taşel (PhD)

» Mustafa Kahraman (PhD)

» Ersin Kamberli (PhD)

» Emrah Akkoyun (PhD)

» Salih Caner (MSc)

» Negin Bagherzadi (MSc)

» Mustafa Çöçelli (MSc)

» Ainaz Muhammedi (MSc)

Research Groups

Publications: 

International Citations

» Times cited: 376 (self-citations excluded)

» h-index: 7

 

International Patents

» LOFTMAN RC, MORGAN KE, MUMCUOGLU E, USTUNER KF, BANJANIN Z (05.19.2005), Transmit Based Axial Whitening, US Patent no: US2005107699

 

International Journal Papers

» Mumcuoğlu EU, Long FR, Castile RG, Gurcan MN, (2013), Image Analysis for Cystic Fibrosis: Computer-Assisted Airway Wall and Vessel Measurements from Low-Dose, Limited Scan Lung CT Images, Journal of Digital Imaging, 26(1): 82-96.

» EH Kale, EU Mumcuoglu, S Hamcan, (2012), Automatic segmentation of human facial tissue by MRI–CT fusion: A feasibility study, Computer Methods and Programs in Biomedicine, 108(3): 1106-20.

» EU Mumcuoglu, R. Hassanpour, SF Tasel, G. Perkins, ME Martone, MN Gurcan, (2012), Computerized detection and segmentation of mitochondria on electron microscope images, Journal of Microscopy, Volume: 246, Page: 248–265.

» EU Mumcuoglu, FM Bozkurt, M Aslan, E Sener, O Ugur, (2011), Computerized scar detection on renal cortical scintigraphy images. Nuclear Medicine Communications, 32:1070–1078.

» Konukseven EI, Onder ME, Mumcuoglu E, Kisnisci RS. (2010), Development of a Visio-Haptic Integrated Dental Training Simulation System, Journal of Dental Education, 74 (8): 880-891. (Times Cited: 1)

» Oğul, H., Mumcuoğlu EÜ (2007) A discriminative method for remote homology detection based on n-peptide compositions with reduced amino acid alphabets, BioSystems, January, 87 (1), pp.75-81. (Times Cited: 10)

» H.Ogul, E.Mumcuoglu, (2007), Subcellular Localization Prediction with New Protein Encoding Schemes, IEEE-ACM Transactions on Computational Biology and Bioinformatics, 4 (2): 227 – 232. (Times Cited: 6

» Mumcuoğlu EÜ, Nar F, Yardımcı Y, Koçak U, Ergün EL, Volkan Salancı B, Uğur O, Erbaş B (2006) Simultaneous Surface Registration of Ictal, Interictal SPECT and MR Images for Epilepsy Studies, Nuclear Medicine Communications, Jan;27(1):45-55. (Times Cited: 4)

» H.Ogul, E.Mumcuoglu, (2006), SVM-based Detection of Distant Protein Structural Relationships Using Pairwise Probabilistic Suffix Trees, Computational Biology and Chemistry, 30 (4): 292-299. (Times Cited: 5)

» Celasun B, Mumcuoglu EÜ, Kalkan H (2005), A Simulation Study on the Sampling of Sentinel Lymph Nodes, Analytical and Quantitative Cytology and Histology, vol. 27, no. 4, pg. 187-194. (Times Cited: 3)

» Singh M., Mumcuoglu EÜ (1998) Design of a CZT Based BreastSPECT System, IEEE Transactions on Nuclear Science, vol. 45., no. 3, pg. 1158-1165. (Times Cited: 22)

» Chan M.T., Leahy R.M., Mumcuoglu EÜ, Cherry S.R, Czernin J., Chatziioannou A. (1997) Comparing Lesion Detection Performance for PET Image Reconstruction Algorithms: A Case Study, IEEE Transactions on Nuclear Science, vol. 44, no. 4, pg. 1558-1563. (Times Cited: 15)

» Mumcuoglu EÜ, Leahy R., Cherry S.R. (1996) Bayesian Reconstruction of PET Images: Methodology and Performance Analysis, Physics in Medicine and Biology, vol. 41., pg. 1777-1807. (Times Cited: 99)

» Cherry S.R., Shao Y., Siegel S., Silverman R.W., Mumcuoglu E., Meadors K., Phelps K. (1996) Optical Fiber Readout of Scintillators Arrays using a Multi-Channel PMT: A High Resolution PET Detector for Animal Imaging, IEEE Transactions on Nuclear Science, vol. 43, no. 3, pg. 1932-1937. (Times Cited: 60)

» Mumcuoglu EÜ, Leahy R., Cherry S.R., Zhou Z.Y. (1994) Fast Gradient-Based Methods for Bayesian Reconstruction of Transmission and Emission PET Images, IEEE Transactions on Medical Imaging, vol. 13, no.4, pg. 687-701. (Times Cited: 139)

 

International Conference Presentations

» Mumcuoglu EU, Prescott J, Baker BN, Clifford B, Long F, Castile R, Gurcan MN., Image analysis for cystic fibrosis: Automatic lung airway wall and vessel measurement on CT images, Conf Proc IEEE Eng Med Biol Soc.,1:3545-8, 2009.

» E. Mumcuoğlu, F. Nar, Ö. Uğur, MF. Bozkurt, M. Aslan, Image-based retrieval system and computer-aided diagnosis system for renal cortical scintigraphy images, Medical Imaging 2008: Computer-Aided Diagnosis, Maryellen L. Giger; Nico Karssemeijer, Editors, 69153J, Proceedings Vol. 6915, SPIE 2008.

» Ogul, H; Mumcuoglu, EU, Protein solvent accessibility prediction using support vector machines and sequence conservations, Artificial Intelligence and Neural Networks, Published in Lecture Notes in Artificial Intelligence, Volume: 3949 Pages: 141-148, 2006

» V. Kılıç, U. Koçak, İ. Konukseven, E. Mumcuoğlu, GPU Supported Haptic Device Integrated Dental Simulation Environment, Proceedings of Eurohaptics’2006, Paris, France, pp. 135-140.

» F. Nar, E. Mumcuoglu, Y. Yardimci, U. Kocak, Simultaneous Registration of Ictal SPECT, Interictal SPECT and MR Images for Epilepsy Studies: Method and Simulations, Proceedings of the IASTED International Conference on Biomedical Engineering, pp. 11-16, Feb. 16-18 2005, Innsbruck, Austria, ACTA Press, Editors: K.-P. Adlassnig, M. Bracale.

» E. Mumcuoglu, F. Nar, Y. Yardimci, U. Kocak, E.L. Ergün, B. Volkan, Ö. Uğur, B. Erbaş, Simultaneous Triple-Registration of Ictal SPECT, Interictal SPECT and MR Images for Epilepsy Studies: Method and Validation, Proceedings of the International Europian Signal Processing Conference (Eusipco), Antalya - Turkey, September 2005, ISBN: 975-00188-0-X, pp. 100-103.

» H Oğul, EÜ Mumcuoğlu, Prediction of Protein Subcellular Localization Using Support Vector Machines and Probabilistic Suffix Trees, Proceedings of International Symposium on Health Informatics and Bioinformatics, Antalya - Turkey Nov. 2005, ISBN 429-239-6, pp. 56-62.

» K Kuru, B Celesun, E Mumcuoğlu, The Use of Lab Color Model for Sharpening and Optimization of Digital Images of Hematoxylin & Eosin Stained Microscopical Materials, Proceedings of International Symposium on Health Informatics and Bioinformatics, Antalya - Turkey Nov. 2005, ISBN 429-239-6, pp. 210-218.

» Ogul, H; Mumcuoglu, UE, Discriminative remote homology detection using maximal unique sequence matches, Advances in Intelligent Data Analysis, Published in Lecture Notes in Computer Science, A.F. Famili et al. (Eds.):, 3646, pp. 283 – 292, Springer-Verlag, 2005

» E. Ergut, Y. Yardimci, E. Mumcuoglu, O. Konu (2003), Analysis of Microarray Images Using FCM and K-means clustering algorithms, Proceedings of the International conference of Signal Processing, vol:1, no:2, page 8, September 24-26, Turkey

» B. Gulden, E. Mumcuoglu, N. Baykal (2003), A GIS System For Ambulatory Transport, BIOMED 2003, 10th Biomedical Science and Technology Symposium, P83, Turkey (also in the Proceedings of the Second IASTED International Conference on Biomedical Engineering Pages: 431-435)

» Singh M, Mumcuoglu E (1997), Design of a CZT Based BreastSPECT System, IEEE Nuclear Science Symposium - Conference Record, Vols 1 & 2 Pages: 1150-1154 Published: 1998

» Leahy, RM; Chan, MT; Cherry, SR; Mumcuoglu EU; et al. Comparison of lesion detection performance for PET image reconstruction using channelized hotelling observers, Society of Nuclear Medicine Meeting, Journal of Nuclear Medicine Volume: 38 Issue: 5 Pages: 286-286, 1997 (Times Cited: 1)

» Mumcuoglu EU., et.al. (1996) Bayesian Image Reconstruction for Cardiac PET, The Society of Nuclear Medicine Meeting, Denver, Colorado, Journal of Nuclear Medicine Volume: 37 Issue: 5 Pages: 510-510 Published: MAY 1996
Mumcuoglu EU, Leahy R. et.al. (1996), Accurate Geometric and Physical Response Modeling for Statistical Image Reconstruction in High Resolution PET, IEEE Nuclear Science Symposium, Vols 1-3 Pages: 1569-1573 Published: 1997, Anaheim, CA

» Chan MT, Leahy R, Mumcuoglu EU, et.al. (1996), Comparing Lesion Detection Performance for PET Image Reconstruction Algorithms: a Case Study, IEEE Nuclear Science Symposium - Conference Record, Vols 1-3 Pages: 1552-1556 Published: 1997, Anaheim, CA

» Cherry S.R., Shao Y., Siegel S., Silverman R.W., Meadows K., Mumcuoglu E.U et.al. (1996) Micropet: A Dedicated PET Scanner for Small Animal Imaging, IEEE Nuclear Science Symposium - Conference Record, Vols 1-3 Pages: 1120-1124 Published: 1997, Anaheim, CA

» Cherry, SR; Shao, YP; Siegel, S; et al. Fiber readout of scintillator arrays using a multi-channel PMT: A high resolution PET detector for animal imaging, IEEE Nuclear Science Symposium and Medical Imaging Conference Record, Vols 1-3 Pages: 1766-1770 Published: 1996

» Cherry, SR; Shao, Y; Silverman, RW; et al. Micropet: A dedicated PET scanner for small animal imaging. The Society of Nuclear Medicine Meeting, Journal of Nuclear Medicine Volume: 37 Issue: 5 Pages: 334-334 Published: MAY 1996 (Times Cited: 3)

» Mumcuoglu E.U., Leahy R., et.al. (1995) A Phantom Study of the Quantitative Behavior of Bayesian PET Reconstruction Methods, IEEE Nuclear Science Symposium and Medical Imaging Conference Record, Vols 1-3 Pages: 1703-1707 Published: 1996, San Francisco, CA

» Zhou Z., Leahy R., Mumcuoglu E.U. (1995) Simultaneous Hyperparameter Estimation and Bayesian Image Reconstruction for PET, Nuclear Science Symposium & Medical Imaging Conference - 1994 IEEE Conference Record, Vols 1-4 Pages: 1604-1608 Published: 1994, San Francisco, CA

» Zhou Z., Leahy R., Mumcuoglu E.U. (1995), Maximum Likelihood Hyperparameter Estimation for Gibbs Priors from Incomplete Data with Applications to Positron Emission Tomography, Information Processing in Medical Imaging Conference, Volume: 3 Pages: 39-51

» Mumcuoglu E.U., Leahy R., et.al. (1994) Bayesian Reconstruction for Attenuation Corrected Whole-Body PET Using Very Low Count Data, The Society of Nuclear Medicine Meeting, Orlando, Florida, Journal of Nuclear Medicine Volume: 35 Issue: 5 Pages: P34-P34 Published: MAY 1994

» Zhou Z., Leahy R., Mumcuoglu E.U. (1994), On the Effects of Hyper-Parameter Estimation on ROI Bias and Variance in Bayesian PET, The Society of Nuclear Medicine Meeting, Orlando, Florida, Journal of Nuclear Medicine Volume: 35 Issue: 5 Pages: P72-P72 Published: MAY 1994

» Mumcuoglu E.U., Leahy R., et.al. (1994) A Gradient Projection Conjugate Gradient Algorithm in Bayesian PET Reconstruction, Nuclear Science Symposium & Medical Imaging Conference - 1994 IEEE Conference Record, Vols 1-4 Pages: 1212-1216 Published: 1994, Norfolk, Virginia

» Mumcuoglu E.U., Leahy R., et.al. (1993) Fast Bayesian Techniques for Attenuation Corrected Whole-Body PET, Nuclear Science Symposium & Medical Imaging Conference, Vols 1-3 Pages: 1902-1906 Published: 1993, San Francisco, CA

» Zhou Z., Leahy R., Mumcuoglu E.U. (1993), A Comparative Study of the Effects of Using Anatomical Priors in PET Reconstruction, Nuclear Science Symposium & Medical Imaging Conference, Vols 1-3 Pages: 1749-1753 Published: 1993, San Francisco, CA

» Mumcuoglu E.U., Leahy R., et.al. (1992) A Statistical Approach to Transmission Image Reconstruction from Ring Source Calibration Measurements in PET, Conference Record of the 1992 IEEE Nuclear Science Symposium and Medical Imaging Conference, Vols 1 and 2 Pages: 910-912 Published: 1992, Orlando, Florida (Times Cited: 2)

» Mumcuoglu E.U., Sezer M.E., (1990) On Ripple-Free Deadbeat Control Problem, Paper presented at the IEEE Bilkent International Conference on New Trends in Communication, Control and Signal Processing, Ankara, Turkey

 

National Conference Presentations

» P. YILDIRIM, UE. MUMCUOĞLU, MR. TOLUN, MN. ÖZMEN, M. ULUDAĞ, Klinik Veritabanlarında Etkin Veri Madenciliği Amacıyla Çoklu-ilişkisel Veri Madenciliği Yaklaşımı, 5. Ulusal Tıp Bilişimi Kongresi/Medical Informatics 2008 Turkey

» E. Şener, E. Mumcuoğlu, E. Kale, V Akgün, BT ve MR Görüntülerini 3 Boyutta Çakıştırarak ve Birlikte Kullanarak, Otomatik ve Yarı-Otomatik Bölütleme Yöntemleri Geliştirilmesi ve Bu Yöntemlerin Kafa Modeli Oluşturma ve Yüz Mimik Kaslarının Bölütlenmesine Uygulanması, 5. Ulusal Tıp Bilişimi Kongresi/Medical Informatics 2008 Turkey

» F. NAR, E. Mumcuoğlu, U. Koçak, Ö. Uğur, F. Bozkurt, M. Aslan, K. Güneştepe, M. Cerrahoğlu, Sintigrafik Böbrek Görüntüleri için İçerik Tabanlı Arama Sistemi, IEEE 14th Signal Processing and Communications Applications, 17-19 April 2006, pg. 1-4, Antalya.

» K. KURU, H. GÜL, G. GÜRSEL, K. ARDA, E. MUMCUOĞLU, N. BAYKAL, Sağlık Hizmetlerinde Kaynakların Doğru Kullanımında Bilgisayar Benzetim Yönteminin Kullanılması: Bir Poliklinik Çalışması, 2. Ulusal Tıp Bilişimi Kongresi/Medical Informatics 2005 Turkey Bildiriler/Proceedings, pp. 14-20 (Editör: K. Hakan Gülkesen)

» B. Volkan, E.L. Ergün, F. Nar, E. Mumcuoğlu, Y. Yardımcı, A. Cila, S. Saygı, Ö. Uğur, B. Erbaş (2004), Geliştirdiğimiz Yazılım ile Epilpsi odağı oluşturulmuş beyin fantomu kullanılarak Siscom algoritmasının uygulanması: Analyze 5.0 ile sonuçlarının kıyaslanması, (6th International Congress of Nuclear Oncology and 17th National Congress of Turkish Nuclear Medicine), Turkish Journal of Nuclear Medicine, Vol.13, No.1, Page:10.

» H. Oğul, Ü.E. Mumcuoğlu, Protein Ailelerinde En Büyük Ortak İkincil Yapı Eşleşmelerinin Bulunması, Biyomedikal Müh. Toplantısı (BIYOMUT), sayfa 107-113, Mayıs 2004, İstanbul.

» F. Nar, C. Gencel, B. Volkan, E. Mumcuoglu, Y. Yardimci, A. Erol, O. Ugur, B. Er (2003), 3-boyutlu ve Moduler Tibbi Imge Analizi Yazilimi, Sinyal Isleme ve Iletisim Uygulamalari Kurultayi, Koc University, Pages:753-756, Turkey