Ulas Bagci, Ph.D., Curriculum Vitae (CV) December 2017   

Education and Qualifications 

  4328 Scorpius Street, HEC 221, Center for Research in Computer Vision (CRCV), University of Central Florida (UCF), Orlando, 32816 FL USA Emails: ulasbagci@gmail.com or bagci@ucf.edu Phone: +1 407 823 1047 

2010 PhD  University of Nottingham, UK.  School of Computer Science,   In collaboration with Dept. of Radiology, University of Pennsylvania, PA, USA.   Thesis: Automatic Anatomy Recognition and Registration.   Advisers: Prof. Jayaram K. Udupa (UPenn) and Prof. Li Bai (UNott). 

 2009 Visiting Fellow Dept. of Radiology, University of Pennsylvania, PA, USA. 

   2005 MSc  Koc University, Turkey.EECS.   

  Thesis: Boosting Classifiers for Automatic Music Genre Classification.   Adviser: Prof. Engin Erzin.    

2003 BSc  Bilkent University, Turkey.     Electrical and Electronics Engineering.   Adviser: Prof. Enis Cetin.   

  Research Interests  Developing effective and high-throughput scientific methods in the following majors:  

● Medical Image Analysis and Biomedical Imaging ● Machine Learning 

 My expertise include the following keywords:  

Computer Vision and Image Processing: Image Segmentation, Image Registration, Shape Analysis, Object Tracking, Image Quantification, Image Enhancement, Object Recognition, Joint segmentation of multiple images, Eye-tracking, visual attention modeling and perception. 

Pattern Analysis: Deep learning, Support vector machines, Computer aided diagnosis methods, boosting, random forest, graph-cut, random walk, graph search, probabilistic graphical models, radiomics. 

Clinical and preclinical applications: Cardiac Imaging, ZIKA, MERS, Tuberculosis, pulmonary imaging, infectious lung disease, lung cancer, kidney cancer, liver cancer, pancreas cancer, nuclear medicine imaging, radiology,preclinical imaging, fat quantification, brown fat identification, prostate cancer imaging and analysis, eye tracking in radiology, perceptual process of screening in radiology. 

Biomedical Imaging Modalities that I have expertise: MRI, PET, CT, PET/CT, fMRI, PET/MRI, DTI, DWI, OCT, Histology 

  

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  Employment  12/14-now    Center for Research in Computer Vision (CRCV), University of Central Florida, 

Orlando, FL. Position    Assistant Professor of Computer Science 

 3/13-12/14    Radiology and Imaging Sciences, National Institutes of Health (NIH), Bethesda, MD. Position    Staff Scientist (Title 42) Duties    1) Staff scientist and  Lab Manager at the CIDI lab, 

  2) Supervising postdocs, post-bacs, and interns.   3) Research: Computational Radiology and Biomedical Imaging.   4) Image analysis lead of the IRF-NIAID projects (MERS1, MERS5, H1N1, etc).  

08/12-03/13 

  Radiology and Imaging Sciences, National Institutes of Health (NIH), Bethesda, MD. 

Position    Senior Research Fellow Duties 

         

  Research in Computational Radiology and Biomedical Imaging.   

08/10-08/12    Radiology and Imaging Sciences, National Institutes of Health (NIH), Bethesda, MD. Position    Imaging Science Training Program (ISTP) Research Fellow Duties 

       

  Research in Computational Radiology and Biomedical Imaging.   

02/2009-06/2009   Department of Radiology, University of Pennsylvania, PA, USA. Position    Visiting Research Fellow Duties 

     

  Research in Medical Image Processing and Analysis.   

06-09  School of Computer Science, University of Nottingham, UK Position    Marie Curie Research Fellow   Duties    Research in Medical Image Processing and Analysis. 

  

03-06  Electrical & Electronics and Computer Engineering, Koc University, Istanbul, Turkey Position    Research and Teaching Assistant Duties 

   

  Research in Signal and Image Processing, Teaching in Computer Science.   Honors & Awards  • 2017: RSNA Merit Award (Deep Learning for Radiology Applications) • 2017: Brain Computer Interface (BCI) Award Nominee (My PhD student’s work: Harish RaviPrakash) • 2017: IEEE SMC 2017 Best Student Paper Finalist (My Phd student’s work: Harish RaviPrakash) • 2017: IEEE SMC 2017 Best Conference Paper Finalist (My Phd student’s work: Harish RaviPrakash) • 2017: NASCI (North America Society of Cardiovascular Imaging) 2017 Best Young Investigator 

Finalist (My PhD student’s work-AliAsghar Mortazi) • 2017: IEEE ISBI 2017 - Travel Award (My PhD student’s work-Neslisah Torosdagli) • 2017: Highlighted in the cover of “Tomography” journal for CT standard and low dose quantitative 

comparison study. • 2016: The Best Scientific Reviewer Award at MICCAI 2016. • 2015: Recognized Reviewer for Distinguished Service at IEEE ISBI 2015. • 2014: Selected as Distinguished Reviewer by Elsevier. 

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• 2014: RSNA Certificate of Merit: The State-of-the-Art and Recent Advances in Pulmonary Image Analysis Techniques. 

• 2014: RSNA Certificate of Merit: Computerized Detection and Classification of Pulmonary Pathologies from CT Images: Current Approaches, Challenges, and Future Trends. 

• 2014: Highlighted in the cover of IEEE Transactions on Biomedical Engineering Journal for in Novel PET Image Segmentation/Quantification study. 

• 2013: Winner of the Fellows Award for Research Excellence (FARE) Award by NIH. • 2013: Highlighted in MDLinx due to the first MRI-PET, PET-CT, and MRI-PET-CT 

co-segmentation software. • 2013: Highlighted in AuntMinnie due to the first MRI-PET, PET-CT, and MRI-PET-CT 

co-segmentation software. • 2012: Best Poster Prize (Molecular Imaging of Infectious Diseases, co-author). • 2012: Winner of the Fellows Award for Research Excellence (FARE) Award by NIH. • 2011: RSNA Education Exhibit Merit Award (co-author). • 2010-2012: NIH Imaging Sciences Training Program (ISTP) Fellowship. • 2006-2009: Marie Curie Research Fellowship, Fp6 Marie Curie Action Programme. • 2006: IEEE Best Student Paper Award-IEEE Conference on Signal Processing and Communications 

Applications. • 2005-2006: DPT Grant for Graduate Study in Koc¸ University, Drive-Safe Project. • 2003-2005: Honored with Vehbi Koc Scholarship, Full Graduate Fellowship, from Koc University. • 1998-2003: Honored with Full-Scholarship by Bilkent University for Undergraduate Study. • 1998-2003: Outstanding Student-Scholarship by Turk Telecom. • 1998: Ranked 1st on the Eastern Anatolia and had several high ranks in University entrance exam 

OYS-98 over 1.5 million students in Turkey.  Computer Skills  • Programming: C/C++, Unix Shell Scripting, Java, Processing, R, Python • Scientific Tools/Software: TensorFlow, ITK/VTK, Slicer, Matlab, 3DViewnix, CAVASS, 

Mathematica, Octave, OpenGL, PACS, OSIRIX • OS: Unix/Linux, MacOS, Windows   Teaching Experience  UCF Computer Science: 

• Robot Vision (Undergraduate Level), Spring 2018 

• Computer Vision (Graduate Level, CAP 5415), Fall 2015 (Evaluation: 4.35/5) Fall 2016 (Evaluation: 4.00/5) Fall 2017 (Evaluation: 4.21/5) 

• Medical Image Computing (Graduate Level, CAP 5937). Spring 2016 (Evaluation: ) Spring 2017 (Evaluation: 4.67/5) 

 UCF REU (research experiences for undergraduates) Courses 

• Algorithms and Methods for Quantitative Radiology (Summer-2015, Summer-2016), • Introduction to Medical Imaging (Summer-2015, Summer-2016) • Machine Learning in Medical Imaging (Summer-2017) 

  CIDI Seminars, NIH (2012-2014): 

• Clinical Image Processing and Analysis, • Computational Radiology, • Statistical Machine Learning, • Computer Graphics and Visualization. 

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 Teaching Assistant, Koc University (2003-2006): • Introduction to C programming, • Introduction to Java programming, • Digital Systems Design and CAD CAM Lab.   

Invited Talks & Lectures Delivered  • 10-2017: Computer Aided Diagnosis in the Deep Learning Era. Johns Hopkins University, Baltimore, 

MD. • 10-2017: Deep Learning and Diagnostic Imaging for Clinical Studies. EMO, Ankara, Turkey. • 9-2016: Developing Next Generation Image Analysis Methods for Infectious Diseases. Imaging of 

Infection and Inflammation” track of World Molecular Imaging Congress (WMIC), NYC, NY. • 5-2016: Advances in Lesion Quantification from PET/CT and PET/MRI. SIAM-Imaging Science 

conference, Albuquerque, New Mexico. • 3-2016: Automatic Quantification of Whole Body Adiposity. Soochow University, Suzhou, China. • 10-2015: The Role of Imaging and Image Analysis in Public Threatening Diseases. Soochow 

University, Suzhou, China. • 4-2015: Quantitative PET Image Analysis: Applications in Cancer and Infectious Diseases. Moffitt 

Cancer Center, Tampa, FL, USA. • 12-2014: Recent Advances in Clinical Image Processing: Quantification of PET/CT and PET/MR 

Images. Center for Medical Image Computing, University of College London (UCL), London, United Kingdom. 

• 9-2014: Fuzzy Connectedness Image Co-Segmentation for Hybrid PET/MRI and PET/CT Scans. Computational Methods for Molecular Imaging Workshop-MICCAI, Boston, MA, USA. 

• 8-2014: Advanced Methods for Quantification of PET, PET/CT, and MRI/PET Images. CRCV Invited Talk, Department of Computer Engineering, University of Central Florida, Orlando, FL, USA. 

• 5-2014: Advanced Methods for Quantification of PET, PET/CT, and MRI/PET Images. MIPG Seminar Series, Department of Radiology, University of Pennsylvania, Philadelphia, PA, USA. 

• 2-2014: Advanced Methods in Pulmonary Image Analysis: Applications in Infectious Lung Diseases. Brown Bag Lecture Series, National Library of Medicine (NLM), Bethesda, MD, USA. 

• 10-2013: Predicting Future Morphological Changes of Lesions from Radiotracer Uptake in 18F-FDG-PET Images. NIAID Integrated Research Facility (IRF), Fort Detrick, Frederick,, MD, USA. 

• 09-2013: Computational Radiology Approaches for Quantifying Pulmonary Infections in Small Animal Images. The third Annual Seminar on Molecular Imaging of Infectious Diseases, School of Medicine, Johns Hopkins University, Baltimore, MD, USA. 

• 03-2012: Hierarchical Scale Based Multi-Object Recognition of 3D Anatomical Structures. MIPG, Department of Radiology, University of Pennsylvania, PA, USA. 

• 12-2011: Clinical Image Processing and Analysis - Automated methods for detection, recognition, and                         segmentation of anatomical and functional objects. National Cancer Institute-Frederick, SAIC. 

• 10-2011: Hierarchical Scale Based Multi-Object Recognition of 3D Anatomical Structures. Imaging Biomarkers and Clinical Image Processing Group, NIH, USA. 

• 03-2011: Automatic Detection of Tree-in-Bud Patterns from CT scans. Clinical Image Processing Group, NIH, USA. 

• 10-2009: Automatic Best Reference Slice Selection for 3D Volume Reconstruction from 2D Histological Slices, Computational Biomedicine Lab, University of Houston, USA. 

• 10-2009: Localisation of Abdominal Organs for Medical Image Analysis. Computational Biomedicine Lab, University of Houston, USA. 

• 2009: Oriented Model Based Localisation of Abdominal Organs in Medical Images.Marie Curie Workshop, on Medical Image Analysis, University of Nottingham, UK. 

• 04-2009: Automatic Best Reference Slice Selection for 3D Volume Reconstruction of a Mouse Brain From Histological Sections, MIPG, University of Pennsylvania. 

• 07-2008: The Role of Intensity Standardization in Medical Image Registration, Port d’Informacio Cientifica (PIC), Universitat Autonoma de Barcelona (UAB), Barcelona. 

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• 10-2007: Registration of Standardized Histological Images in Feature Space for 3D Volume Reconstruction, Academic Radiology, Queen’s Medical Centre, Nottingham. 

• 07-2007: Multi-resolution Elastic Image Registration in Standard Intensity Scale,Marie Curie Workshop on Medical Image Analysis, Nottingham. 

• 05-2007: Dual-Tree Complex Wavelet Transform. CMIAG, University of Nottingham, UK. • 02-2007: Brain Image Warping. CMIAG, University of Nottingham, UK. • 12-2006: Brain Image Analysis in Alzheimer’s Disease. CMIAG, University of Nottingham, UK. • 2005: MATLAB tutorial for machine learning. Koc University, Istanbul, Turkey. • 2004: Musical Genre Classification. SIGNALIST, Istanbul Technical University, Istanbul, Turkey.   Memberships in Societies  • ACM (Association for Computing Machinery) Member • RSS (Royal Statistical Society) Member • ASA (American statistical association) Member • IEEE Senior Member • IEEE Engineering in Medicine and Biology Society Member • AAAS Member • MICCAI Member • RSNA (Radiological Society of North America) Associate Member • SNMMI (Society of Nuclear Medicine and Molecular Imaging) • SPIE Member   

Services-Reviewer  • IEEE Transactions on Medical Imaging • IEEE Transactions on Image Processing • IEEE Transactions on Biomedical Engineering • IEEE Transactions on Signal Processing • IEEE Transactions on Computational Biology and Bioinformatics • IEEE Transactions on Information Forensics and Security • IEEE Signal Processing Letters • IEEE Journal of Biomedical and Health Informatics • Medical Image Analysis (Elsevier) • Computer Vision and Image Understanding (Elsevier) • Computers in Biology and Medicine (Elsevier) • Computerized Medical Imaging and Graphics (Elsevier) • Pattern Recognition Letters (Elsevier) • Artificial Intelligence in Medicine (Elsevier) • NeuroComputing (Elsevier) • Intern. Journal of Computer Assisted Tomography • Plos One • ACM Computing Reviews • Machine Vision and Applications • The Visual Computer • Information • Journal of Infection and Public Health • RadioGraphics (RSNA) • Medical Physics (RSNA) • Nature Scientific Reports • Human Brain Mapping • Magnetic Resonance Materials in Physics, Biology and Medicine (MAGMA) • Molecular Imaging and Biology   

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Services-Conferences, Workshops, and Editorial  Services to UCF 

• Faculty Senate Member, 2017-now. • CRCV Faculty Search Committee Chair 2017-2018 • Graduate Committee Member, Computer Science, UCF (completed as of 2016). 

 Editorial Board 

• Associate Editor, Medical Physics Journal. • Editorial Board Member of Computers in Biology and Medicine Journal (Elsevier). • Editorial Board Member of World Journal of Radiology. • Area Editor (Artificial Intelligence), Information 

 PhD/MSc/BSc Thesis Committee 

• Ph.D. Dissertation Committee Member of Khurram Soomro (completed as of 3 November 2017). 

• Ph.D. Dissertation Committee Member of Nasim Souly (completed as of 3 November 2017). • MSc. Dissertation Committee Chair of Nandakishore Puttasamachar (completed as of 3 

November 2017). • Ph.D. Dissertation Committee Member of Vildan Atalay (completed as of 27 October 2017). • Ph.D. Dissertation Committee Member of Waqas Sultan (completed as of 7 July 2017). • Ph.D. Dissertation Committee Member of Syed Alam (completed as of 21 April 2017). • Ph.D. Dissertation Committee Member of Dong Zhang (completed as of 11 July 2016). • Ph.D. Dissertation Committee Member of Afshin Deghan (completed as of 4 April 2016). • MSc. Dissertation Committee Member of Lahari Tumuliri (completed as of 7 April 2016). • BSc. Dissertation Committee Chair of Arjun Watane (completed as of 6 April 2017). • Senior Design Project - Review Panel Member (2017, 3 projects). • Senior Design Project - Review Panel Member (2016, 1 project). 

 Conference Committee 

• Program Committee Member, Computational Methods and Clinical Applications in Spine Imaging, Workshop, MICCAI 2013. 

• Program Committee Member, Computational Methods and Clinical Applications in Spine Imaging, Workshop, MICCAI 2014. 

• Program Committee Member, Computational Methods and Clinical Applications in Spine Imaging, Workshop, MICCAI 2015. 

• Program Committee Member, Computational Methods and Clinical Applications in Spine Imaging, Workshop, MICCAI 2017. 

• Program Committee Member, Ophthalmic Medical Image Analysis, Workshop, MICCAI 2014. • Program Committee Member, Computational Methods for Molecular Imaging (CMMMI), 

Workshop, MICCAI 2014. • Program Committee Member, Computational Methods for Molecular Imaging (CMMMI), 

Workshop, MICCAI 2015. • Program Committee Member, Computational Methods for Molecular Imaging (CMMMI), 

Workshop, MICCAI 2017. • Program Committee Member, SPIE Medical Imaging, 2017. • Session Chair, SPIE Medical Imaging-Image Processing Track, 2017. 

 Grant Reviews 

• Review Panel Member - Czech Science Foundation Grants • Review Panel Member - AAAS Grants • Review Panel Member - Breast Cancer Now (UK) • Review Panel Member - Fondation Recherche Medicale (FR) • Review Panel Member - The Netherlands Organization for Scientific Research (NWO) • Review Panel Member - The Austrian Science Fund (FWF) • Review Panel Member - NSF 

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Supervised Students  UCF (PhD Students): 

• Sarfaraz Hussein, (2015-...) • AliAsghar Mortazi, (2016-...) • Naji Khosrovan, (2016-...) • Harish RaviPrakash, (2016-...) • Neslisah Torosdagli, (2016-...) • Rodney LaLonde, (2017-...) 

 UCF (MSc Students): 

• Sumit Laha, MSc. Student, (2017-...) • Nandakishore Puttashamachar, (2016-2017). Now: Disney Research/Orlando. 

  Alumni: 

• Ismail Irmakci, Ph.D Student, CRCV, UCF and Ege University Turkey (2016-2017).  Now: He is with Ege University, Turkey. 

• Arjun Watane, Undergraduate CS Student, UCF (2015-2017).  Now: He is with Medical School, University of Miami, FL. 

• Poay Hoon Lim, Ph.D Student, University of Nottingham, UK (2011-2014).  Now: She is with University of Calgary, Canada. 

• Ziyue Xu, Post-Doctoral Fellow, CIDI, NIH (2012-2015).  Now: He is staff scientist at NIH, Bethesda, MD. 

• Awais Mansoor, Post-Doctoral Fellow, CIDI, NIH (2012-2014).  Now: He is with George Washington University, Washington, DC. 

• Mingchen Gao, Post-Doctoral Fellow, CIDI, NIH (2014-2015).  Now: She is faculty at University at Buffalo SUNY. 

• Mario Buty, Post-Bac Fellow, CIDI, NIH (2014-2015).  Now: He is with IMPAQ International, Seattle, WA. 

• Aaron Wu, Post-Bac Fellow, CIDI, NIH (2014-2015).  Now: He is with CuraCloud, Seattle, WA. 

• Brent Foster, Post-Bac Fellow, CIDI, NIH (2012-2014).  Now: He is with UC Davis. 

 • Kirsten Miller-Jaster, Post-Bac Fellow, CIDI, NIH (2011-2012). 

Now: She is with Cleveland Clinics. • Neil Mendhiratta, Summer Intern, MD student, NYU (2012).  

Now: He is with UCLA.   

Publications  I have authored 165 papers on relevant topics (3 book (book chapter, book review), 51 journal articles, 54 peer-reviewed conference proceedings and/or lecture notes, and 58 abstracts).  * indicates students under my direct supervision (including postdocs, postbacs, and summer interns), and in those studies I am the corresponding author.  Google Scholar h-index: 21 Google Scholar i10-index: 37    

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Books  

1. Xu, Z., G. Z. Papadakis, D. J. Mollura, and Bagci, Ulas (2017). Chapter 11: Image Analyses. Ed. by S. Jain. Imaging Infection. Springer. 

 2. A.Statnikov, C. Aliferis, D. Hardin, and I. Guyon (2013). A Gentle Introduction to Support Vector 

Machines in Biomedicine Volume 2: Case Studies and Benchmarks. http://www.worldscientific. com/worldscibooks/10.1142/7923. 

 3. U. Bagci (2010). Automatic Anatomy Recognition and Registration-Medical Image Processing and 

Analysis. LAP LAMBERT Academic Publishing.   Journal Papers  

1. Xiang, D., Bagci, U., Jin, C., Shi, F., Zhu, W., Yao, J., Chen, X (2017). CorteXpert: A model-based method for automated renal cortex segmentation. Medical Image Analysis 42, 257-273. 

 2. Green, A., Bagci, U., S. Hussein, and M. Osman (2017). Brown Adipose Tissue Detected by 

PET/CT Imaging is Associated with Less Central Obesity. Nuclear Medicine Communication 38(7), 537-539. 

 3. M.Buty, Z.Xu, A.Wu, M. Gao, C. Nelson, G. Papadakis, U.Teomete, H. Celik, B. Turkbey, P. 

Choyke, D. Mollura, U.Bagci, and L. Folio (2017). Quantitative Image Quality Comparison of Reduced and Standard Dose Dual Energy Multiphase Chest, Abdomen, and Pelvis CT. Tomography 3 (2), 114–122. 

 4. Papadakis, G. Z., S. Jha, T. Bhattacharyya, C. Millo, T.-W. Tu, Bagci, Ulas, K. Marias, A. H. 

Karan-tanas, and N. J. Patronas (2017). 18F-NaF PET/CT in Extensive Melorheostosis of the Axial and Appendicular Skeleton With Soft-Tissue Involvement. Clinical Nuclear Medicine 42(7), 537–539. 

 5. Papadakis, G. Z., D. Mavroudis, V. Georgoulias, J. Souglakos, A. K. Alegakis, G. Samonis, Bagci, 

Ulas, A. Makrigiannakis, and O. Zoras (2017). Serum IGF-1, IGFBP-3 levels and circulating tumor cells (CTCs) in early breast cancer patients. Growth Hormone & IGF Research. 

 6. Papadakis, G. Z., C. Millo, A. H. Karantanas, Bagci, Ulas, and N. J. Patronas (2017). Avascular 

Necrosis of the Hips With Increased Activity on 68Ga-DOTATATE PET/CT. Clinical Nuclear Medicine.  

 7. Papadakis, G. Z., C. Millo, S. M. Sadowski, A. H. Karantanas, Bagci, Ulas, and N. J. Patronas 

(2017). Breast Fibroadenoma With Increased Activity on 68Ga DOTATATE PET/CT. Clinical Nuclear Medicine 42(2), 145–146.  

 8. Papadakis, G. Z., C. Millo, S. M. Sadowski, A. H. Karantanas, Bagci, Ulas, and N. J. Patronas 

(2017). Fibrous Dysplasia Mimicking Malignancy on 68Ga-DOTATATE PET/CT. Clinical Nuclear Medicine.  

 9. Candemir, S., S. Jaeger, S. Antani, Bagci, Ulas, L. R. Folio, Z. Xu, and G. Thoma (2016). Atlas-based 

rib-bone detection in chest X-rays. Computerized Medical Imaging and Graphics 51, 32–39.   

10. Hussein, S., A. Green, A. Watane, D. Reiter, X. Chen, G. Z. Papadakis, B. Wood, A. Cypess, M. Osman, and Bagci, Ulas (2016). Automatic Segmentation and Quantification of White and Brown Adipose Tissues from PET/CT Scans. IEEE Transactions on Medical Imaging 36(3), 734–744.  

 

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11. Johnson, R. F. et al. (2016). 3B11-N, a monoclonal antibody against MERS-CoV, reduces lung pathology in rhesus monkeys following intratracheal inoculation of MERS-CoV Jordan-n3/2012. Virology 490, 49–58. 

 12. Kopriva, I., W. Ju, B. Zhang, F. Shi, D. Xiang, K. Yu, X. Wang, Bagci, Ulas, and X. Chen (2016). 

Single-channel Sparse Nonnegative Blind Source Separation Method for Automatic 3D Delineation of Lung Tumor in PET Images. IEEE Journal of Biomedical and Health Informatics.  

 13. Papadakis, G. Z., C. Millo, Bagci, Ulas, J. Blau, and M. T. Collins (2016). 18F-NaF and 18F-FDG 

PET/CT in Gorham-Stout Disease. Clinical Nuclear Medicine 41(11), 884–885.   

14. Papadakis, G. Z., C. Millo, S. M. Sadowski, Bagci, Ulas, and N. J. Patronas (2016). Endolymphatic Sac Tumor Showing Increased Activity on 68Ga DOTATATE PET/CT. Clinical Nuclear Medicine 41(10), 783–784.  

 15. Papadakis, G. Z., C. Millo, S. M. Sadowski, Bagci, Ulas, and N. J. Patronas (2016). Epididymal 

Cystadenomas in von Hippel-Lindau Disease Showing Increased Activity on 68Ga DOTATATE PET/CT. Clinical Nuclear Medicine 41(10), 781–782.  

 16. Papadakis, G. Z., C. Millo, S. M. Sadowski, Bagci, Ulas, and N. J. Patronas (2016). Kidney Tumor 

in a von Hippel-Lindau (VHL) Patient With Intensely Increased Activity on 68Ga-DOTA-TATE PET/CT. Clinical Nuclear Medicine 41(12), 970–971.  

 17. Papadakis, G. Z., S. M. Sadowski, Bagci, Ulas, and C. Millo (2016). Application of 

68Ga-DOTATATE PET/CT in metastatic neuroendocrine tumor of gastrointestinal origin. Annals of Gastroenterology 30(1), 130.  

18. Zhou, Y., U. Teomete, O. Dandin, O. Osman, T. Dandinoglu, Bagci, Ulas, and W. Zhao (2016). Computer-Aided Detection (CADx) for Plastic Deformation Fractures in Pediatric Forearm. Computers in Biology and Medicine 78, 120–125.  

 19. Camp, J., U. Bagci, Y. Chu, B. Squier, M. Fraig, S. Uriarte, H. Gu, D. Mollura, & C. Jonsson (2015). 

Lower Respiratory Tract Infection of the Ferret by 2009 H1N1 Pandemic Influenza A Virus Triggers Biphasic Systemic and Local Neutrophil Recruitment. Journal of Virology.  

 20. L.Wang et al. (2015). Evaluation of Candidate Vaccine Approaches for MERS-CoV. Nature 

Communications.  

21. Mansoor*, A., U. Bagci, B. Foster, Z. Xu, G. Papadakis, L. Folio, J. Udupa, and D. Mollura (2015). Segmentation and Image Analysis of Abnormal Lungs at CT: Current Approaches, Challenges, and Future Trends. Radiographics 35(4).  

 22. Papadakis*, G. Z., C. Millo, U. Bagci, N. J. Patronas, and C. A. Stratakis (2015). Talc Pleurodesis 

with intense 18F-FDG activity but no 68Ga-DOTATATE activity on PET/CT. Clinical Nuclear Medicine.  

 23. Papadakis*, G. Z., U. Bagci, S. M. Sadowski, N. J. Patronas, and C. A. Stratakis (2015). Ectopic 

ACTH and CRH co-secreting tumor localized by 68Ga-DOTATATE PET/CT. Clinical Nuclear Medicine.  

 24. Papadakis, G., C. Millo, U. Bagci, S. Sadowski, and C. Stratakis (2015). Schmorl Nodes Can 

Cause Increased 68Ga DOTATATE Activity on PET/CT, Mimicking Metastasis in Patients With Neuroendocrine Malignancy. Clinical Nuclear Medicine.  

 

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25. U. Bagci, J.K.Udupa, X. Chen, D. Zhou, and B.Li (2017 (submitted)). Efficient Anatomical Structure Localization Strategies Using Non-Euclidean Metrics and Multi-Object Shape Models. Information.  

 26. Xu*, Z., U. Bagci, B. Foster, A. Mansoor, J. K. Udupa, and D. Mollura (2015). A hybrid method 

for airway segmentation and estimation of its wall boundary surfaces at CT. Medical Image Analysis 24(1), 1–17.  

 27. Xu*, Z., U. Bagci, A. Mansoor, G. Kramer-Marek, B. Luna, A. Kubler, B. Dey, B. Foster, G. Z. 

Papadakis, J. Camp, C. Jonsson, W. Bishai, S. Jain, J. Udupa, and D. Mollura (2015). Computer-Aided Pulmonary Image Analysis of Infectious Lung Diseases in Small Animal Models. Medical Physics 42(7), 3896–3910.  

 28. A.Mansoor*, U. Bagci, Z. Xu, B. Foster, J. Elinoff, K. Olivier, A. Suffredini, J. K. Udupa, and D. 

Mollura (2014). A Generic Approach for Pathological Lung Segmentation. IEEE Transactions on Medical Imaging 33 (12), 2293–2310. 

 29. Elinoff, J. M. et al. (2014). Recombinant Human Factor VIIa as Adjunctive Therapy for Alveolar 

Hemorrhage Following Allogeneic Hematopoietic Stem Cell Transplantation. Biology of Blood and Marrow Transplantation 20(7), 969–978.  

 30. Foster*, B., U. Bagci, Z. Xu, B. Dey, B. Luna, W. R. Bishai, S. Jain, and D. J. Mollura (2014). 

Segmentation of PET Images for Computer Aided Functional Quantification of Tuberculosis in Small Animal Models. IEEE Transactions on Biomedical Engineering 61(3), 711–724.  

31. Foster*, B., U. Bagci, Z. Xu, A. Mansoor, and D. J. Mollura (2014). A Review on Image Segmentation Methods for Positron Emission Tomography. Computers in Biology and Medicine 50, 76–96.  

 32. Kubler, A., B. Luna, C. Larsson, N. C. Ammerman, B. B. Andrade, M. Orandle, K. W. Bock, Z. 

Xu, Bagci, Ulas, D. J. Molura, et al. (2014). Mycobacterium tuberculosis dysregulates MMP/TIMP balance to drive rapid cavitation and unrestrained bacterial proliferation. The Journal of Pathology 253(3), 431–444.  

 33. Luna, B., A. Kubler, C. Larsson, B. Foster, U. Bagci, D. Mollura, S. Jain, and W. Bishai (2014). In 

vivo Prediction of Tuberculosis Cavity Formation in Rabbits. Journal of Infectious Diseases 11(3), 481–485.  

 34. Lim*, P., U. Bagci, and L. Bai (2013). Introducing Willmore Flow into Level Set Segmentation of 

Spinal Vertebrae. IEEE Transactions on Biomedical Engineering 60(1), 115–122.   

35. U. Bagci, B. Foster, K. Miller-Jaster, B. Luna, B. Dey, W. R. Bishai, C. B. Jonsson, S. Jain, and D. J. Mollura (2013). A computational pipeline for quantification of pulmonary infections in small animal models using serial PET-CT imaging. European Journal of Nuclear Medicine and Molecular Imaging Research 3(55), 1–20.  

 36. U. Bagci, G. Kramer-Marek, and D. Mollura (2013). Automated computer quantification of 

breast cancer in small-animal models using PET-guided MR image co-segmentation. European Journal of Nuclear Medicine and Molecular Imaging Research 3(49), 1–13.  

 37. U. Bagci, K. Miller-Jaster, J.Yao, and D. Mollura (2013). Synergistic combination of clinical and 

imaging features predicts abnormal imaging patterns of pulmonary infections. Computers in Biology and Medicine 43(9), 1241–1251.  

 38. U. Bagci, J. K. Udupa, N. Mendhiratta, B. Foster, Z. Xu, J. Yao, X. Chen, and D. Mollura (2013). 

Joint Segmentation of Anatomical and Functional Images: Applications in Quantification of 

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Lesions from PET, PET-CT, MRI-PET, and MRI-PET-CT Images. Medical Image Analysis 17(8), 929– 945.  

 39. U. Bagci, J. Yao, K. Miller, X. Chen, and D. Mollura (2013). Predicting Future Morphological 

Changes of Lesions from Radiotracer Uptake in 18F-FDG-PET Images: Longitudinal Assessment of Diseases through Automated Volume Delineations and Texture Correlations. PlosOne 8(2), e57105.  

 40. Xu*, Z., U. Bagci, A. Kubler, B. Luna, S. Jain, W. Bishai, and D. Mollura (2013). Computer-aided 

detection and quantification of cavitary tuberculosis from CT scans. Medical Physics 40(11), 113701, 1–14.  

 41. Chen, X., R. Summers, M. Cho, U. Bagci, and J. Yao (2012). An Automatic Method for Renal 

Cortex Segmentation on CT images: Evaluation on Kidney Donors. Academic Radiology 19(5), 562– 570.  

 42. Chen, X., J. K. Udupa, U. Bagci, Y. Zhuge, and J. Yao (2012). Medical Image Segmentation by 

Combining Graph Cut and Oriented Active Appearance Models. IEEE Transactions on Image Processing 21(4), 2035–2046.  

43. Kramer-Marek, G., M. Bernardo, D. O. Kiesewetter, U. Bagci, M. Kuban, A. Omer, R. Zielinski, J. Seidel, P. Choyke, and J. Capala (2012). PET Imaging of HER2+ Pulmonary Metastases with 18F-ZHER2:342-Affibody in a Mouse Model; Comparison with 18F-Fluorodeoxyglucose (18F-FDG). Journal of Nuclear Medicine 53(6), 939–946.  

 44. U. Bagci, M. Bray, J. Caban, J. Yao, and D. Mollura (2012). Computer-Assisted Detection of 

Respiratory Tract Infections: A Review. Computerized Medical Imaging and Graphics 36(1), 72–84.  

45. U. Bagci, X. Chen, and J. K. Udupa (2012). Hierarchical Scale-Based Multi-Object Recognition of 3D Anatomical Structures. IEEE Transactions on Medical Imaging 31(3), 777–789.  

 46. U. Bagci, J. Yao, A. Wu, J. Caban, A. Suffredini, T. Palmore, O. Aras, and D. J. Mollura (2012). 

Detection and Quantification of Tree-in-Bud (TIB) Opacities from CT Scans. IEEE Transactions on Biomedical Engineering 59(6), 1620–1632.  

 47. Chen, X. and U. Bagci (2011). 3D Automatic Anatomy Segmentation Based on Iterative 

Graph-Cut-ASM. Medical Physics 38(8), 4610–4622.   

48. U. Bagci and L. Bai (2010). Automatic Best Reference Slice (BRS) Selection for Smooth Volume Reconstruction of a Mouse Brain From Histological Sections. IEEE Transactions on Medical Imaging 29(9), 1688–1696.  

 49. U. Bagci, J. K. Udupa, and L. Bai (2010). The Role of Intensity Standardization in Medical Image 

Registration. Pattern Recognition Letters 31(4), 315–323.   

50. U. Bagci and D. Mamurekli (2009). Determination of Onset of Failure of Rocks in Multiple Failure State Triaxial Tests Using Scale-Based Differential Geometry. Arch. Min. Sci. 54(1), 55–78.  

 51. U. Bagci and E. Erzin (2007). Automatic Classification of Musical Genres Using Inter-Genre 

Similarity. IEEE Signal Processing Letters 8(14), 521–524.    Peer Reviewed Conference Papers  

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1. Chuquicusma, MJM, Hussein, S., Burt, J., and Bagci, U (2018). How to Fool Radiologists with Generative Adversarial Networks (GANs) ? A Visual Turing Test for Lung Cancer Diagnosis. IEEE ISBI 2018. 

  2. Hussein, S., Kandel, P., Corral, JE., Bolan, CW, Wallace, MB, and Bagci, U (2018). Deep Multi-Modal 

Classification of Intraductal Papillary Mucinous Neoplasms (IPMNs) with Canonical Correlation Analysis. IEEE ISBI 2018. 

 3. Morley, D., Foroosh, H., Shaikh, S., and Bagci, U (2017). Simultaneous Detection and Quantification 

of Retinal Fluid with Deep Learning. MICCAI-RETOUCH Challenge, 2017.  

4. Mortazi, A., Burt, J., Bagci, U (2017). Multi-planar Deep Segmentation Networks for Cardiac Substructures from MRI and CT. MICCAI STACOM / MM-WHS Challenge 2017.  

 5. Hussein, S., Q. Cao, Q. Song, and U. Bagci (2017). Risk Stratification of Lung Nodules Using 3D 

CNN Multi-Task Learning. Information Processing in Medical Imaging (IPMI), 249–259.  

6. Hussein, S., R. Gillies, K. Cao, Q. Song, and Bagci, U (2017). TumorNet: Lung Nodule Characterization Using Multi-View Convolutional Neural Network with Gaussian Process. In: IEEE International Symposium on Biomedical Imaging-2017. IEEE. 

 7. Mortazi, A., R. Karim, K. Rhode, J. Burt, and U. Bagci (2017). CardiacNET: Segmentation of Left 

Atrium and Proximal Pulmonary Veins from MRI using Multi-View CNN. In: MICCAI 2017.  

8. RaviPrakash, H., M. Korostenskaja, E. Castillo, K. Lee, J. Baumgartner, and Bagci, Ulas (2017). Automatic Response Assessment in Regions of Language Cortex in Epilepsy Patients Using ECoG-based Functional Mapping and Machine Learning. In: IEEE SMC. [Best conference and student paper nominee] 

 9. Torosdagli, N., D. K. Liberton, P. Verma, M. S. J. Lee, S. Pattanaik, and Bagci, Ulas (2017). Robust and 

fully automated segmentation of mandible from CT scans. In: IEEE ISBI 2017. [Oral, Travel Grant Awardee] 

 10.Buty, M., Z. Xu, M. Gao, Bagci, Ulas, A. Wu, and D. J. Mollura (2016). Characterization of Lung                                   

Nodule Malignancy Using Hybrid Shape and Appearance Features. In: International Conference on                       Medical Image Computing and Computer-Assisted Intervention-MICCAI. Springer International               Publishing, pp.662–670. 

 11.Khosravan, N., H. Celik, B. Turkbey, R. Cheng, E. McCreedy, M. McAuliffe, S. Bednarova, E. Jones,                               

Chen, and Ulas Bagci (2016). Gaze2Segment: A Pilot Study for Integrating Eye-Tracking                       Technology into Medical Image Segmentation. MICCAI-Medical Computer Vision.  

 12.Gao, M., U. Bagci, L. Lu, A. Wu, M. Buty, H.-C. Shin, H. Roth, G. Papadakis, A. Depeursinge, R.                                     

Summers, Z. Xu, and D. Mollura (2015). Holistic Classification of CT Attenuation Patterns for                           Interstitial Lung Diseases via Deep Convolutional Neural Networks. In: Deep Learning in Medical                         Image Analysis, MICCAI 2015.  

 13.Hussein, S. and U. Bagci (2015). Transferability of 3D CNN features for Organ Detection. In: NIPS                               

2015 Workshop on Machine Learning in Healthcare. {Travel Grant Awardee]   

14.Xu*, Z., U. Bagci, J. Udupa, and D. Mollura (2015). Fuzzy Connectedness Image Co-Segmentation                           for Hybrid PET/MRI and PET/CT Scans. In: Lecture Notes in Computer Vision and Biomechanics, In:                             Workshop of Computational Methods for Molecular Imaging-MICCAI 2014.  

 

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15.Z.Xu*, U. Bagci, M.Gao, and D. Mollura (2015). Highly Precise Partial Volume Correction for PET                             Images: An Iterative Approach via Shape Consistency. In: In: IEEE 10th International Symposium on                           Biomedical Imaging (ISBI).  

 16.Foster*, B., U. Bagci, and D. Mollura (2014). QAV-PET: A Free Software for Quantitative Analysis                             

and Visualization of PET Images. In: IEEE EMBC 2014.   

17.Mansoor*, A., U. Bagci, B. Foster, Z. Xu, J. Solomon, D. Douglas, J. Udupa, and D. Mollura (2014).                                   CIDI-Lung-Seg: A Single-Click Annotation Tool for Automatic Delineation of Lungs from CT Scans.                         In: IEEE EMBC 2014.  

 18.Mansoor*, A., U. Bagci, and D. Mollura (2014). Near-optimal Keypoint Sampling for Fast                         

Pathological Lung Segmentation. In: IEEE EMBC 2014.   

19.Mansoor*, A., U. Bagci, and D. Mollura (2014). Optimally Stabilized PET Image Denoising Using                           Trilateral Filtering. In: Medical Image Computing and Computer-Assisted Intervention - MICCAI 2014.  

 20.Xu*, Z., U. Bagci, and D. Mollura (2014). Accurate and Efficient Separation of Left and Right Lungs                                 

from 3D CT Scans: a Generic Hysterisis Approach. In: IEEE EMBC 2014.   

21.Xu*, Z., U. Bagci, and D. Mollura (2014). Efficient Ribcage Segmentation from CT Scans Using                             Shape Features. In: IEEE EMBC 2014.  

 22.Xu*, Z., U. Bagci, J. Seidel, D. homasson, J. Solomon, and D. Mollura (2014). Segmentation Based                               

Denoising of PET Images: An Iterative Approach via Regional Means and Affinity Propagation. In:                           Medical Image Computing and Computer-Assisted Intervention - MICCAI 2014.  

 23.Foster*, B., U. Bagci, B. Luna, B. Dey, W. Bishai, S. Jain, Z. Xu, and D. J. Mollura (2013). Robust                                       

Segmentation and Accurate Target Definition for Positron Emission Tomography Images Using Affinity                       Propagation. In: Biomedical Imaging (ISBI), 2013 IEEE 10th International Symposium on, pp.1461–1464.   

 24.U. Bagci and D. J. Mollura (2013). Denoising PET Images Using Singular Value Thresholding and                             

Stein’s Unbiased Risk Estimate. In: Medical Image Computing and Computer-Assisted Intervention -                       MICCAI 2013. Ed. by K. Mori, I. Sakuma, Y. Sato, C. Barillot, and N. Navab. Vol. 8151. Lecture                                   Notes in Computer Science. Springer Berlin Heidelberg, pp.115–122.   

 25.Xu*, Z., U. Bagci, B. Foster, A. Mansoor, and D. J. Mollura (2013). Spatially Constrained Random Walk                                 

Approach for Accurate Estimation of AirwayWall Surfaces. In: Medical Image Computing and                       Computer-Assisted Intervention - MICCAI 2013. Ed. by K. Mori, I. Sakuma, Y. Sato, C. Barillot, and N.                                 Navab. Lecture Notes in Computer Science. Springer Berlin Heidelberg, pp.559–566.  

 26.Xu*, Z., U. Bagci, B. Foster, and D. J. Mollura (2013). A Hybrid Multi-Scale Approach to Automatic                                 

Airway Tree Segmentation From CT Scans. In: Biomedical Imaging (ISBI), 2013 IEEE 10th International                           Symposium on, pp.1308–1311.  

 27.Caban, J., U. Bagci, A. Mehari, S. Alam, J. R. Fontana, G. J. Kato, and D. J. Mollura (2012).                                     

Characterizing NonLinear Dependencies Among Pairs of Clinical Variables and Imaging Data. In:                       IEEE EMBC 2012, pp.2700–2703.  

 28.Lim*, P. H., U. Bagci, O. Aras, Y. Wang, and B. Li (2012). A Novel Spinal Vertebrae Segmentation                                   

Framework Combining Geometric Flow and Shape Prior with Level Set. In: IEEE International                         Symposium in Biomedical Imaging, ISBI-2012, pp.1703–1706.  

 

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29.U. Bagci, K. Miller-Jaster, J. Yao, A. Wu, O. Aras, and D. J. Mollura (2012). Automatic Quantification                                 of Tree-In-Bud Patterns from CT Scans. In: IEEE International Symposium in Biomedical Imaging,                         ISBI-2012, pp.1459–1462.   

 30.U. Bagci, J. K. Udupa, J. Yao, and D. J. Mollura (2012). Co-segmentation of Functional and                               

Anatomical Images. In: Medical Image Computing and Computer-Assisted Intervention - MICCAI 2012.                       Ed. by N. Ayache, H. Delingette, P. Golland, and K. Mori. Vol. 7512. Lecture Notes in Computer                                 Science. Springer Berlin Heidelberg, pp.459–467. 

 31. Caban, J., J. Yao, U. Bagci, and D. J. Mollura (2011). Monitoring Pulmonary Fibrosis by Fusing                                 

Clinical, Physiological, and Computed Tomography Features. In: 33rd Annual International                   Conference of IEEE Engineering in Medicine and Biology Society (EMBC 11), pp.6216–6219.  

 32.Lim*, P. H., U. Bagci, O. Aras, and B. Li (2011). Identification of Spinal Vertebrae Using                               

Mathematical Morphology and Level Set Method. In: Nuclear Science Symposium and Medical Imaging                         Conference (NSS/MIC), 2011 IEEE, pp.3105–3107.  

 33.Lim*, P. H., U. Bagci, and B. Li (2011). A New Prior Shape Model for Level Set Segmentation. In:                                     

Progress in Pattern Recognition, Image Analysis, Computer Vision, and Applications. Ed. by C. San                           Martin and S.-W. Kim. Vol. 7042. Lecture Notes in Computer Science. Springer Berlin Heidelberg,                           pp.125–132.  

 34.U. Bagci, J. K. Udupa, and X. Chen (2011). Intensity Non-Standardness Affects Computer                         

Recognition of Anatomical Structures. In: Proc. of SPIE Medical Imaging 2011. Vol. 7964, pp.79642M.   

35.U. Bagci, J. K. Udupa, and X. Chen (2011). Orientation Estimation of Anatomical Structures in                             Medical Images for Object Recognition. In: Proc. of SPIE Medical Imaging 2011. Vol. 7962, pp.79622L.  

 36.U. Bagci, J. Yao, J. Caban, B. E. Turkbey, O. Aras, and D. J. Mollura (2011). A Graph-Theoretic                                   

Approach for Segmentation of PET Images. In: 33rd Annual International Conference of IEEE                         Engineering in Medicine and Biology Society (EMBC 11), pp.8479–8482.  

 37.U. Bagci, J. Yao, J. Caban, B. E. Turkbey, O. Aras, and D. J. Mollura (2011). Automatic Detection of                                     

Tree-in-Bud Patterns for Computer Assisted Diagnosis of Respiratory Tract Infections. In: 33rd Annual                         International Conference of IEEE Engineering in Medicine and Biology Society (EMBC 11), pp.5096–5099.  

 38.U. Bagci, J. Yao, J. Caban, A. F. Suffredini, T. N. Palmore, and D. J. Mollura (2011). Learning Shape                                     

and Texture Characteristics of CT Tree-in-Bud Opacities for CAD Systems. In: Medical Image                         Computing and Computer-Assisted Intervention – MICCAI 2011. Ed. by G. Fichtinger, A. Martel, and T.                             Peters. Vol. 6893. Lecture Notes in Computer Science. Heidelberg: Springer, pp.215–222.  

 39.Chen, X., J. K. Udupa, and U. Bagci (2010). 3D Automatic Anatomy Segmentation Based on                             

Iterative-Graph-Cut Active Shape Model. In: Proc. of SPIE Medical Imaging 2010. Vol. 7625,                         pp.76251T.  

 40.Chen, X., J. Yao, Y. Zhuge, and U. Bagci (2010). 3D Automatic Anatomy Segmentation Based on                               

Graph Cut - Oriented Active Appearance Models. In: IEEE International Conference on Image                         Processing (ICIP), pp.3653–3656.  

 41.U. Bagci, J. K. Udupa, and L. Bai (2010). Influences of Standardization on Medical Image                             

Registration. In: Proc. of SPIE Medical Imaging 2010. Vol. 7625, pp.76251X.   

42.U. Bagci, J. K. Udupa, and X. Chen (2010). Ball-Scale Based Multi-Object Recognition in a                             Hierarchical Framework. In: Proc. of SPIE Medical Imaging 2010. Vol. 7623, pp.762345.  

 

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43.U. Bagci and L. Bai (2008). Fully Automatic 3D Reconstruction of Histological Images. In: IEEE                             International Symposium on Biomedical Imaging (ISBI), pp.991–994.  

 44.U. Bagci and L. Bai (2008). Parallel AdaBoost Algorithm for Gabor Wavelet Selection in Face                             

Recognition. In: IEEE International Conference on Image Processing (ICIP), pp.1640–1643.   

45.U. Bagci and L. Bai (2008). Registration of histological images in feature space. In: Proc. of SPIE                                 Medical Imaging 2008. Vol. 6914, pp.69142V.  

 46.U. Bagci and B. Li (2008). Doku Imgelerinin Tam Otomatik Geri Catilmasi. In: Proc. of IEEE Conf. on                                   

Processing and Communications Applications (SIU’08), pp.1–4.   

47.U. Bagci and B. Li (2008). Medikal Imgelerin Standart Yeginlik Olceginde, Esnek ve Cok                           Cozunurluklu Cakistirilmasi. In: Proc. of IEEE Conf. on Processing and Communications Applications                       (SIU’08), pp.1–4.  

 48.U. Bagci and L. Bai (2007). A Comparison of Daubechies and Gabor Wavelets for Classification of                               

MR Images. In: IEEE International Conference on Signal Processing and Communications (ICSPC),                       pp.676–679.  

 49.U. Bagci and L. Bai (2007). Multi-resolution Elastic Medical Image Registration in Standard                         

Intensity Scale. In: IEEE Brazilian Symposium on Computer Graphics and Image Processing (SIBGRAPI),                         pp.305–312.  

 50.U. Bagci and B. Li (2007). Detecting Alzheimer Disease in Magnetic Resonance Brain Images Using                             

Gabor Wavelets. In: Proc. of IEEE Conf. on Processing and Communications Applications (SIU’07),                         pp.1–4.  

 51.U. Bagci and E. Erzin (2006). Inter Genre Similarity Modelling for Automatic Music Genre                           

Classification. In: Digital Audio Effects-DAFx-2006, pp.153–156.   

52.U. Bagci and E. Erzin (2006). Muzik Turlerinin Siniflandirilmasinda Benzer Kesisim Bilgileri                       Uygulamalari. In: Proc. of IEEE Conf. on Processing and Communications Applications (SIU’06), pp.1–4.  

 53.U. Bagci and E. Erzin (2006). Muzik Turlerinin siniflandirilmasinda Siniflandiricilarin                   

Yuk-seltilmesi. In: Proc. of IEEE Conf. on Processing and Communications Applications (SIU’06), pp.1– 3.   

54.U. Bagci and E. Erzin (2005). Boosting Classifiers for Music Genre Classification. In: International                           Symposium on Computer and Information Sciences (ISCIS). Vol. 33. Lecture Notes in Computer Sci-ence,                           pp.575–584. 

  Abstracts & Thesis & Technical Reports  

1. Mortazi, A., Burt, J., and Bagci, U (2017). Deep Learning for Cardiac MRI: Automatically Segmenting Left Atrium Expert Human Level Performance. Radiological Society of North America (RSNA), 103rd Scientific Assembly and Annual Meeting, November 26- December 1, 2017 McCormick Place, Chicago. [Oral] 

 2. Hussein, S., Mortazi, A., RaviPrakash, H., Burt, J., and Bagci, U (2017). Deep Learning Applications in 

Radiology, Recent Developments, Challenges, and Potential Solutions. Radiological Society of North America (RSNA), 103rd Scientific Assembly and Annual Meeting, November 26- December 1, 2017 McCormick Place, Chicago. [Certificate of Merit Awardee] 

 

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3. Celik, H., B. Turkbey, P. Choyke, R. Cheng, E. McCreedy, M. McAuliffe, N. Khosravan, Ulas Bagci, and B. Wood (2017). Eye Tracking System for Prostate Cancer Diagnosis Using Multi-Parametric MRI. In: ISMRM. 

 4. Mortazi, A., Bagci, Ulas, and J. Burt (2017). Machine Learning for Cardiac MRI: Automated Mapping 

of Left Atrium and Pulmonary Veins with Human Level Performance. In: 45th Annual Meeting of North American Society for Cardiovascular Imaging. [Young Investigator Award Nominee] 

 5. Shaikh, S., T. Ozerderm, A. Carmack, B. Thiel, Bagci, Ulas (2017). Motion Stabilization in Retinal 

Video Angiography Using Serial Rigid Registration. In: 50th Annual Retina Society Meeting.  

6. Papadakis, G., C. Millo, Bagci, U, N. Patronas, and M. Collins (2016). Value of F-18-NaF PET/CT imaging in the assessment of Gorham-Stout disease activity. In: European Journal of Nuclear Medicine and Molecular Imaging. Vol. 43. SPRINGER 233 SPRING ST, NEW YORK, NY 10013 USA, pp.S597–S597. [Oral] 

 7. Green, A., U. Bagci, P. V. Kelly, and M. Osman (2015). Brown adipose tissue detected by FDG 

PET/CT is associated with less central obesity compared to body mass index matched controls. In: SNMMI (Society of Nuclear Medicine and Molecular Imaging). 

 8. Green, A., U. Bagci, P. V. Kelly, and M. Osman (2015). Brown Adipose Tissue Detected by FDG 

PET/CT is Associated with Less Visceral Fat. In: SNMMI (Society of Nuclear Medicine and Molecular Imaging). 

 9. Papadakis, G., A. Karageorgiadis, U. Bagci, R. Casas, C. Millo, N. Patronas, and C. Stratakis (2015). 

Value of 18F-FDG-PET/CT in Localizing Ectopic ACTH/CRH Co-secreting Tumors, Causing Cushing Syndrome (CS), in Children and Adolescents. In: Radiological Society of North America (RSNA), 101st Scientific Assembly and Annual Meeting, November 29 - December 4, 2015, McCormick Place, Chicago.  [Oral] 

 10.Souly, N., G. Papadakis, U. Teomete, and U. Bagci (2015). A New Saliency Metric for Precise 

Denoising PET Images for Better Visualization and Accurate Segmentation. In: Radiological Society of North America (RSNA), 101st Scientific Assembly and Annual Meeting, November 29 - December 4, 2015, McCormick Place, Chicago. [Oral] 

 11.Teomete, U., G. Papadakis, O. Osman, O. Dandin, and U. Bagci (2015). From Signal to Screen: The 

Science Behind Radiologic Images. In: Radiological Society of North America (RSNA), 101st Scientific Assembly and Annual Meeting, November 29 - December 4, 2015, McCormick Place, Chicago. 

 12. Teomete, U., Y. Zhou, O. Dandin, W. Zhao, T. Dandinoglu, O. Osman, and U. Bagci (2015). Plastic 

Bowing Fractures of the Pediatric Forearm: Evaluation of a Novel Computer Aided Method for Detection. In: Radiological Society of North America (RSNA), 101st Scientific Assembly and Annual Meeting, November 29 - December 4, 2015, McCormick Place, Chicago. [Oral] 

 13. U. Bagci, G. Papadakis, Z. Xu, A. Green, M. Osman, and M. Shah (2015). Nuclear Medicine Meets 

Computer Vision: Increasing Role of Computerized Detection, Tracking, Diagnosis, and Quantification of PET/CT and PET/MRI Studies. In: SNMMI (Society of Nuclear Medicine and Molecular Imaging). 

 14. Xu, Z., M. Gao, U. Bagci, and D. Mollura (2015). Recent Advances in Techniques for PET Image 

Denoising and Partial Volume Correction. In: Radiological Society of North America (RSNA), 101st Scientific Assembly and Annual Meeting, November 29 - December 4, 2015, McCormick Place, Chicago.  

 

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15. Xu*, Z., U. Bagci, M. Gao, and M. Shah (2015). Improved PET image quantification via iterative                               denoising and partial volume correction. In: SNMMI (Society of Nuclear Medicine and Molecular                         Imaging). 

 16. A.Mansoor*, U. Bagci, and D. Mollura (2014). Noise Adaptive Multi-resolution technique to                       

accurately denoise PET, MRI-PET, and PET-CT images. In: J Nucl Med. 2014; 55 (Supplement                           1):2050. 

 17. Camp, J. V., U. Bagci, M. Fraigb, H. Guoc, S. M. Uriarte, D. J. Mollura, and C. B. Jonsson (2014).                                       

Multifocal neutrophil infiltration and inflammation in lungs of ferrets infected with 2009 H1N1                         Influenza A virus clinical isolate. In: Annual Meeting of the American Society for Virology. 

 18. Johnson, R. F., D. J. Mollura, L. E. Via, U. Bagci, N. Oberlande, C. J. Bartos, J. Solomon, J. Johnson, R.                                         

Holbrook, D. Thomasson, G. G. Olinger, L. E. Hensley, and P. B. Jahrling (2014). Evaluation of                               MERS CoV Induced Disease in Two Species of Nonhuman Primate the Common Marmoset and                           Rhesus Monkey by Computed Tomography. In: 13th International Nidovirus Symposium. 

 19. Johnson, R. F., U. Bagci, D. J. Mollura, C. J. Bartos, N. Oberlander, M. R. Holbrook, D. Thomasson, G.                                     

Olinger, P. B. Jahrling, and L. E. Hensley (2014). Evaluation of MERS CoV Induced Disease in                               the Rhesus Macaque by Computed Tomography. In: ASM Biodefence. 

 20. Mansoor, A., U. Bagci, B. Foster, Z. Xu, G. Papadakis, J. Udupa, and D. Mollura (2014).                               

Computerized detection and classification of pulmonary pathologies from CT images: current                     approaches, challenges, and future trends. In: Radiological Society of North America (RSNA). 

 21. Mansoor, A., U. Bagci, Z. Xu, B. Foster, G. Papadakis, and D. Mollura (2014). Lung Lobe                               

Volume-try as a Reliable Biomarker: Methods for Automatic Extraction of Lobes from CT Scans,                           and Fissure Integrity Scoring. In: Radiological Society of North America (RSNA). 

 22. Ollinger, G. G., R. F. Johnson, U. Bagci, L. Via, J. Solomon, D. Hammoud, D. J. Mollura, R. C.                                     

Reba, N. Oberlander, C. Bartos, D. Douglas, K. Cooper, M. R. Holbrook, L. E. Hensley, and P. B.                                   Jahrling (2014). Use of Imaging for development of animal models of Biosafety Level (BSL) 3                             and 4 agents. In: World Molecular Imaging Congress. 

 23. Papadakis, G., U. Bagci, B. Foster, Z. Xu, A. Mansoor, N. Patronas, C. Stratakis, and D. Mollura                                 

(2014). Automated Computer-derived SUV and Metabolic Tumor Volume Measurements of                   Biopsy Proven Lesions: Comparison with Radiologist-derived PET-CT Imaging. In: Radiological                   Society of North America (RSNA). 

 24. Papadakis, G., U. Bagci, Z.Xu, C. S. K.A. Kissell, and D. Mollura (2014). Detection and                             

Quantification of Brown Fat Tissue using PET-CT Scans: A Novel Computer Aided Detection                         System. In: Annual Congress of the European Association of Nuclear Medicine-EANM. 

 25. Spergel, A. R., C. Chen, C. Beegle, P. Littel, M. Garofalo, S. Anaya-O’Brien, M. Marquesen, U.                               

Bagci, D. Mollura, J. Gallin, and H. Malech (2014). The use of radiolabelled 18-F-2-deoxy-                           2-fluro-glucose (18F-FDG) in combined positron emission tomography-computed tomography               (PET-CT) to evaluate infection: lessons learned from a case series of 23 patients with Chronic                             Granulomatous Disease (CGD). In: American Academy of Allergy, Asthma & Immunology Annual                       Meeting. 

 26. U. Bagci, Z.Xu, and D. Mollura (2014). Recent Advances in PET, PET-CT, and MRI-PET Image                             

Segmentation Techniques. In: J Nucl Med. 2014; 55 (Supplement 1):1280.  

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27. Xu, Z., U. Bagci, A. Mansoor, B. Foster, G. Papadakis, J. J. Udupa, and D. Mollura (2014). The                                   State-of-the-art and Recent Advances in Pulmonary Image Analysis Techniques. In: Radiological                     Society of North America (RSNA). 

 28. Z.Xu*, U. Bagci, and D. Mollura (2014). Diffusion based enhancement of PET images for                           

improved diagnostic measurements in clinical nuclear medicine. In: J Nucl Med. 2014; 55                         (Supplement 1):2051. 

 29. Foster*, B., U. Bagci, A. Mansoor, Z. Xu, and D. Mollura (2013). Challenges, Techniques, and                             

Advancements for State-of-the-Art PET Image Segmentation. In: Radiological Society of North America                       (RSNA), 99th Scientific Assembly and Annual Meeting, Dec 1-6, 2013, McCormick Place, Chicago. 

 30. Foster*, B., U. Bagci, Z. Xu, B. Dey, B. Luna, W. Bishai, S. Jain, and D. Mollura (2013). Affinity                                     

Propagation Clustering Determines Distributed Uptake Regions in PET Images: A                   Computer-Aided Approach for Quantification of Pulmonary Infections in Small Animals. In: J                       Nucl Med. 2013; 54 (Supplement 2):313. [Oral]  

 31. Foster*, B., U. Bagci, Z. Xu, A. Mansoor, B. Luna, B. Dey, W. BIshai, C. Jonson, S. Jain, and D.                                       

Mollura (2013). Quantitative Analysis of Infectious Lung Disease from Serial PET-CT Scans in Small                           Animal Models. In: Radiological Society of North America (RSNA), 99th Scientific Assembly and                         Annual Meeting, Dec 1-6, 2013, McCormick Place, Chicago.  

 32. Foster*, B., U. Bagci, X. Zu, A. Mansoor, B. Dey, B. Luna, W. Bishai, S. Jain, and D. Mollura                                     

(2013). A Method for Segmenting Multi-Focal Radiotracer Uptake in PET Images to Quantify                         Tuberculosis in Rabbits. In: Radiological Society of North America (RSNA), 99th Scientific Assembly                         and Annual Meeting, Dec 1-6, 2013, McCormick Place, Chicago. [Oral] 

 33. Mansoor*, A., U. Bagci, B. Foster, Z. Xu, and D. Mollura (2013). How to Correctly Denoise PET                                 

and MRI-PET Images: Current Approaches, Constraints, and Future Trends. In: Radiological                     Society of North America (RSNA), 99th Scientific Assembly and Annual Meeting, Dec 1-6, 2013,                           McCormick Place, Chicago. 

 34. Mansoor*, A., U. Bagci, B. Foster, Z. Xu, J. Udupa, and D. Mollura (2013). A Robust Pathological                                 

Lung Segmentation Platform Using Fuzzy-Connectedness with Patient-specific Modeling. In:                 Radiological Society of North America (RSNA), 99th Scientific Assembly and Annual Meeting, Dec 1-6,                           2013, McCormick Place, Chicago. 

 35. Mansoor*, A., U. Bagci, B. Foster, Z. Xu, J. Udupa, and D. Mollura (2013). Pathological Lung                               

Segmentation in Computed Tomography (CT) Images. In: Radiological Society of North America                       (RSNA), 99th Scientific Assembly and Annual Meeting, Dec 1-6, 2013, McCormick Place, Chicago. 

 36. Sandouk*, A., U. Bagci, Z. Xu, A. Mansoor, B. Foster, and D. Mollura (2013). Accurate                             

Quantification of Brown Adipose Tissue through PET-guided CT Image Segmentation. In: J                       Nucl Med. 2013; 54 (Supplement 2):318. 

 37. U. Bagci, B. Foster, Z. Xu, B. Luna, B. Dey, W. Bishai, C. Jonsson, S. Jain, and D. Mollura (2013).                                       

A Computational Platform for Quantification of Infectious Lung Disease Using PET-CT                     Imaging. In: J Nucl Med. 2013; 54 (Supplement 2):314. 

 38. Xu*, Z., U. Bagci, J. Udupa, and D. Mollura (2013). Simultaneous Segmentation from Hybrid                           

MRI-PET and PET-CT Images Using Fuzzy Connectedness Image Co-segmentation. In:                   Radiolog-ical Society of North America (RSNA), 99th Scientific Assembly and Annual Meeting, Dec 1-6,                           2013, McCormick Place, Chicago. 

 

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39. Luna, B. B., K. Miller-Jaster, B. Foster, U. Bagci, D. Mollura, S. Jain, and W. Bishai (2012).                                 Qualitative and Quantitative Analysis of Inflammation in Pulmonary Tuberculosis in Rabbit                     using F18-FDG-PET/CT Imaging: A multi-Parametric Approach. In: Molecular Imaging of                   Infectious Diseases: Current Status and Future Challenges. 

 40. N.Mendhiratta*, Z. Xu*, B. Foster*, U. Bagci, and D. Mollura (2012). Accurate and Robust                           

Quantification of Hybrid MRI-PET and PET-CT Images through a Novel Joint-Segmentation                     Method. In: Molecular Imaging of Infectious Diseases: Current Status and Future Challenges BEST                         POSTER PRIZE. 

 41. U. Bagci, O. Aras, and D. Mollura (2012). Correlation of Anatomical and Functional Information                           

from PET-CT Images. In: J Nucl Med. 2012; 53 (Supplement 1):2266.  42. U. Bagci, J. Udupa, K. Jaster-Miller, and D. Mollura (2012). Automatic Segmentation Methods                         

for Abnormal Activities from PET, PET-CT, and MRI-PET Images. In: RSNA.  43. U. Bagci, J. Udupa, K. Jaster-Miller, and D. Mollura (2012). Simultaneous Segmentation of                         

Abnormal Activities from Hybrid MRI-PET. In: RSNA Highlighted in AuntMinnie.  44. Caban, J., J. Yao, U. Bagci, and D. J. Mollura (2011). Computer-based Quantitative Modeling of                             

Chest CT findings in Pulmonary Hypertension and its Association with Physiologic and Clinical                         Variables. In: Radiological Society of North America (RSNA), 97th Scientific Assembly and Annual                         Meeting, Nov 27-Dec 2, 2011, McCormick Place, Chicago. 

 45. Caban, J., J. Yao, U. Bagci, and D. J. Mollura (2011). Quantitative Measurements of Chest CT Using                                 

Texture Analysis (RSNA MERIT AWARD). In: Radiological Society of North America (RSNA), 97th                         Scientific Assembly and Annual Meeting, Nov 27-Dec 2, 2011, McCormick Place, Chicago. 

 46. U. Bagci, X. Chen, L. Bai, D. Mollura, B. Turkbey, and O. Aras (2011). Registration, Reconstruction,                               

and Analysis of Serial Histological Sections. In: Radiological Society of North America (RSNA), 97th                           Scientific Assembly and Annual Meeting, Nov 27-Dec 2, 2011, McCormick Place, Chicago.  

 47. U. Bagci, X. Chen, J. K. Udupa, L. Bai, D. J. Mollura, B. Turkbey, and O. Aras (2011). Model                                     

Based Segmentation Methods: Multi-Organ Segmentation Platform. In: Radiological Society of                   North America (RSNA), 97th Scientific Assembly and Annual Meeting, Nov 27-Dec 2, 2011,                         McCormick Place, Chicago.  

48. U. Bagci, X. Chen, J. K. Udupa, B. Li, S. Messian, B. Turkbey, and O. Aras (2011). Quantitative                                   Assessment of Multiple Sclerosis (MS) Lesions in Longitudinal MRI Studies. In: Radiological                       Society of North America (RSNA), 97th Scientific Assembly and Annual Meeting, Nov 27-Dec 2, 2011,                             McCormick Place, Chicago.  

 49. U. Bagci, X. Chen, J. Udupa, S. Histed, S. Perez-Pujol, B. Turkbey, and O. Aras (2011).                               

Automated Analysis of Multi-detector CT images for Preoperative Assessment of Living Renal                       Donors. In: Radiological Society of North America (RSNA), 97th Scientific Assembly and Annual                         Meeting, Nov 27-Dec 2, 2011, McCormick Place, Chicago.  

 50. U. Bagci, B. Turkbey, S. Perez-Pujol, D. Mollura, and O. Aras (2011). Is There a Reliable                               

Correlation Between computer-aided diagnosis (CAD) Results from CT Images and Information                     from PET Images in Longitudinal Studies: An Example Study in Interstitial Lung Disease. In:                           Radiological Society of North America (RSNA), 97th Scientific Assembly and Annual Meeting, Nov                         27-Dec 2, 2011, McCormick Place, Chicago.  

 51. U. Bagci and X.Chen (2011). Characteristics of Shape Functional in Iterative Graph Cut Active Shape                             

Model Segmentation (IGCASM). Tech. rep. NIH, Technical Report.   

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52. U. Bagci, J. Yao, J. Caban, T. N. Palmore, A. F. Suffredini, and D. J. Mollura (2011). CAD for                                     Pulmonary Infections: Automatic Detection of Tree-in-Bud Opacities. In: Radiological Society of                     North America (RSNA), 97th Scientific Assembly and Annual Meeting, Nov 27-Dec 2, 2011,                         McCormick Place, Chicago.  

 53. U. Bagci, J. Yao, J. Caban, T. Palmore, A. Suffredini, A. Wu, and D. Mollura (2011).                               

Quantification of Small Airway Pulmonary Infections: Subjective Visual Grading versus                   Objective Quantification Through a CAD System. In: Radiological Society of North America                       (RSNA), 97th Scientific Assembly and Annual Meeting, Nov 27-Dec 2, 2011, McCormick Place,                         Chicago.  

 54. U. Bagci (2010). “Automatic Anatomy Recognition and Registration”. PhD thesis. University of                       

Nottingham.   55. U. Bagci and J. K. Udupa (2008). The Role of Standardization in Medical Image Registration. Tech.                               

rep. MIPG Technical Report-341.   56. U. Bagci and J. K. Udupa (2008). Towards Efficient Medical Image Registration Methods. In:                           

Marie Curie Workshop-Barcelona.  57. U. Bagci (2007). Fundamental Issues of Registration: Applications for change analysis in health and                           

disease. Tech. rep. CMIAG Technical Report.   58. U. Bagci (2005). Boosting Classifiers for Automatic Music Genre Classification. Tech. rep. MSc Thesis,                           

Koc University.                                    

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