Some Peer Reviewed Representative Publications

Book Chapters

Book Chapter(s)
  1. S. Kockara, N. Ali, S. Dagtas, “Immersive Visualization of Cellular Structures”, Data Engineering Mining, Information and Intelligence, ISBN:978-1-4419-0175-0, pages 388-402, Springer, 2009.
  2. S. Kockara, M. Mete, and S. Suer, “Color and Spatial Features Integrated Normalized Distance for Density Based Border Detection in Dermoscopy Images”, Book Chapter, Springer, Color Medical Image Analysis, Editors: M. E. Celebi and G. Schaefer, Springer (ISBN: 9789400753884), Chapter 4, pp. 41-62, 2013.

Conferences

  1. F. Dinc, K. Oumimoun, W. Kwable, S. Kockara, T. Halic, S. Arikatla, S. Ahmadi, “Towards Real-time Bone Drilling Simulation for Anchor Placement in VR Based Arthroscopic Rotator Cuff Surgery Simulation”, Accepted for American Medical Informatics Association (AMIA) 2022 Informatics Summit, Chicago, March 21-24, 2022.
  2. S.Shedage, J.Farmer, D.Demirel, T.Halic, S.Kockara, V.Arikatla, K. Sexton, and S. Ahmadi, “Development of Virtual Skill Trainers and Their Validation Study Analysis Using Machine Learning”. In 2021 the 5th International Conference on Information System and Data Mining (ICISDM 2021), Association for Computing Machinery, 8–13, DOI:https://doi.org/10.1145/3471287.3471296, New York, 2021.
  3. J. Farmer, M. Tunc, D. Ahmadi, D. Demirel, T. Halic , S. Arikatla, S. Kockara , and S. Ahmadi, “Virtual Rotator Cuff Arthroscopic Skill Trainer: Results and Analysis of a Preliminary Subject Study”, ICISDM 2020: Proceedings of the 2020 the 4th International Conference on Information System and Data Mining, pages 139-143, 2020.
  4. D. Demirel, A. Yu, S. Cooper-Baer, T. Halic, S. Kockara, and S. Ahmadi. “Difficulty Scenario Modeling for Virtual Arthroscopic Rotator Cuff Surgery with GAML”. 5th International Conference on Computational and Mathematical Biomedical Engineering, Pittsburgh, PA, vol. 2, pp. 814-817, 2017.
  5. A. Yu, D. Demirel, T. Halic, S. Kockara, “Virtual Intraoperative Cholangiogram Using WebCL”. Studies in health technology and informatics, emphMed. Meets Virtual Real. 22 NextMedMMVR22, vol. 220, p. 459, 2016.
  6. S. Kockara, M. Mete, T. Halic, N. Yuruk, M. Ercan, and A. Lawrence, "Fractals for Malignancy Detection in Dermoscopy Images", IEEE ICHI, 2015, Dallas (Long Paper, Acceptance rate ~10.95%).
  7. S. Kockara, T. Halic, A. Looney, C. Hudson, and A. Crawford “Portable Malignant Lesion Detection with Low Cost Mobile Infrared Thermography” , IEEE Innovations in Technology conference (InnoTek2014), Rhode Island, May 16, 2014.
  8. D. Demirel, A. Yu, T. Halic, and S. Kockara, “Web-Based Camera Navigation for Virtual Pancreatic Cancer Surgery:  Whipple Surgery Simulator (VPenSS)”, IEEE Innovations in Technology conference (InnoTek2014), Rhode Island, May 16, 2014.
  9. T. Halic, S. Kockara, M. Willey, K. Eichelberger, and D. Demirel, “MoMiReS: Mobile Mixed Reality System for Physical & Occupational Therapies for hand and wrist ailments”, IEEE Innovations in Technology conference (InnoTek2014), Rhode Island, May 16, 2014.
  10. R. Avci, T. R. Stovall, S. Kockara, J. Bian, W. Hogan, U. Topaloglu, “Discovering Semantic Classes of Elligibility Criteria for Clinical Trials using Semantic Types and Network Clustering”, AMIA Clinical Research Informatics (AMIA CRI 2013), San Francisco, CA, 2013.
  11. V. Yip, S. Kockara , and C. Hu, “Efficient Calculation of Structural Similarity Threshold for the SCAN Network Clustering Algorithm”, Accepted for publication in IEEE International Conference on Bioinformatics & Biomedicine (BIBM), pp. 600-603, 2011. (Full Paper Acceptance Rate: ~20%)
  12. V. Yip,  M. Mete, U. Topaloglu, S. Kockara, “Concept Discovery for Pathology Reports using an N-gram Model”,  AMIA Summits Transl Sci Proc. 2010; pp. 43–47, 2010 (Acceptance Rate ~20%).
  13. B. Chen, M. Mete, and S. Kockara, "Parameter-free Multi-level Fuzzy C-means Clustering For Unsupervised Structure Detection in Histological Images", SDPS 2010 Transformative Systems Conference, Dallas, USA, 2010.  Proceeding Available Under: http://sdps.omnibooksonline.com/2010/index.html
  14. S. Kockara, T. Halic, and C. Bayrak, "Real-time Minute Change Detection on GPU for Cellular and Remote Sensor Imaging", IEEE 23rd International Conference on Advanced Information Networking and Applications, IEEE AINA 2009 (Acceptance Rate for 2009: ~33%).
  15. B. Chen and S. Kockara, "Mining Positional Association Super-Rules on Fixed-Size Protein Sequence Motifs", IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2009, pp. 1-8, 2009. (Acceptance Rate: 32%)
  16.  E. Ermisoglu, F. Sen, S. Kockara, T. Halic, C. Bayrak, and R. Rowe, "Scooping Simulation Framework for Artificial Cervical Disc Replacement Surgery", IEEE International Conference on Systems, Man, and Cybernetics, SMC 2009, pp. 900-905, 2009.
  17. T. Halic., S.Kockara., Bayrak C, Rowe R., and Chen B., " Soft Tissue Deformation and Optimized Data Structures for Mass Spring Methods", IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2009, pp. 45-52, 2009. (Acceptance Rate: 32%)
  18. S. Kockara, V. Yip, and M. Mete, "Balls Hierarchy: Image Segmentation by a Graph Spanner ", IEEE International Symposium on Biomedical Imaging (ISBI’09), 2009, (Podium presentations acceptance rate ~17%)
  19.  S. Kockara, "Balls Hierarchy: A Proximity Query for Metric Spaces and Covering Theorem", International Conference on Network-Based Information Systems, NBIS 2009, (Acceptance Rate: ~37%).
  20. S. Kockara, T. Halic, K.Iqbal, C. Bayrak, and R. Rowe, “Collision Detection: A Survey”, ", IEEE International Conference on Systems, Man, and Cybernetics, SMC 2007, pp. 4046-4051, 2007.
  21. S. Kockara, S. Dagtas, K. Aydin, N. Ali, and K. Iqbal, "New Set of Algorithms to Create 3D Images of Cellular Structures using Light Microscopy", IEEE International Conference on Engineering of Intelligent Systems, 2006.
  22. S. Kockara, N. Ali, and S. Dagtas, "Efficient 3-D Visualization of Cellular Structures through Reuse of Multi-focal 2-D Images", IEEE International Conference on Information Reuse and Integration, pp. 298-302, Sept. 2006.
  23. S. Kockara, S. Dagtas, K. Aydin, N. Ali, and K. Iqbal, "New Set of Algorithms to Create 3D Images of Cellular Structures using Light Microscopy", IEEE International Conference on Engineering of Intelligent Systems, 2006.  

Journals

  1. D. Demirel, B. Cetinsaya, T. Halic, S. Kockara, D. Reiners, S. Ahmadi, and S. Arikatla, “A partition-based optimization model and its performance benchmark for Generative Anatomy Modeling Language”, Elsevier, Computers in Biology and Medicine, vol. 119, 103695, ISSN 0010-4825, (IF: 4.589), 2020.
  2. J. Farmer, D. Demirel, R. Erol, D. Ahmadi, T. Halic, S. Kockara, S. Arikatla, K. Sexton, and S. Ahmadi, “Systematic approach for content and construct validation: Case studies for arthroscopy and laparoscopy”, International Journal of Medical Robotics and Computer Assisted Surgery, Wiley, (IF: 2.547), Aug;16(4):e2105. doi: 10.1002/rcs.2105. Epub Apr 4, 2020.
  3. M. Bayraktar, S. Kockara, T. Halic, M. Mete, H. K. Wong, and K. Iqbal. “Local Edge-Enhanced Active Contour for Accurate Skin Lesion Border Detection”, BMC Bioinformatics, 20 (2):105, (IF: 3.169), 2019.
  4. D. Demirel, B. Cetinsaya, T. Halic, S. Kockara, S. Ahmadi, “Partition-based optimization model for generative anatomy modeling language (POM-GAML)”, BMC Bioinformatics, 20 (2):105, (IF: 3.169), 2019
  5. R. Erol, M. Bayraktar, S. Kockara, S. Kaya, and T. Halic, "Texture based skin lesion abruptness
  6. quantification to detect malignancy", BMC Bioinformatics 2017.
  7. S. Kaya, M. Bayraktar, S. Kockara, M. Mete, T. Halic, H. E. Field, H. K. Wong, "Abrupt skin lesion border cutoff measurement for malignancy detection in dermoscopy images", BMC Bioinformatics 2016 (MCBIOS proceedings Impact Factor: 4.45).
  8. D. Demirel, A. Yu, T. Halic, S. Kockara, ...,N. Kockara, S. Ahmadi, "A Hierarchical Task Analysis of Shoulder Arthroscopy for a Virtual Arthroscopic Tear Diagnosis and Evaluation Platform (VATDEP)", The International Journal of Medical Robotics and Computer Assisted Surgery, 2016 (Accepted) (Impact Factor: 1.511).
  9. Lemon J, Kockara S, Halic T, Mete M., "Density-based parallel skin lesion border detection with webCL", BMC Bioinformatics. 2015;16 Suppl 13:S5. doi: 10.1186/1471-2105-16-S13-S5. Epub 2015 Sep 25 , PMID: 26423836 
  10. T. R.Stovall, S. Kockara, and R. Avci, “GPUSCAN: GPU-Based Parallel Structural Clustering Algorithm for Networks”, submitted to IEEE Transactions on Parallel and Distributed Systems. (SCI, Impact Factor 1.80), 2015.
  11. S. Suer, S. Kockara, and Mete M., "An Improved Border Detection in Dermoscopy Images for Density Based Clustering", BMC Bioinformatics, ISSN:1471-2105, vol. 12-S8, 2011. (SCI-Expanded, Impact Factor 3.03)
  12. M. Mete, S. Kockara, and K. Aydin, "Fast Density-Based Lesion Detection in Dermoscopy Images", Elsevier, Computerized Medical Imaging and Graphics, 35(2):128-36, 2011. (Impact factor 1.954)
  13. S. Kockara, M. Mete, V. Yip, B. Lee, and  Aydin K., "A soft kinetic data structure for lesion border detection", Oxford Bioinformatics, vol. 26: pages i21-i28, 2010. (SCI indexed, Impact factor 6.911)
  14. T. Halic, S. Kockara, et al., “Mixed Reality Simulation of Rasping Procedure in Artificial Cervical Disc Replacement (ACDR) Surgery”, BMC Bioinformatics, 2010; Vol. 11, S11 . (SCI-Expanded  indexed, Co-Corresponding author, Impact factor 3.78)
  15.  S. Kockara, M. Mete, B. Chen, K. Aydin, "Analysis of density based and fuzzy c-means clustering methods on lesion border extraction in dermoscopy images", BMC Bioinformatics. 2010; Vol. 11, S26. (SCI-Expanded  indexed, Impact factor 3.78)
  16. S. Kockara, T. Halic, C. Bayrak, K. Iqbal, R. Rowe, "Contact Detection Algorithms", Academy publisher, The Journal of Computers (JCP, ISSN1796-203X), 2009.