TOLGA CAN

Curriculum Vitae

 

Associate Professor

Department of Computer Engineering,
Middle East Technical University,
06531, Ankara, Turkey

               

Tel : (312) 210-5537
Fax : (312) 210-1259
Email : tcan@ceng.metu.edu.tr
www: http://www.ceng.metu.edu.tr/~tcan

RESEARCH INTERESTS

 

Bioinformatics:

Protein structure analysis, molecular surface generation and comparison, construction and analysis of protein networks, classification of bio-images.

 

General:

Computer graphics, computer vision, machine learning, statistical methods: support vector machines, hidden Markov models, Bayesian networks, decision trees.

EDUCATION

 

2000-2004:

University of California, Santa Barbara,
M.S. (Fall 2003) + Ph.D. (Summer 2004), Computer Science.

Title: Efficient and Automated Analysis of Protein Structures

Advisor: Prof. Yuan-Fang Wang

 

1998-2000:

Middle East Technical University, Ankara, Turkey,
M.S. Student, Computer Engineering.

 

1994-1998:

Middle East Technical University, Ankara, Turkey,
B.S. (Spring 1998), Computer Engineering, GPA: 3.57/4.0.

HONORS AND AWARDS

 

2000-2002:

Fulbright Fellowship awarded by IIE (International Institute of Education)

 

Nov. 2001:

Department of Energy Travel Grant for Georgia Tech-Emory International Conference on Bioinformatics.

 

Jun. 1998:

High-Honor Student, Class of 1998 at Middle East Technical University, Ankara, Turkey.

 

Dec. 1993:

3rd Prize in Black Sea Region, TUBITAK I. National Science Olympics in Informatics, Ankara, Turkey.

 

RESEARCH & WORK EXPERIENCE

 

Fall 2005-

present:

Associate Professor, Department of Computer Engineering, Middle East Technical University, Ankara, Turkey

 

Fall 2004-

Fall 2005:

Postdoctoral Researcher, University of California, Santa Barbara,
Working as a researcher at the Center for Bio-image Informatics. Developing algorithms for classification and querying of retinal and microtubule images. Currently working on methods that support user relevance feedback in content based image similarity queries.
Supervisor : Prof. Ambuj K. Singh

 

Fall 2001-Summer 2004:

Research Assistant, Department of Computer Science, University of California, Santa Barbara,
Developed efficient and automated methods for protein structure analysis.

Supervisor : Prof. Yuan-Fang Wang

 

Fall 1998-Summer 2000:

Researcher at MODSIM (Modeling and Simulation) Laboratory, Middle East Technical University, Ankara, Turkey,
Worked on a project funded by Turkish Department of Defense, on sensor optimization in a virtual environment. Modeled an existing area using digital elevation maps (DEM) and aerial photos and simulated virtual sensors (IR, Seismic, Thermal) to find optimal coverage of the area.

Supervisor : Dr. Veysi Isler

 

Fall 1997- Fall 1998

Technical Assistant, Oracle Ankara Office, Ankara, Turkey,
Worked at the technical support group and performed installation, maintenance, upgrade and migration tasks for ORACLE databases.

 

Fall 1996- Fall 1997

Part-time Engineer, ASELSAN Electronic Industries Inc., Ankara, Turkey,
Designed and implemented an application specific text editor under X-Windows environment on a Sun Solaris machine.

TEACHING EXPERIENCE

 

Summer 2003:

Instructor of Record, University of California, Santa Barbara,
Course: Introduction to Computer Programming (in Java).

 

Fall 2002:

Instructor of Record, University of California, Santa Barbara,
Course: Programming Methods in C.

 

2000-2001:

Teaching Assistant, at University of California, Santa Barbara,
Course: Data Structures and Algorithms II (2 quarters).
Graded homeworks, midterms, and finals. Managed office hours and discussion sessions regularly.

 

1998-2000:

Teaching Assistant, at Middle East Technical University, Ankara, Turkey,
Courses: C Programming (2 semesters), Language Processors/Compilers (2 semesters). Graded homeworks, projects, midterms, and finals. Managed office hours and discussion sessions.

REFEREED PUBLICATIONS (also available at http://www.ceng.metu.edu.tr/~tcan/)

 
  •  

Orhan Camoglu, Tolga Can, and Ambuj K. Singh, “Integrating Multi-Attribute Similarity Networks for Robust Representation of the Protein Space,” Bioinformatics, accepted for publication.

 
  •  

Tolga Can, Chao-I Chen, and Yuan-Fang Wang, “Molecular Surface Generation and Interior Cavity Detection Using Level-Set Methods,” submitted to Journal of Molecular Graphics and Modeling.

 
  •  

Tolga Can, Orhan Camoglu, and Ambuj. K. Singh, “Analysis of protein-protein interaction networks using random walks,” In Proceedings of the 5th ACM SIGKDD Workshop on Data Mining in Bioinformatics, Chicago, August 2005.

 
  •  

Orhan Camoglu, Tolga Can, Ambuj K. Singh, and Yuan-Fang Wang, “Decision Tree Based Information Integration for Automated Protein Classification,” Journal of Bioinformatics and Computational Biology (JBCB), Vol. 3, No. 3 (June 2005), 717-742.

 
  •  

Tolga Can, Orhan Camoglu, Ambuj K. Singh, and Yuan-Fang. Wang, “Automated Protein Classification Using Consensus Decision,” in Proceedings of the Third International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2004, pp. 224-235, Stanford, CA, August, 2004.

 
  •  

Tolga Can and Yuan-Fang Wang, “Protein Structure Alignment and Fast Similarity Search Using Local Shape Signatures,” Journal of Bioinformatics and Computational Biology (JBCB), Vol. 2, No. 1 (March 2004), 215-239.

 
  •  

Arnab Bhattacharya, Tolga Can, Tamer Kahveci, Ambuj K. Singh, and Yuan-Fang Wang, “ProGreSS: Simultaneous Searching of Protein Databases by Sequence and Structure,” in Proceedings of the 9th Pacific Symposium on Biocomputing (PSB2004), 9:264-275, Hawaii, 2004.

 
  •  

Yujun Wang, Tolga Can, Yuan-Fang Wang, and Jianwen Su, “Personalized Annotation and Information Sharing in Protein Science with Information-Slips,” in the 2nd IASTED International Conference on Information and Knowledge Sharing (IKS 2003), pp. 299-304, Scottsdale, AZ, November, 2003.

 
  •  

Tolga Can and Yuan-Fang Wang, “CTSS: A Robust and Efficient Method for Protein Structure Alignment Based on Local Geometrical and Biological Features,” in Proceedings of the Second International IEEE Computer Society Computational Systems Bioinformatics Conference, CSB 2003, pp. 169-179, Stanford, CA, August, 2003.

 
  •  

Tolga Can, Yujun Wang, Yuan-Fang Wang and Jianwen Su, “FPV: fast protein visualization using Java 3D,” Bioinformatics, 19(8):913-922, 2003.

 
  •  

Tolga Can, Yujun Wang, Yuan-Fang Wang and Jianwen Su, “FPV: Fast Protein Visualization Using Java 3D,” in Proceedings of the 18th Annual ACM Symposium on Applied Computing, SAC 2003, pp. 88-95, Melbourne, FL, March, 2003.

 
  •  

Tolga Can, Yujun Wang, Yuan-Fang Wang, and Jianwen Su, “A Distributed Protein Visualization Application,” in Proceedings of the 3rd Georgia Tech-Emory International Conference on Bioinformatics, Poster Paper, Atlanta, GA, Nov., 2001.

 
  •  

Tolga Can, Veysi Isler, and Ziya Ipekkan, “Sensor Optimization In a Virtual Environment,” in Proceedings of the 9th Conference on Computer Generated Forces and Behavioral Representation, Orlando, FL, May, 2000.

SELECTED TALKS

 

August 2004:

CSB’04 Stanford, CA, “Automated Protein Classification Using Consensus Decision”.

 

January 2004:

PSB’04, Big Island, Hawaii, “ProGreSS: Simultaneous Searching of Protein Databases by Sequence and Structure”.

 

August 2003:

CSB’03 Stanford, CA, “CTSS: A Robust and Efficient Method for Protein Structure Alignment Based on Local Geometrical and Biological Features”.

 

March 2003:

SAC’03, Melbourne, FL, “FPV: Fast Protein Visualization Using Java 3D”.

SELECTED PROJECTS

  •  

LSMS: Molecular Surface Generation and Interior Cavity Detection Using Level Set Methods
Developed a tool for generation and visualization of molecular surfaces (along with interior inaccessible cavities) using level-set methods. The developed tols is ~3 times faster than other molecular surface generation tools.

Link: http://www.ceng.metu.edu.tr/~tcan/LSMS
  •  

CTSS: Protein Structure Alignment Using Local Geometrical Features
Developed a method for comparison and similarity search of protein structures. The method utilizes local shape signatures computed based on the theory of differential geometry. CTSS is up to 30 times faster than CE, a widely used method for structure comparison, while achieving similar levels of accuracy.

Link: http://www.ceng.metu.edu.tr/~tcan/CTSS
  •  

FPV: Fast Protein Visualization Using Java 3D
Developed a tool for efficient visualization of protein structures using a scene-graph based graphics library. We propose techniques to optimize the constructed scene-graph to enable real-time visualization of very large protein complexes. FPV achieves up to 8 times interactive speed compared to existing methods. FPV is listed at the World Index of BioMolecular Visualization Resources.

Link: http://www.ceng.metu.edu.tr/~tcan/fpv