This document is a resume for Gokcen Cilingir. It summarizes her education, including a Master's degree in Computer Engineering from Middle East Technical University with honors, work experience including research assistantships and software engineering roles, skills in languages like C++, Java and tools like Visual Studio, research interests in bioinformatics and machine learning, and publications in those areas. References are also provided.

1. Gokcen Cilingir
17766 NE 90th ST, APT R189, Redmond, WA 98052
Mobile phone: 425 591 2221
Home phone: 425 358 3204
Email: gokcen.cilingir@gmail.com
Web site: http://www.ceng.metu.edu.tr/~gokcen/
Education
• M.Sc. in Computer Engineering, Middle East Technical University*, Ankara, Turkey
(September 2007, GPA: 3.64 out of 4)
 Worked full time as a Teaching/Research Assistant while attending university for 2
years.
 Attended I-Cancer Bioinformatics Research Group and participated in a
Bioinformatics project.
 Prepared a Master’s thesis entitled “A Classification System for the Problem of
Protein Subcellular Localization”.
• B.Sc. in Computer Engineering, Middle East Technical University, Ankara, Turkey (June
2005, High Honors Degree, GPA: 3.31 out of 4)
 Worked part time as a Software Engineer in the last year of university.
 Led a graduation project team who successfully completed design and development
of a project on restaurant automation.
 Took two six week internships at two software development companies where
actively participated in the assigned projects.
* Middle East Technical University is considered to be the leading university in terms of
scientific and engineering research in Turkey. Computer Engineering Department is
periodically reviewed and deemed "substantially equivalent to similarly titled and accredited
programs in the U.S.A." by the Accreditation Board for Engineering and Technology (ABET)

2. Work Experience
• Teaching/Research Assistant in the Computer Engineering Department of the Middle
East Technical University (and also as a member of the I-Cancer Bioinformatics
Research Group) for 2 years (2005 - 2007)
 Worked on a supervised learning problem where the goal was predicting a certain
feature of a given protein from its sequence. Conducted experiments using various
statistics, data mining, and machine learning techniques on a dataset which
contained approximately ten thousand protein sequences. Mainly focused on pattern
discovery process and the effect of feature selection methods on the classification
performance. Perl, C++ languages and some Matlab code are used for the
experiments which are performed mainly in Linux environment.
 Designed, implemented and evaluated a classification system for an important prob-
lem in Bioinformatics and outperformed the existing methods in terms of prediction
accuracy and time efficiency.
 Designed and implemented a plug-in for the Cytoscape tool (a popular biological net-
work visualization and analysis tool) which is used to annotate biological networks
with the predicted features that are obtained by our prediction tool. Java is used as
the programming language.
 Built a client-server application where the plug-in was the client side. Server side
contained a web service implementation (based on SOAP messaging) and a
database application. Worked on UniProtKB and Uniref100 databases which contain
approximately eight and fifteen million protein records, respectively.
• Software Engineer at MIKES for 1 year (2004 – 2005)
 Shipped an internal product. Designed, implemented and fully documented a multi-
threaded application that simulates a number of devices working simultaneously
using C# and .NET Framework. Made use of synchronization objects like semaphore
and mutex. Also used threads for I/O operations (i.e. serial port communication).
 Gained great amount of invaluable experience in object oriented design, software
development strategies, documentation and testing policies.
• Intern at MIKES for 8 weeks (2004)
 Developed an application similar to hyper terminal for serial port monitoring.
 Implemented a PC-based application using Visual C++ for the programming and
debugging of Dallas Semiconductor microcontrollers equipped with a ROM loader.
Communication is performed over a standard, asynchronous serial communications
port using a terminal emulator program with 8-N-1 protocol settings. For testing
purposes, a simulator for the microcontroller side is also implemented.
• Intern at MILSOFT for 8 weeks (2003)

3.  Implemented an XML file parser/generator application with a GUI using C++ (with
Visual Studio) for verification and testing purposes.
Computer Skills
• Languages: C/C++, C# (.Net), Java, Perl, HTML, XML, SQL
• Tools: Visual Studio 6.0, Visual Studio .Net, J Builder, Open Perl IDE, Oracle, MS SQL,
MySQL, Matlab
• Windows and UNIX (Linux) operating systems
Research Interests
Bioinformatics, Machine Learning, Data Mining, Statistical Data Analysis
Publications
• Gokcen Cilingir, Tolga Can, Volkan Atalay, “Protein Classification by Feature Mapping
based on Frequent Subsequences”, 15th Annual International Conference on Intelligent
Systems for Molecular Biology (ISMB 2007) and 6th European Conference
Computational Biology, Vienna, Austria, July 21-25, 2007. (Poster Presentation)
• Gokcen Alay , Tolga Can and Volkan Atalay, “A Feature Mapping Technique for Protein
Classification Problem Based on Frequent Patterns”, International Symposium on Health
Informatics and Bioinformatics Turkey’07, Antalya, Turkey, April 30 - May 2, 2007.
(Poster Presentation)
Scholarships and Honors
• Full scholarship for Machine Learning Summer School (MLSS), Taipei, Taiwan, 2006.
• Full Scholarship for graduate education, The Scientific and Technological Research
Council of Turkey, Ankara, Turkey, 2005.
• High Honors Degree, Middle East Technical University, Ankara, Turkey, 2005.
Attended Conferences and Summer Schools

4. • International Symposium on Health Informatics and Bioinformatics Turkey’07, April 30 -
May 2, Antalya, Turkey
• MLSS Taipei 2006, Machine Learning Summer School, July 24 - August 4, Taipei,
Taiwan
Languages
• Turkish (native language)
• Fluent in written and spoken English
References
• Prof. Dr. Volkan Atalay (Chair of Department), Department of Computer Engineering
Middle East Technical University, 06531, Ankara, TURKEY.
E-mail: volkan@ceng.metu.edu.tr, Phone: (90-312) 210 2080
• Assistant Prof. Dr. Tolga Can, Department of Computer Engineering
Middle East Technical University, 06531, Ankara, TURKEY.
E-mail: tcan@ceng.metu.edu.tr, Phone: (90-312) 210 5537
• Assistant Prof. Dr. Rengul Cetin Atalay, Department of Molecular Biology and Genetics
Bilkent University, 06800, Ankara, TURKEY.
E-mail: rengul@bilkent.edu.tr, Phone: (90-312) 290 2503