BIOINFORMATICS and COMPUTATIONAL BIOLOGY RESEARCH LABORATORY

 

Laboratory History and Mission

 

Our laboratory is officially established in 2006 with the goal of uniting ongoing bioinformatics research in the department. We focus on developing and applying computational techniques for the analysis of data and modeling of processes related to molecular biology. The broad aim of our research is to provide computational tools to assist researchers in understanding, explaining, and predicting the behavior of complex biological systems. We utilize methodologies from the areas of machine learning, statistical modeling, graph theory to provide solutions to bioinformatics problems such as protein functional classification, gene expression analysis, protein-protein interaction network analysis. To give a couple of examples, for protein sequences, we work on machine learning techniques for feature extraction and feature selection; for gene expression arrays, we work on extraction of gene expression patterns and try to explore a group of genes with similar behaviors; and for protein-protein interaction networks, we integrating multiple data sources using statistical techniques to construct and analyze these networks.

 

People

  • Faculty: Prof. Volkan Atalay and Assist. Prof. Tolga Can
  • Students:
    • Ömer Sinan Saraç (CENG PhD student, TUBITAK 105E035 project researcher)
    • Gökçen Alay (CENG MSc student, teaching assistant)
    • Zerrin Sökmen (CENG PhD student, TUBITAK 105E068 project researcher)
    • Oral Dalay (CENG PhD student, OYP assistant)
    • M. Ersan Topaloğlu (CENG PhD student, TUBITAK 105E068 project researcher)
    • Ş. Özge Gürsoy (Bilkent MBG MSc student, TUBITAK 105E035 project researcher-not located in the lab)
    • Alper Söyler (FDE PhD student, teaching assistant)
    • Bahar Pamuk (CENG MSc student, teaching assistant)
    • Merter Sualp (CENG PhD student)
    • Sevgi Yaşar (CENG MSc student)

 

Completed Theses

  • Biter Bilen, MSc Thesis, “Analyses and Web Interfaces for Protein Subcellular Localization and Gene Expression Data,” February 2007.
  • Perit Bezek, MSc Thesis, “A Clustering Method for the Problem of Protein Subcellular Localization,” December 2006.

 

Current Projects

  • SYSPATHO:EU-FP7 Research Project, New Algorithms for Host Pathogen Systems Biology
  • Genome Annotation based on Subsequence Analysis, TUBITAK 105E035, 2005-2007, $120,000
  • Construction and Analysis of Genome-Scale Protein Networks using Statistical Methods, TUBITAK 106E128, 2007-2010, 96K YTL
  • Cancer Gene Promoter Related Motif Search (CAPRIS), Bilkent University-METU joint project, non-funded
  • Large Scale Microarray Analysis, Bilkent University-METU joint project, non-funded

 

Past Projects

  • LSMS: Level Set methods for Molecular Surface Generation

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

  • CTSS: Protein Structure Alignment Using Local Geometrical Features

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

  • FPV: Fast Protein Visualization Using Java 3D       

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

 

Selected Publications

 

  • M.E. Turanalp, T. Can, “Finding frequent patterns in protein-protein interaction networks,” in preparation.
  • M.A. Bayir, T.D. Güney, and T. Can, “Integration of topological measures for eliminating non-specific interactions in protein interaction networks,” accepted to Discrete Applied Mathematics special issue on Networks in Computational Biology.
  • T. Can, C.-I. Chen, Y.-F. Wang, “Efficient molecular surface generation using level-set methods,” Journal of Molecular Graphics and Modelling (JMGM), 25(4):442-454, 2006.
  • O. Çamoğlu, T. Can, and A.K. Singh, “Integrating multi-attribute similarity networks for robust representation of the protein space,” Bioinformatics, 22(13):1585-1592, 2006.
  • V. Atalay, R. Cetin-Atalay, “Implicit Motif Distribution based Hybrid Computational Kernel for Sequence Classification”, Bioinformatics, 21(13), pp.1429-1436, 2005.