Bioinformatics and Computational Biology

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http://bioserver.ceng.metu.edu.tr/

Our laboratory was 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, we work on machine learning techniques for feature extraction and feature selection for protein sequences, we work on extraction of gene expression patterns and try to explore a group of genes with similar behaviors for gene expression arrays, and we integrate multiple data sources using statistical techniques to construct and analyze these networks for protein-protein interaction networks.

Members

  • Prof. Dr. Volkan Atalay
  • Asst. Prof. Dr. Tolga Can
  • Merter Sualp (PhD.St)
  • Alper Söyler (FDE PhD.St)
  • Ayse Gül Yaman (PhD.St)
  • Zerrin Sökmen (PhD.St)
  • Bahar Pamuk (PhD.St)
  • Oral Dalay (PhD.St)
  • Sevgi Yasar (MSc.St)
  • M. Ersan Topaloğlu (PhD.St)
  • S. Özge Gürsoy (Bilkent MBG MSc.St)

Current Projects

  • Genome Annotation based on Subsequence Analysis, TUBITAK 105E035, 2005-2007,
  • Construction and Analysis of Genome-Scale Protein Networks using Statistical Methods, TUBITAK 106E128, 2007-2010,
  • Cancer Gene Promoter Related Motif Search (CAPRIS), METU - Bilkent University joint project,
  • Large Scale Microarray Analysis, METU - Bilkent University joint project,

Past Projects

Selected Publications

  1. Turanalp, M. E., & Can, T. (2010). Finding frequent patterns in protein-protein interaction networks. [bib]
  2. Camoğlu, O., Can, T., & Singh, A. K. (2006). Integrating multi-attribute similarity networks for robust representation of the protein space. Bioinformatics, 22(13), 1585-1592. [bib]
  3. Can, T., Chen, C. -I., & Wang, Y. -F. (2006). Efficient molecular surface generation using level-set methods. Journal of Molecular Graphics and Modelling (JMGM), 25(4), 442-454. [bib]
  4. Atalay, V., & Cetin-Atalay, R. (2005). Implicit Motif Distribution based Hybrid Computational Kernel for Sequence Classification. Bioinformatics, 21(13), 1429-1436. [bib]
  5. Bayir, M. A., Güney, T. D., & Can, T. Integration of topological measures for eliminating non-specific interactions in protein interaction networks. Discrete Applied Mathematics special issue on Networks in Computational Biology. [bib]

Alumni

Name Current Position & Affiliation
Ömer Sinan Sarac, Ph.D. Post-Doc, BIOTEC DU Dresden
research/bioinfo/index.txt · Last modified: 2011/01/28 13:28 by Ayse Gul YAMAN