Welcome to my homepage!

I am a fifth year PhD student in Language Technologies Institute of School of Computer Science in Carnegie Mellon University. Prior to CMU, I was an undergraduate in Biological Sciences and Bioengineering Program in Sabanci University, Turkey. My Ph.D. advisors are Prof. Jaime G. Carbonell and Prof. Judith Klein-Seetharaman. My interests are in machine learning, computational biology and sytems biology. Currently my focus is infering and analyzing host-virus protein-protein interactions. I am a member of  Pittsburgh Center for HIV Interactions. Previously, I have worked in transmembrane protein structure/folding related problems.

Teaching
  • In Fall 2009, I was the teaching assistant for the Machine Learning course, course website.
  • In Spring 2007, I assisted the Foundations of Molecular Biophysics III course.
  • In my senior year at Sabanci University, I assisted the sophomore/junior level computational biology course.

    • Publications

    Journal Publications
  • Tastan O, Yu E, Ganapathiraju M, Aref A, Rader AJ and Klein-Seetharaman, J.  Comparison of stability predictions and simulated unfolding of rhodopsin structures.Photobiology and photochemistry, Volume 63, Issue 2, pp 351-363, 2006. Supplementary Website.


  • Tastan O, Meirovitch H, Klein-Seetharaman, J. The effect of loops on the structural organization of α-helical membrane proteins. Biophysical Journal. Volume 96, Issue 6, 2299-2312, 2009. Supplementary Website.


  • Balakrishnan S, Tastan O, Carbonell JG and Klein-Seetharaman J. (2009) Alternative paths in HIV-1 targeted human signal transduction pathways. BMC Genomics 10 Suppl 3, S30.


  • Venkatachari NJ, Le T, Tastan O, Timothy MD, Walker L, Ricciuti A, Yanamala N, Srinivasan A, Klein-Seetharaman J, Ramachandran M, Montelaro RC, and Ayyavoo,V. Oligomerization of HIV-1 Vpr: Identification of essential domains/residues using structure based approaches and evaluation of its relevance to Vpr functions. (2010) Virology Journal, 7: 119.


  • Tastan O , Rose JJ, Gibson GA, Singh I, Salter R, Ambrose Z, Watkins S, Klein-Seetharaman J, Aiken C. Mapping functionally important interactions between HIV-1 and human proteins, in preparation.


    • Peer Reviewed Conference Publications
  • Tastan O, Qi Y, Carbonell, JG, and Klein-Seetharaman, J. Prediction of Interactions between HIV-1 and Human Proteins by Information Integration. Pacific Symposium on Biocomputing 14:516-527(2009). Supplementary Website


  • Qi Y, Tastan O, Carbonell JG, Klein-Seetharaman J and Weston J. Semi-Supervised Multi-Task Learning for Predicting Interactions between HIV-1 and Human Proteins (2010) Bioinformatics, 9th European Conference on Computational Biology (ECCB). Supplementary Website.


  • Singh I, Tastan O, Klein-Seetharaman J. Comparison of virus interactions with human signal transduction pathways. (2010) ACM International Conference on Bioinformatics and Computational Biology.


  • Tastan O, Carbonell JG and Klein-Seetharaman J. Assessing confidence in literature-curated protein interactions in a probabilistic framework through community opinion., in review.


    • Selected Peer Reviewed Conference Posters and Talks
  • Tastan O, Carbonell JG, and Klein-Seetharaman J. Refining the HIV-1, human protein interaction network with multiple expert opinions . The 23rd Annual Meeting of the Groups Studying the Structures of AIDS-Related Systems and their Application to Targeted Drug Design, Satellite Session, Jun 25-26, 2009, Bethesda, Maryland.


  • Venkatachari NJ, Le T, Tastan O et al. Oligomerization of HIV-1 Vpr:Identification of essential domains/residues using structure based approaches and evaluation of its relevance to Vpr functions. The 23rd Annual Meeting of the Groups Studying the Structures of AIDS-Related Systems and their Application to Targeted Drug Design. Jun 25-26, 2009, Bethesda, Maryland.


  • Tastan O , Meirovitch H, Klein-Seetharaman, J. The effect of loops on the structural organization of alpha-helical membrane proteins. 3Dsig: Structural Bioinformatics and Computational Biophysics an ISMB Satellite Meeting. Jun 27-28, 2009, Stockholm, Sweeden.


  • Tastan O , Qi Y, Carbonell JG, and Klein-Seetharaman J. (2009) Prediction of HIV-1, human protein interactome . VIII European Symposium of the Protein Society, Jun 14-18, 2009, Zurich, Switzerland.


  • Tastan O . A machine learning approach for predicting HIV-1, human protein-protein interactions. University of Pittsburgh, Department of Structural Biology Data and Literature Seminar Series, Apr 9, 2008, Pittsburgh, PA (Invited talk).


  • Tastan O , Yu E, Rader AJ and Klein-Seetharaman J. Comparison of simulated unfoldings of alpha-helical membrane proteins. Biophysical Society Annual Meeting, Mar 3-7, 2007, Baltimore, Maryland.

    • Links
  • SCS Events Calendar
  • Machine Learning Lunch Seminar
  • Lane Center Seminar
  • Intelligence Seminar