Research

Interests My research interests fall into the areas of information visualization (e.g. biological pathway and social network visualization), bioinformatics (pathway informatics), and graph algorithms (e.g. graph layout algorithms and query algorithms for graph-based knowledgebases) under i-Vis Research Group. Even though I've worked on purely theoretical problems (my Erdös number is 3) in the past, my current philosophy in research is to identify and tackle complex real-life problems and develop solutions of practical value. Such problems typically embrace challenging theoretical problems as well.
Selected Recent Publications
Projects & Software
Theses Supervised
In Progress

  • Istemi Bahceci, Ph.D. candidate
  • Hasan Balci, Ph.D. candidate
  • Enes Karaca, M.S. candidate
  • Ilkin Safarli, M.S. candidate
  • Leonard Dervishi, M.S. candidate
  • Umut Utku Calis, M.S. candidate

Completed

  • Metin Can Siper, (M.S.), July 2017, "Libraries and Tools for Viewing and Editing Biological Maps in SBGN",
    currently a Software Engineer at the Demir Lab at OHSU, Portland.
  • Istemi Rahman Bahceci, (M.S.), August 2016, "Software Tools for Visual Analysis of Cancer Genomics Data in the Context of Pathways".
  • Can Cagdas Cengiz, (M.S.), July 2014, "A Layout Algorithm for Graphs with Overlapping Clusters",
    currently a Software Engineer at ASELSAN.
  • Begum Genc, (M.S.), July 2014, "Automated Layout of Process Description Maps Drawn in SBGN",
    currently a (Ph.D.) candidate at Insight Centre for Data Analytics.
  • Mecit Sari, (M.S.), July 2014, "Methods & Tools for Visualization and Management of SBGN PD Maps",
    currently a Software Engineer at ESEN Sistem Entegrasyon, Ankara.
  • Merve Cakir, (M.S.), July 2013, "Integrating Biological Pathways and Genomic Profiles with ChiBE 2",
    currently a [Computational Biology and Bioinformatics] (Ph.D.) candidate in Duke University.
  • Alper Karacelik, (M.S.), August 2012, "An Improved Spring Embedder Layout Algorithm for Compound Graphs",
    currently a Software Engineer at Havelsan, Ankara.
  • Selcuk Onur Sumer, (M.S.), March 2012, "Chisio Web: Customizable Web-Based Visualization of Relational Information",
    currently a Software Engineer in Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York.
  • Ozgun Babur, (Ph.D.), Jan 2010, "Causality Analysis in Biological Networks", (M.S.), Sep 2003, "Methods for Signaling Pathway Analysis using Microarray Data".
    currently a [Biomedical Engineering] Research Assistant Professor at Oregon Health & Science University, Portland, OR.
  • Alptug Dilek, (M.S.), Aug 2009, "VISIBIOweb: a web-based visualization and layout service for biological pathways",
    currently a Senior Software Engineer at BILGEM, TUBITAK, Ankara.
  • Mehmet Esat Belviranli, (M.S.), Aug 2009, "A Circular Layout Algorithm for Clustered Graphs".
  • Ahmet Cetintas, MS, Jul 2007, "Algorithms for Effective Querying of Graph-Based Pathway Databases",
    currently a Senior Software Engineer at Mobile Action, Ankara.
  • Cihan Kucukkececi, MS, Jun 2007, "Chisio: A Visual Framework for Compound Graph Editing and Layout",
    currently a Software Team Lead and Software Architect at AYESAS, Ankara.
  • Emek Demir, (Ph.D.), Oct 2005, "An Ontology for Computer-Aided Modeling of Cellular Processes",
    currently currently a [Biomedical Engineering] Assistant Professor at Oregon Health & Science University, Portland, OR.
  • Erhan Giral, (M.S.), Aug 2005, "A Layout Algorithm for Undirected Compound Graphs",
    currently a Chief Architect in Computer Associates, San Francisco, CA.
  • E.Zeynep Erson, (M.S.), Jul 2005, "PATIKAweb: A Web Service for Accessing and Visualizing Pathway Data in PATIKA Database",
    currently an Associate Research Scientist at Yale University School of Medicine, New Haven, CT.
  • Asli Ayaz, (M.S.), Aug 2004, "Clustering Protein-Protein Interactions Based on Conserved Domain Similarities",
    currently a Research Associate at University of Zurich, Switzerland.
  • Gurcan Gulesir, (M.S.), Sep 2003, "A Framework for Management of Multiple Views of Cellular Pathway Graphs",
    currently a Project Manager at BMW Group, Munich, Germany.
  • Cihad Baskoy, MS, Jan 2003, "Polygon Packing Approach to Disconnected Graph Layout",
    currently a Java Developer at Credit Suisse, London, United Kingdom.
  • Burkay Genc, MS, Sep 2002, "Complexity Management Techniques in Graph Visualization",
    currently a [Institution of Population Studies] faculty in Hacettepe University, Ankara.
  • Alpay Erdem [co-advised with A. Gursoy], (M.S.), Apr 2002, "Time Domain Based Web Usage Mining for Web Site Improvement".
  • H.Mehmet Yuksel, (M.S.), Jan 2002, "Extending Hierarchical Graph Layout for Drawing UML Activity Diagrams".
    currently a Group Manager at Havelsan, Ankara.