Ugur Dogrusoz

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 the roofs of i-Vis Research Group and BCBI. My 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
In Progress
Projects
Theses Supervised
In Progress

  • Alper Karacelik, PhD candidate
  • Merve Cakir, MS candidate
  • Can Cagdas Cengiz, MS candidate
  • Begum Genc, MS candidate
  • Marzieh Eslami Rasekh, MS candidate
  • Mecit Sari, MS candidate

Completed

  • Alper Karacelik, MS, August 2012, An Improved Spring Embedder Layout Algorithm for Compound Graphs,
    currently a Software Engineer at Havelsan, Ankara.
  • Selcuk Onur Sumer, MS, 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, PhD, Jan 2010, Causality Analysis in Biological Networks, MS, Sep 2003, Methods for Signaling Pathway Analysis using Microarray Data.
    currently a [Computational Biology] Post-doc at Memorial Sloan-Kettering Cancer Center, New York.
  • Alptug Dilek, MS, Aug 2009, VISIBIOweb: a web-based visualization and layout service for biological pathways,
    currently a Researcher at UEKAE, TUBITAK, Ankara.
  • Mehmet Esat Belviranli, MS, Aug 2009, A Circular Layout Algorithm for Clustered Graphs,
    currently a [CSE] PhD candidate in UC Riverside.
  • Ahmet Cetintas, MS, Jul 2007, Algorithms for Effective Querying of Graph-Based Pathway Databases,
    currently a Software Engineer at OSYM, Ankara.
  • Cihan Kucukkececi, MS, Jun 2007, Chisio: A Visual Framework for Compound Graph Editing and Layout,
    currently an Intermediate Software Engineer at Siemens IT Solutions, Ankara.
  • Emek Demir, PhD, Oct 2005, An Ontology for Computer-Aided Modeling of Cellular Processes,
    currently a [Computational Biology] Research Associate at Memorial Sloan-Kettering Cancer Center, New York.
  • Erhan Giral, MS, Aug 2005, A Layout Algorithm for Undirected Compound Graphs,
    currently with Computer Associates, San Francisco, CA.
  • E.Zeynep Erson, MS, Jul 2005, PATIKAweb: A Web Service for Accessing and Visualizing Pathway Data in PATIKA Database,
    currently a [Bioinformatics] Post-doc at Yale University, School of Medicine, New Haven, CT.
  • Asli Ayaz, MS, Aug 2004, Clustering Protein-Protein Interactions Based on Conserved Domain Similarities,
    currently a [Visual Neuroscience] Research Associate at University College London.
  • Gurcan Gulesir, MS, Sep 2003, A Framework for Management of Multiple Views of Cellular Pathway Graphs,
    currently a Senior Software Architect at BMW, Munich, Germany.
  • Cihad Baskoy, MS, Jan 2003, Polygon Packing Approach to Disconnected Graph Layout,
    currenly a Software Engineering Manager at Vodafone, Istanbul.
  • Burkay Genc, MS, Sep 2002, Complexity Management Techniques in Graph Visualization,
    currently a [CS] faculty in TED University, Ankara.
  • Alpay Erdem [co-advised with A. Gursoy], MS, Apr 2002, Time Domain Based Web Usage Mining for Web Site Improvement.
  • H.Mehmet Yuksel, MS, Jan 2002, Extending Hierarchical Graph Layout for Drawing UML Activity Diagrams.
    currenly an Infrastructure Group Leader at Havelsan, Ankara.