Ugur Dogrusoz

Research

Interests My research interests fall into the areas of big data analytics and 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 Lab. Even though I've worked on purely theoretical problems (both my Erdos number and Knuth number are 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 Publications See related i-Vis page for Selected Publications and CV for a complete list.
Projects & Software See related i-Vis page for Projects & Software
Supervision

Theses In Progress

  • M. Mahdi Khosravi, M.S. candidate
  • Sinan Havus, M.S. candidate
  • Melisa Tanrikulu, MS Candidate
  • Alperen Tolga Karacam, MS Candidate
  • Pouya Rashidi Kia, MS Candidate
  • Syed Ebad Hyder, M.S. candidate

Theses Completed

  • Noor Muhammad, (M.S.), February 2026, "A framework for collaborative integration and effective querying of biological pathways in a graph database"
  • Yusuf Ziya Ozgul, (M.S.), Februray 2026, "A framework for validation and error resolution of biological pathway maps"
  • Hamza Islam, (M.S.), September 2023, "HySE: A spring embedder approach for layout of hybrid graphs"
    currently a software engineering contractor
  • Osama Zafar, (M.S.), August 2023, "CMGV: a unified framework for complexity management in graph visualization"
    currently a PhD student at CS Dept, Case Western Reserve University, Cleveland.
  • Huseyin Eren Calik, (M.S.), September 2022, "An ensemble classification model for detecting voice phishing in telecommunication networks and its integration into a visual analysis tool"
    currently a software engineer at Havelsan, Ankara.
  • Hasan Balci, (Ph.D.), August 2022, "Fast Compound Graph Layout with Constraint Support"
    currently a Postdoctoral Researcher at NLM/NIH, USA
  • Mubashira Zaman, (M.S.), October 2021, "An Orthogonal Layout Algorithm for Small Compound Graphs"
    currently a Senior Specialist Engineer - R&D at Beko Global, Pakistan.
  • Yusuf Sait Canbaz, (M.S.), September 2021, "Visuall: A Quickly Customizable Library for Jumpstarting Visual Graph Analysis Components",
    currently a Software Engineer at GraphAware (London).
  • Alihan Okka, (M.S.), October 2020, "A Compound Graph Layout Algorithm With Support for Ports",
    currently a Software Engineer at Ekinoks Software, Ankara.
  • Umut Utku Calis, (M.S.), September 2019, "Semantic Validation of Biological Maps in SBGN",
    currently a software engineer in Central Bank of Turkey, Ankara.
  • Enes Karaca, (M.S.), February 2019, "Efficient querying of SBGN maps stored in a graph database",
    currently a Lead Software Engineer at Aselsan, Ankara.
  • Ilkin Safarli, (M.S.), July 2018, "Methods and Tools for Synchronized Visualization of Evolving Networks",
    currently a Software Engineer at Google, Mountain View, California.
  • Leonard Dervishi, (M.S.), July 2018, "Improvements on PathwayMapper: A collaborative Pathway Curation Tool",
    currently a Data Scientist at Fraunhofer Institute, Germany.
  • Metin Can Siper, (M.S.), July 2017, "Libraries and Tools for Viewing and Editing Biological Maps in SBGN",
    currently a fullstack developer (freelance).
  • Istemi Rahman Bahceci, (M.S.), August 2016, "Software Tools for Visual Analysis of Cancer Genomics Data in the Context of Pathways".
    currently a Software Engineer at HOLO-LIGHT, Munich, Germany.
  • Can Cagdas Cengiz, (M.S.), July 2014, "A Layout Algorithm for Graphs with Overlapping Clusters",
    currently a Senior Software Developer at Booking.com, Netherlands.
  • Begum Genc McEvoy, (M.S.), July 2014, "Automated Layout of Process Description Maps Drawn in SBGN",
    currently a Data Scientist at Apple and Women in AI Ireland Ambassador, Ireland.
  • Mecit Sari, (M.S.), July 2014, "Methods & Tools for Visualization and Management of SBGN PD Maps",
    currently a Software Design Engineer at ASML, Eindoven.
  • Merve Cakir, (M.S.), July 2013, "Integrating Biological Pathways and Genomic Profiles with ChiBE 2",
    currently a Specialist in Univ of California, San Francisco.
  • Alper Karacelik, (M.S.), August 2012, "An Improved Spring Embedder Layout Algorithm for Compound Graphs",
    currently a Tech Lead at EUROCONTROL, France.
  • 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 an Assistant Professor of Network Data Science at University of Massachusetts, Boston.
  • Alptug Dilek, (M.S.), Aug 2009, "VISIBIOweb: a web-based visualization and layout service for biological pathways",
    currently a Staff Engineer at Tekmetric (Houston, Texas, USA).
  • Mehmet Esat Belviranli, (M.S.), Aug 2009, "A Circular Layout Algorithm for Clustered Graphs",
    currently an Associate Professor at Colorado School of Mines, Denver.
  • Ahmet Cetintas, MS, Jul 2007, "Algorithms for Effective Querying of Graph-Based Pathway Databases",
    currently CTO at Matchingam Games, Ankara.
  • Cihan Kucukkececi, MS, Jun 2007, "Chisio: A Visual Framework for Compound Graph Editing and Layout",
    currently a Software Development Platform and Process Owner at EUROCONTROL, Belgium.
  • Emek Demir, (Ph.D.), Oct 2005, "An Ontology for Computer-Aided Modeling of Cellular Processes",
    currently a [Biomedical Engineering] Associate Professor at Oregon Health & Science University, Portland.
  • Erhan Giral, (M.S.), Aug 2005, "A Layout Algorithm for Undirected Compound Graphs",
    currently a VP of AI Strategy & Innovation at BMC Helix, Santa Clara, California.
  • E.Zeynep Erson Omay, (M.S.), Jul 2005, "PATIKAweb: A Web Service for Accessing and Visualizing Pathway Data in PATIKA Database",
    currently an Assistant Professor at Yale University School of Medicine, New Haven.
  • Asli Ayaz, (M.S.), Aug 2004, "Clustering Protein-Protein Interactions Based on Conserved Domain Similarities",
    currently a Expert Research Scientist at Nerf - empowered by imec, KU Leuven and VIB, Belgium.
  • Gurcan Gulesir, (M.S.), Sep 2003, "A Framework for Management of Multiple Views of Cellular Pathway Graphs",
    currently a Principal Techincal Program Manager at Microsoft, Germany.
  • Cihad Baskoy, MS, Jan 2003, "Polygon Packing Approach to Disconnected Graph Layout",
    currently a Senior Agile/Java and Kotlin Developer at Fleetnest and a Director at Kaan IT Ltd, London.
  • Burkay Genc, MS, Sep 2002, "Complexity Management Techniques in Graph Visualization",
    currently a [Computer Science] Associate Professor 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",
    currently Senior Software Architect at Spectrum Automative Holdings Corp, USA.
  • H.Mehmet Yuksel, (M.S.), Jan 2002, "Extending Hierarchical Graph Layout for Drawing UML Activity Diagrams".
    currently Modelling and Software Engineering Group Leader in Simulation at Havelsan, Ankara.