Theses In Progress

• Noor Muhammad, M.S. candidate
• Yusuf Ziya Ozgul, M.S. candidate

Theses Completed

• Hamza Islam, (M.S.), September 2023, "HySE: A spring embedder approach for layout of hybrid graphs"
• 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"
• Hasan Balci, (Ph.D.), August 2022, "Fast Compound Graph Layout with Constraint Support"
  currently a Postdoctoral Researcher at Maastricht Centre for Systems Biology, Netherlands.
• 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 Senior Researcher at TUBITAK BILGEM, 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 PhD student at CS Dept, Case Western Reserve University, Cleveland.
• Metin Can Siper, (M.S.), July 2017, "Libraries and Tools for Viewing and Editing Biological Maps in SBGN",
  currently a Research 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".
  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, (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 Postdoctoral Researcher in Univ of California, San Francisco.
• Alper Karacelik, (M.S.), August 2012, "An Improved Spring Embedder Layout Algorithm for Compound Graphs",
  currently a Team Leader 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 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 Senior Software Engineer at Tekmetric, Ankara.
• Mehmet Esat Belviranli, (M.S.), Aug 2009, "A Circular Layout Algorithm for Clustered Graphs",
  currently an Assistant 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 Corporate Architect at BMC Software, Danville, California.
• E.Zeynep Erson, (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 Co-Lead 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 Senior 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".
• H.Mehmet Yuksel, (M.S.), Jan 2002, "Extending Hierarchical Graph Layout for Drawing UML Activity Diagrams".
  currently RTOS and Platform Management Group Leader at Havelsan, Ankara.