[2025-2027] Static and incremental automatic layout algorithms for compound graphs
[Funded by TUBITAK (ARDEB #125E061)]
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[2024-2025] SAA: Supporting the software development process with visualization-based methods using software analytics
[Funded by TUBITAK (ARDEB #123E492)]
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[2022] Security and management of cloud users and resources via graph-based visualization
[Funded by Slauth.io Inc (now called Armo Ltd)]
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[2021-2024] Effective analysis of big data through graph visualization with a unified complexity management framework
[Funded by TUBITAK (ARDEB #121E230)]
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[2021-2022] Detecting and preventing fraud in telecom networks through graph based modeling, querying and visualization
[Funded by TUBITAK (TEYDEB #5200049) and Turkcell Technology]
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[2021-2022] Custom technologies for visual graph-based analysis of lifecycle management
[Funded by Tripudio/Glide Systems Inc, USA]
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[2019-2021] Big graph visualization and analysis using advanced querying, fast layout and complexity management techniques
[Funded by TUBITAK (TEYDEB #5180088) and Huawei-Turkey]
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[2018-2020] Efficient layout algorithms for compound graphs with support for ports and constraints
[Funded by TUBITAK (ARDEB #118E131)]
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[2014-]  Newt Pathway Viewer and Editor
[In collaboration with the Demir Lab at OHSU, USA, and EISBM, France]
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[2016-] PathwayMapper (An interactive and collaborative graphical curation tool for cancer pathways)
[In collaboration with MSKCC, USA]
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[2014-2016] SBGNViz (Methods and tools for effective Analysis of Biological Processes with SBGN Diagrams)
[In collaboration with the Demir Lab at OHSU, USA][Funded by TUBITAK]
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[2011-]  cBio cancer genomics portal pathway views
[In collaboration with MSKCC & Dana-Farber Cancer Institute / Harvard Medical School, USA, and others]
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[2014-]  Cytoscape.js compound support and various extensions
[In collaboration with Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Canada]
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[2011-2013] Cytoscape Web compound support
[In collaboration with Donnelly Centre for Cellular & Biomolecular Research, University of Toronto, Canada]
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[2007-]  ChiBE (Chisio BioPAX Editor)
[In collaboration with Net Bio Lab at UMass Boston, USA]
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| [2006-2009] PVS - VISIBIOweb (Pathway Visualization Services)
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[2006-2014] Chisio (Compound or clustered graph visualization tools)
[Funded by TUBITAK (ARDEB #111E036)]
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[2000-2011] PATIKA (Pathway analysis tool for integration and knowledge acquisition)
[Funded by TUBITAK (ARDEB #104E049)]
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[2000-2001] Complexity management techniques in graph visualization cntd.
[Funded by Tom Sawyer Software, USA]
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[2000] Complexity management techniques in graph visualization
[Funded by Tom Sawyer Software, USA]
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