Alexander Lex

I am a post-doctoral researcher and lecturer at the Institute for Computer Graphics and Vision at the Graz University of Technology. In 2011 I was a visiting researcher at the Computational Genomics Research Group which is part of the Center for Biomedical Informatics at Harvard Medical School.

My primary research interests are Information Visualization, Bioinformatics and Human Computer Interaction. My focus is my work on Caleydo, which is both, software that can be used by life science experts to visualize biomolecular data and pathways, but also a platform for implementing prototypes of more radical visualization ideas.

I am particularly interested in divide and conquer visualization for multidimensional inhomogeneous our heterogeneous datasets in a molecular biology context. I have investigated using multiform views, often containing disjoint subsets of data and align and connect them in non-traditional, flexible setups. I have used visual linking to connect these different views.

A recent application example of this research is StratomeX, a Caleydo view for cancer subtype analysis. For more information visit http://stratomex.caleydo.org or look at the video.

Publications
Projects
Teaching and Student Projects
Curriculum Vitae

Publications

Peer Reviewed Publications

2012

Alexander Lex, Marc Streit, Hans-Jörg Schulz, Christian Partl, Dieter Schmalstieg, Peter J. Park and Nils Gehlenborg: StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization To appear in: Computer Graphics Forum (EuroVis '12), pp. fff-lll, 31(3), June 2012
Clemens Holzhüter, Alexander Lex, Dieter Schmalstieg, Hans-Jörg Schulz, Heidrun Schumann and Marc Streit: Visualizing Uncertainty in Biological Expression Data Proceedings of the SPIE Conference on Visualization and Data Analysis (VDA '12), pp. 82940O, San Francisco, CA, USA, 2012.

2011

Alexander Lex, Hans-Jörg Schulz, Marc Streit, Christian Partl and Dieter Schmalstieg: VisBricks: Multiform Visualization of Large, Inhomogeneous Data IEEE Transactions on Visualization and Computer Graphics (InfoVis'11), 17(12), pp. 2291-2300, Dec. 2011.
Markus Steinberger, Manuela Waldner, Marc Streit, Alexander Lex and Dieter Schmalstieg: Context-Preserving Visual Links - Best paper award IEEE Transactions on Visualization and Computer Graphics (InfoVis'11), 2249-2258, 17(12), Dec. 2011.
Marc Streit, Hans-Jörg Schulz, Alexander Lex, Dieter Schmalstieg, Heidrun Schumann: Model-Driven Design for the Visual Analysis of Heterogeneous Data To appear in: IEEE Transactions on Visualization and Computer Graphics, 2011.
Thomas Geymayer, Alexander Lex, Marc Streit, Dieter Schmalstieg: Visualizing the Effects of Logically Combined Filters Proceedings of the Conference on Information Visualisation (IV’2011), pp. 47-52, London, UK, 2011.

2010

Alexander Lex, Marc Streit, Christian Partl, Karl Kashofer, Dieter Schmalstieg: Comparative Analysis of Multidimensional, Quantitative Data IEEE Transactions on Visualization and Computer Graphics (Proceedings Visualization / Information Visualization 2010), 16(6), pp. 1027-1035, Nov.-Dec. 2010
Manuela Waldner, Werner Puff, Alexander Lex, Marc Streit, Dieter Schmalstieg: Visual Links across Applications - Best student paper award Proceedings of the Graphics Interface (GI) 2010, Ottawa, Ontario, Canada, May 31 - June 2 2010.
Alexander Lex, Marc Streit, Ernst Kruijff, Dieter Schmalstieg: Caleydo: Design and Evaluation of a Visual Analysis Framework for Gene Expression Data in its Biological Context Proceedings of 2010 IEEE Pacific Visualization Symposium, pp. 57-64, Taipeh, Taiwan, 2010.

2009

Marc Streit, Alexander Lex, Michael Kalkusch, Kurt Zatloukal, Dieter Schmalstieg: Caleydo: Connecting Pathways with Gene Expression Bioinformatics, Oxford Journals, 25(20), pp. 2760-2761, 2009.
Manuela Waldner, Alexander Lex, Marc Streit, Dieter Schmalstieg: Design Considerations for Collaborative Information Workspaces in Multi-Display Environments Procceedings of Workshop on Collaborative Visualization on Interactive Surfaces (CoVIS'09), in conjunction with VisWeek, ISSN 1862-5207, pp. 5-8, Atlantic City, USA, 2009.
Heimo Müller, Robert Reihs, Stefan Sauer, Kurt Zatloukal, Marc Streit, Alexander Lex, Bernhard Schlegl, Dieter Schmalstieg: Connecting Genes with Diseases Symposium on Information Visualization in Biomedical Informatics, 13th International Conference on Information Visualization, Barcelona, Spain, July 2009.
Marc Streit, Alexander Lex, Heimo Müller, Dieter Schmalstieg: Gaze-Based Focus Adaption in an Information Visualization System Computer Graphics and Visualization and Image Processing 2009 Conference (CGVCVIP), Algarve, Portugal, June 2009.
Gudrun Schmidt-Gann, Katharina Schmid, Monika Uehlein, Joachim Struck, Andreas Bergmann, Dieter Schmalstieg, Marc Streit, Alexander Lex, Douw G. van der Nest, Martijn van Griensven and Heinz Redl: Gene- and Protein Expression Profiling in Liver in a Sepsis-Baboon Model 32nd Annual Meeting on Shock, San Antonio, Texas, June 6-9, 2009.

Talks

• 26.10.2011
  Paper presentation at IEEE InfoVis 2011, Providence, Rhode Island, USA
  VisBricks: Multiform Visualization of Large, Inhomogeneous Data
  Download slides
• 12.08.2011
  Invited talk at CBMI, Harvard Medical School, Boston, Massachusetts , USA
  Visualizing Biomolecular Data with the Caleydo Framework
  Download slides
• 14.07.2011
  Paper presentation at Information Visualization 2011, London, UK
  Visualizing the Effects of Logically Combined Filters
  Download slides
• 28.10.2010
  Paper presentation at IEEE InfoVis 2010, Salt Lake City, Utah, USA
  Comparative Analysis of Multidimensional, Quantitative Data
  Download slides
• 21.09.2010
  Invited talk at the MRC Laboratory of Molecular Biology (LMB), Cambridge, UK
  Caleydo: Visual Analysis of Biomolecular Data
• 20.09.2010
  Invited talk at the European BioInformatics Institute (EBI), Cambridge, UK
  Caleydo: Visual Analysis of Biomolecular Data
  Download slides
• 02.07.2010
  Invited talk at VCBM 2010 Leipzig, Germany
  Caleydo: Visual Analysis of Biomolecular Data
• 11.03.2010
  Invited talk at the VRVis Research Company, Vienna, Austria
  Caleydo and Visual Links
• 03.03.2010
  Paper presentation at PacificVis 2010, Taipei, Taiwan
  Caleydo: Design and Evaluation of a Visual Analysis Framework for Gene Expression Data in its Biological Context.
  Download slides
• 26.02.2009
  Invited talk at the AUVA Research Center for Traumatology, Vienna, Austria
  Caleydo: Visualization of Gene Expression Data in the Context of Biological Processes
• 10.07.2008
  Invited talk at the Institute for Genomics and Bioinformatics, Graz University of Technoloy, Austria
  Novel InfoVis Techniques Applied to Pathways and Gene Expression Data

Posters

• Alexander Lex, Peter J. Park and Nils Gehlenborg:
  Supporting Subtype Characterization through Integrative Visualization of Cancer Genomics Data Sets
  The Cancer Genome Atlas’ 1st Annual Scientific Symposium: Enabling Cancer Research Through TCGA, November 17-18, 2011, Washington, D.C., USA
  
• Marc Streit, Alexander Lex, Helmut Doleisch and Dieter Schmalstieg:
  Does software engineering pay off for research? Lessons learned from the Caleydo project.
  Proceedings of the second Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM), Leipzig, Germany, July 1 - 2 2010.
  
• CALEYDO
  Marc Streit, Alexander Lex, Dieter Schmalstieg, Heimo Mueller, Stefan Sauer, Wilhelm Steiner, Kurt Zatloukal
  ZMF.Day (Center for Medical Research) 2008, Graz, Austria, November 12, 2008.
  

Thesis Papers

• Doctoral Thesis
  Title: Visualization of Multidimensional Data with Applications in Molecular Biology
  Advisor: Univ. Prof. DI. Dr. Dieter Schmalstieg
  Co-Advisor: Dr. Nils Gehlenborg
  Referee: Prof. Dr. Robert Kosara
  Publication date: March 2012
  

• Master's Thesis
  Title: Exploration of Gene Expression Data in a Visually Linked Environment
  Supervision: Univ. Prof. DI. Dr. Dieter Schmalstieg
  Publication date: June 2008
  

• Bachelor's Thesis
  Title: Evaluation of Medical Image Viewers and
  Architectural Software Design for a Medical Image Viewer
  Supervision: Univ. Prof. DI. Dr. Horst Bischof / Dipl-Ing. Dr.techn. Martin Urschler
  Publication date: June 2005
  

Exhibitions

• FWF Austrian Science Fund 40-Year Anniversary
  Marc Streit, Alexander Lex, Dieter Schmalstieg, Heimo Mueller, Kurt Zatloukal
  Graz, Austria, December 2008 - January 2009.

Projects

Project Acquisition

• Co-author of the research proposal: Diagnostics of Tumor Heterogenity - a new Steering Factor for Colorectal Cancer?. Responsible for the Visualization Part. Funded by the state of Styria, 2012.
• Co-author (together with Dieter Schmalstieg, Manuela Waldner, Marc Streit) of the research proposal: Caleydoplex – Collaborative Information Exploration in Multi-Display Environments Funded by FWF, 2011.
• Principal author (together with Dieter Schmalstieg, Marc Streit, Helmut Doleisch) of the research proposal:
  inGeneIous - Visualization of biomolecular and clinical data.
  Funded by FFG, BRIDGE program, 2009.

Software Projects

• Caleydo Visualization Framework (emerged from GeneView)
  Visit caleydo.org

  
  

• iMEDgine - Medical Image Viewer
  Visit imedgine.org
  iMEDgine is open source software that allows visualization and manipulation of medical 3D image data.
  The software itself provides the GUI, basic manipulation functionality and interfaces to algorithms as implemented in ITK.

  iMEDgine was developed from 2005-2006 and is no longer actively maintained.

  

Teaching and Student Projects

Courses

• Selected Topics Computer Grapics (2011/2012, 2010/2011)
  Lectures on Perceptional Issues, Color, Information Visualization, Visual Analytics, Flow Visualization.
• Distributed Systems (2011/2012, 2010/2011, 2009/2010)
  Development and supervision of lab assignments
• Introduction to Scientific Work (2011/2012, 2010/2011)
  Supervision of focus groups.
• Computer Graphics 1 (2011)
  Development and supervision of lab assignments
• Computer Graphics 2 (2011)
  Development and supervision of lab assignments

Student Projects

Curriculum Vitae

Download CV

Grants, achievements

• 2011: Co-recipient of best paper award, IEEE InfoVis
• 2011: Scholarship for short time academic research and expert courses abroad (KUWI). Granted by the Graz University of Technology.
• 2010: Co-recipient of best student paper award, ACM Graphics Interface.
• 2007: Award for excellent performance as a student (Leistungsstipendium) granted by the Faculty of Computer Science at the Graz University of Technology.
• 2007: Research grant for students (Förderstipendium) awarded by the Faculty of Computer Science at the Graz University of Technology
• 2006: Joint Study scholarship for student exchange with McMaster University, Hamilton, On, Canada.