Alexander Lex

data visualization; visualization for molecular biology

Alexander Lex I am a post-doctoral visualization researcher at the Visual Computing Group lead by Hanspeter Pfister at the Harvard School of Engineering and Applied Sciences. I received my PhD, Master's and Undergraduate degrees from the Institute for Computer Graphics and Vision at the Graz University of Technology where I studied under the supervision of Prof. Dieter Schmalstieg. In 2011 I was a visiting researcher at Prof. Peter Park's Computational Genomics Research Group at Harvard Medical School.

My primary research interests are data visualization especially applied to molecular biology, 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 radical visualization ideas.

I am particularly interested in subset visualization (think slice & dice) for heterogeneous datasets in a molecular biology context. A recent application example of this research is StratomeX, a Caleydo view for cancer subtype analysis.

My second major research topic is visualization related to biological networks (pathways). Examples are the Entourage and enRoute techniques which enable users to explore large quantities of experimental data in the context of multiple pathways.

On the more theoretic side I investigate how to visually express relationships between either visible or currently invisible items on the screen.

I also work and consult on projects concerning pharmacology data, text, graphs, proteins, etc.

Current Research Projects

Check out past projects here

Caleydo http://caleydo.org

Caleydo is our open-source visualization framework developed by a team of research labs. Active since 2008 Caleydo is the platform for many bio-related visualization projects.

Caleydo StratomeXhttp://stratomex.caleydo.org

StratomeX is a visual analysis technique for cancer subtype visualization. It's purpose is to enable analysts to investigate groupings of patients (stratifications) across many datasets and properties enabling them to judge and characterize potential cancer subytpes.

LineUphttp://lineup.caleydo.org

LineUp is a visualization technique for multi-attribute rankings. It enables analysts to create and explore custom rankings of datasets with more than one attribute. We also use LineUp for data assignment, querying and to find good matches or supporting evidence for stratifications in StratomeX, Entourage and enRoute.

Caleydo enRoutehttp://enroute.caleydo.org

enRoute is a technique that enables analysts to explore large and heterogeneous experimental datasets in the context of biological pathways. The central idea is to let users specify relevant paths in a pathway and present these paths in a separate view juxtaposed with experimental data.

Caleydo Entouragehttp://entourage.caleydo.org

Entourage works in concert with enRoute to manage multiple pathways, find interdependencies between pathways and discover related pathways. The core idea of Entourage is that of contextual subsets. To manage the limited display space we don't show multiple complete pathways but instead display a contextually relevant subset of nodes and edges.

Mu-8 /ˈmyuteɪt/http://mu-8.com

Mu-8 (from 'mutate') is our approach to uncover which mutation of an amino-acid sequence causes a functional breakdown in a protein. Mu-8 was conceived as a contribution to the 2013 BioVis Contest and was originally developed together with students of Harvards CS 171 - Visualization class.

Mu-8 visualizes differences of principla components of a mutated protein relative to its protein family, in addition to the conservation of regions of the sequence, 3D structure and proximity data.

Publications

Peer Reviewed Publications

Hidden content visualization screenshot
Thomas Geymayer, Markus Steinberger, Alexander Lex, Marc Streit, and Dieter Schmalstieg:
Show me the Invisible: Visualizing Hidden Content - Honorable Mention award
To appear in Proceedings of the SIGCHI Conference on Human Factors in Computing Systems (CHI ’14), 2014.
Entourage screenshot
Alexander Lex, Christian Partl, Denis Kalkofen, Marc Streit, Anne Mai Wasserman, Samuel Gratzl, Dieter Schmalstieg and Hanspeter Pfister:
Entourage: Visualizing Relationships between Biological Pathways using Contextual Subsets
IEEE Transactions on Visualization and Computer Graphics (InfoVis '13), vol. 19, no. 12, pp. 2536–2545, 2013.
LineUp screenshot
Samuel Gratzl, Alexander Lex, Nils Gehlenborg, Hanspeter Pfister, and Marc Streit
LineUp: Visual Analysis of Multi-Attribute Rankings - Best paper award
IEEE Transactions on Visualization and Computer Graphics (InfoVis '13), vol. 19, no. 12, pp. 2277–2286, 2013.
enRoute screenshot
Christian Partl, Alexander Lex, Marc Streit, Denis Kalkofen, Karl Kashofer and Dieter Schmalstieg
enRoute: Dynamic Path Extraction from Biological Pathway Maps for Exploring Heterogeneous Experimental Datasets
BMC Bioinformatics, vol. 14, no. Suppl 19, p. S3, Nov. 2013
enRoute screenshot
Christian Partl, Alexander Lex, Marc Streit, Denis Kalkofen, Karl Kashofer, Dieter Schmalstieg:
enRoute: Dynamic Path Extraction from Biological Pathway Maps for In-Depth Experimental Data Analysis - Best paper award
Proceedings of the IEEE Symposium on Biological Data Visualization (BioVis ’12), 2012, pp. 107–114.
StratomeX screenshot
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 - 3rd best paper award
Computer Graphics Forum (EuroVis '12), pp. 1175-1184, 31(3), June 2012
Uncertainty heatmap illustration
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.
Stack'n'Flip screenshot
Marc Streit, Hans-Jörg Schulz, Alexander Lex, Dieter Schmalstieg, Heidrun Schumann:
Model-Driven Design for the Visual Analysis of Heterogeneous Data
IEEE Transactions on Visualization and Computer Graphics, 18(6), pp.998-1010, 2012.
Caleydo VisBricks screenshot
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.
Visual links routing screenshot
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.
Filter pipeline screenshot
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.
Caleydo Matchmaker screenshot
Alexander Lex, Marc Streit, Christian Partl, Karl Kashofer, Dieter Schmalstieg:
Comparative Analysis of Multidimensional, Quantitative Data
IEEE Transactions on Visualization and Computer Graphics (InfoVis'2010), 16(6), pp. 1027-1035, Nov.-Dec. 2010.
Visual linking screenshot
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.
Caleydo Bucket, heatmap and parallel coordinates screenshot
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.
Hierarchical heat map
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.
Multi-display environment mockup
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), at VisWeek, ISSN 1862-5207, pp. 5-8, Atlantic City, USA, 2009.
Parallel coordinates screenshot
Heimo Müller, Robert Reihs, Stefan Sauer, Kurt Zatloukal, Marc Streit, Alexander Lex, Bernhard Schlegl, Dieter Schmalstieg:
Connecting Genes with Diseases
Proceedings of the Symposium on Information Visualization in Biomedical Informatics, 13th International Conference on Information Visualization, Barcelona, Spain, July 2009.
Gaze-based bucket adaption illustration
Marc Streit, Alexander Lex, Heimo Müller, Dieter Schmalstieg:
Gaze-Based Focus Adaption in an Information Visualization System
IADIS Computer Graphics and Visualization and Image Processing 2009 Conference (CGVCVIP), Algarve, Portugal, June 2009.

Posters and Abstracts

Thesis Papers

Tutorials

Talks

Visualization Approaches for Biomolecular Data

MIT CSAIL, Cambridge, MA, USA. 04.12.2013
UMass Lowell, Lowell, MA, USA. 06.11.2013

Data Visualization in Molecular Biology.

Novartis Institutes for BioMedical Research, Cambridge, MA, USA. 29.07.2013

enRoute: Dynamic Path Extraction from Biological Pathway Maps for Exploring Heterogeneous Experimental Datasets

BioIT World Conference & Expo, Boston, MA, USA. 10.04.2013
Visualizing Biological Data (VIZBI) 2013, Cambridge, MA, USA. 20.03.2013
Symposium on Understanding Cancer Genomics through Information Visualization at Tokyo University, Tokyo, Japan. 22.02.2013

StratomeX: Visual Analysis of Large-Scale Heterogeneous Genomics Data for Cancer Subtype Characterization

IEEE BioVis 2012, Seattle, Washington, USA. 14.10.2012
EuroVis 2012, paper presentation, Vienna, Austria. 07.06.2012

VisBricks: Multiform Visualization of Large, Inhomogeneous Data

IEEE InfoVis 2011, Providence, Rhode Island, USA. Paper presentation. 26.10.2011

Visualizing Biomolecular Data with the Caleydo Framework

CBMI, Harvard Medical School, Boston, Massachusetts , USA. 12.08.2011
MRC Laboratory of Molecular Biology (LMB), Cambridge, UK. 21.09.2010
European BioInformatics Institute (EBI), Cambridge, UK. 20.09.2010

Visualizing the Effects of Logically Combined Filters

Information Visualization 2011, London, UK. Paper presentation. 14.07.2011

Comparative Analysis of Multidimensional, Quantitative Data

IEEE InfoVis 2010, Salt Lake City, Utah, USA. Paper presentation. 28.10.2010

Caleydo: Visual Analysis of Biomolecular Data

VCBM 2010 Leipzig, Germany. 02.07.2010

Caleydo and Visual Links

VRVis Research Company, Vienna, Austria. 11.03.2010

Caleydo: Design and Evaluation of a Visual Analysis Framework for Gene Expression Data in its Biological Context.

PacificVis 2010, Taipei, Taiwan. Paper presentation. 03.03.2010

Caleydo: Visualization of Gene Expression Data in the Context of Biological Processes

AUVA Research Center for Traumatology, Vienna, Austria. 26.02.2009

Novel InfoVis Techniques Applied to Pathways and Gene Expression Data

Institute for Genomics and Bioinformatics, Graz University of Technoloy, Austria. 10.07.2008

Teaching and Student Projects

Guest Lectures

Courses at Harvard University

Courses at TU Graz

Mentored Students

I have supervised many student projects on all levels - PhD, bachelor's thesis, master project and master's thesis, both at Harvard and at TU Graz. For a list of previous and ongoing students go here .

Looking for a Project?

Are you a student at Harvard looking for a visualization project? I'm always looking for students to work on web-based visualization or on projects in Caleydo. Just write me!