Christoph W. Sensen Research Interests and Projects

Phone: [43] (316) 873-4090 | Fax: [43] (316) 873-4071 | E-mail: csensen@tugraz.at


This Web Site is updated infrequently. To get a better idea about current activities, please have a look at the Publications.


Visual Genomics Centre

My laboratory is now working on the creation of 4D (spatial and temporal) systems for genome annotation and the visualization of genomic knowledge. To build the infrastructure for this research, we have collaborated with Sun Microsystems and Fakespace Systems to build a high-performance computing environment, including a Java 3DTM enabled CAVE (CAVE is a recursive acronym. It stands for CAVE Automated Virtual Environment). 

Inside a Model of the Human Heart

picture by Maja Swannie

Highlights and Breakthroughs

The image below shows the layout of the CAVE

Whitepaper

A Technical White Paper about our CAVE installation is now available in PDF format. Click here to go to the white paper.

Middleware: JABIRU

We have created a middleware system called JABIRU, which allows us to manipulate Java 3DTM objects using the magic wand in the CAVE or keyboard and mouse on the standard computer. This allows users of our virtual reality models to work with complex data sets without the need for programming. Details about JABIRU can be found at the JABIRU Website.


The Human Body Project

Picture by Masumi Yajima

With our partners at Kasterstener Publications., Red Deer, AB, we have created an object oriented Model of the Human Anatomy. The model currently consists of over 3000 objects.

Funded by Genome Canada, we are now working to equip this model with functionality for the study of developmental patterns and diseases. More details can be found at the 4D Bioinformatics Web site. The most-asked question is what the "4" in 4D Bioinformatics stands for. This is of course the temporal component of our models. Have a look at the 4D demos (Flash Player required).

The Ontology used for our Project, which encompasses the complete set of terms referenced on Terminologia Anatomica is now available for download as an OBO file via the "Ontology Explorer" section of BRENDA.


An Integrated and Distributed Bioinformatics Platform for Genome Canada

Principal Investigator: Christoph W. Sensen

Co-Investigators (from left to right): David Wishart (University of Alberta), Brian Fristensky (University of Manitoba),  Mark Wilkinson (then at PBI, Saskatoon), 

On April 2nd 2002, Genome Canada funded the Bioinformatics platform project to a total amount of 10 million dollars (5 million dollars from Genome Canada, to be matched by 5 million dollars of industrial and provincial contributions) over three years. The Bioinformatics platform builds on existing infrastructure at the Calgary-based Sun Center of Excellence for Visual Genomics.

The Platform was renewed in 2005 through an additional investement of approximately 5 Million Dollars by Genome Canada and was funded until 2010.

The main scientific research goals of the project focused on data standardization and Web Services (BioMOBY) and the visualization of complex genomic features (Bluejay). A help desk and custom programming facility assisted genomics research projects in Canada on a cost-recovery basis.

The project featured a training component. Two Bioinformatics workshops (approximately 50 students each) were held per year (one in Eastern and one in Western Canada). These workshops were aimed at researchers working in Genome Canada science projects or similar ventures. The goal was to create Bioinformatics “power users” who can efficiently deal with the analysis and organization of the massive amounts of data that will be produced in the currently more than 50 Genome Canada projects.

As a consequence of the Bioinformatics Platform, the Sensen lab still supports three Genome Canada programs until 2018, supported by Alberta Innovates Technology Futures and Genome Alberta (see below).


Major Genome Canada/Genome Alberta Projects , in which Dr. Sensen currently is a Co-Investigator


MAGPIE: Automated Genome Analysis and Annotation

Together with Terry Gaasterland (now at Scripps) I started the MAGPIE project in April 1995. MAGPIE is an automated genome analysis and annotation system. A major aspect of the project is the visualization of genomic features. 

Below is one example of a view into a segment of the Sulfolobus solfataricus P2 genome.

Today, there are two versions of MAGPIE, a U.S. version based in Terry's laboratory and a Canadian version, based at the University of Calgary.  The Canadian MAGPIE code is included on CD in the "Genome Annotation" book.


Bluejay: Graphical Queries of Annotated Genomic Sequence

bluejay.gif (5484 bytes)

Many questions that biologist would like to answer using completely sequenced genomes are complex. The ideal environment for questions like "Tell me where all the tRNA synthetase genes are and if they are co-located with the respective tRNA genes is a graphical environment. Over several years, we have created one of the most powerful  browsers for XML-encoded genomic information. The system can be used free of charge by anyone. The Bluejay web site provides more details. The Bluejay system is also included in the "Genome Annotation" book.

Bluejay Browser in Comparative Genomics Mode


Complete Sequencing of Genomes

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I was part of the multinational Sulfolobus solfataricus P2 genome project, which concluded in 2001 with the publication of the entire genome.

We are now studying the gene expression of Sulfolobus in collaboration with several international collaborators.

The tools that we have developed for the Sulfolobus project, such as Magpie, Bluejay and Osprey, are now in wide use worldwide.


Development of Testing Methods for Transmissible Spongiform Encephalopathies

Together with scientists from the Canadian Food Inspection Agency in Lethbridge and Chronix Biomedical, Inc. in Göttingen, Germany, we have completed a study on the identification of DNA-based markers for transmissible spongiform encephalitis in Elk.

We have also characterized CNA patterns for BSE in an ALMA-funded collaboration with the Friedrich Löffler Institute in Riems, Chronix Biomedical, Inc and the University of Göttingen. We found that markers for the typical form of BSE are present consistently 10 months before clinical signs. Currently, we are transforming the basic research results into a field application.


New Testing Approaches for Chronic Diseases in Mammals

The results from our CWD and BSE work have led to the creation of a new company, CNA Diagnostics Inc. in Calgary. This company plans to develop a comprehensive suite of serum-based markers for chronic diseases in production animals, pets and eventually also for human conditions.


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01.09.2014