Impact

The Center for Bioinformatics Saar has set important scientific impulses on the campus of Saarland University as well as in the German and international bioinformatics scene. In order to continue to be successful, the work of the Center has at seven goals, whioch have been laid out in detail the chapter "About us":

 

Excellent Research

The Center prides itself on excellent research results in a number of research areas pertaining to bioinformatics. The research focuses of the Center include:

 

Epigenetics

In this area, which is central to the modern life sciences, the Center has formed a focus. The large German Epigenome Program (DEEP), which is being funded by the German Federal Ministry of Education and Research ((BMBF) from 2012 two 2017, is directed by Prof. Jörn Walter, Full Professor of Genetics at Saarland University. Prof. Thomas Lengauer from the Max Planck Institute for Informatics coordinates the bioinformatics activities of this project. In addition, in the context of DEEP several interdisciplinary research collaborations have developed and include additional research groups on campus (e.g., Prof. Holmes, Prof. Wolf, and Prof. Hein). The DEEP project has brought forth high-ranking publications and important software which is being used by a large number of scientists worldwide.

 

Biomarkers for the diagnosis of diseases

The research groups around Prof. Keller, Prof. Meese, and Prof. Lenhof in the Center have identified new biomarkers for a number of diseases, among them many types of cancer. The biomarkers for cancer consist of diverse antigens that occur in tumors or of different short RNA molecules (microRNAs). Such composite biomarkers, which are also called molecular signatures, can be detected in the blood of patients. Thus, they can form the basis for minimal - or even noninvasive - diagnostic tests. The diagnostic signatures have been described in more than 50 scientific publications and form the basis of several patent applications and patents. Building on these results, we aim at testing such biomarkers in the clinic.

 

Bacterial resistance — new antibiotics

The cummulative expertise from bioinformatics, biochemistry, pharmaceutics, and chemistry enabled research groups in the Center to isolate promising natural antibacterial compounds and identify their molecular targets. Highlights are the work on a new inhibitor of the protein gyrase as well as translational research on the development of griselimycins as drugs against tuberculosis. The latter show exceptional activity in animal models and, due to their new mechanism of action based on blocking DNA synthesis, exhibit no cross-resistance with known antibiotics.

 

Bacterial resistance — resistance testing

Building on the experience with biomarker panels, the Center is working on improving the diagnosis and therapy selection for patients with bacterial infections. The goal is to replace classic culture-based resistance tests that are used today in genetic testing. The respective tests can potentially lead to decisions on therapy more quickly, thus improving patient treatment.

 

Biotechnology

The Center actively fostered the leading international leading concepts for design and development of microbial cell factories, which form the basis for pioneering sustainable industrial production. This has led to high-ranking publications and international patents as well as to promising materials developed in collaboration with the chemical and pharmaceutical industries. Examples include bio-based plastics and platform chemicals such as biologically produced succinic acid (spirit of amber).

 

Biomolecular interactions

This topic forms a research focus at the Center, to which numerous research groups contribute. Research comprises for instance a novel analysis of transiently, that is intermittently, forming binding pockets in proteins, a result which has generated a new research direction. Furthermore, we have investigated the binding of compounds to proteins, which are relevant for medicine and biotechnology. Another topic is modeling large complexes consisting of many proteins. At a higher level, we analyze networks of molecular interactions comprising a large number of molecules, partly in basic research and partly in veiw of medical issues.

 

Publications

Between 2010 and 2015 the Center for Bioinformatics has published over 500 papers in international journals and refereed conferences. Examples for high-ranking journals include interdisciplinary journals that target at a broad audience (Nature, Science, Cell, PLOS, Proceedings of the National Academy of Sciences (PNAS)) as well as journals targeted specifically to bioinformatics (PLOS Computational Biology, Bioinformatics, BMC Bioinformatics) and leading journals on Genetics (Nucleic Acids Research, Genome Biology, Genome Research). The translational aspect of our research is represented by publications in clinical journals such as Gastroenterology or Cancer Research. However, restricting the attention to leading journals is not adequate for assessing the scientific output of the Center.

Many high-quality publications appear in specific scientific journals or in high-ranking refereed conferences. You can find an overview of the Center's main publications between 2010 and 2015 here.

 

Software

The Center for Bioinformatics has produced widely-used bioinformatics software:

• The geno2pheno server for viral resistance analysis is freely accessible over the Internet and is used worldwide for treating patients with HIV, Hepatitis B, and Hepatitis C.

• Software systems used by many scientists in epigenetics internationally include Rnbeads (analysis of DNA methylation data), BiQAnalyzer (quality control of DNA methylation data), and EpiExplorer (navigation through genomic and epigenomic data)

• The GeneTrail server performs gene set enrichment analysis and is used by many groups worldwide for the analysis of dysregulated biological processes and categories involved in different diseases

• The C++-software library BALL (Biochemical ALgorithms Library) is used in structural biology for modeling proteins and other macromolecules and for designing drugs and has received several software prizes

• FunSimMat, a comprehensive database of functional similarities among proteins and protein families

 

Translation

In the area of viral resistance analysis and through the work of the Lengauer research group the Center has produced internationally leading research results with high translational impact. In addition to high-ranking publications, the Center has also developed software which is directly and widely used for treating HIV patients (see here).

 

Education

Well educated and trained graduates are among the most precious outcomes of the Center for Bioinformatics. In the 15 years of its existence the Center has brought forth 181 graduates from the bachelor's (70 women) and 156 graduates from the master's (48 women)program. 143 of the bachelor graduates have continued in Saarbrücken with their master's studies. Since the master-level courses are held in English, our master's degree recepients have a highly international profile: 48 of them come from abroad.

Since the foundation of the Center, we have graduated 61 PhD students (15 women). About a third of the PhD graduates of the Center have gone into industry. The rest have continued in academia. Furthermore, the Center has conferred the qualification of professor 16 times (4 women); these educators teach and perform research at universities in Germany and abroad.

 

Impact in the region

The founding of the Center for Bioinformatics has opened new doors on the campus of Saarland University. Never before has there been a program with such an interdisciplinary character. This was also a new concept for universities nationally. In fact, the congenial collaboration between faculties as it is practiced in the Center for the benefit of the students, has gained great respect beyond the German borders and has served as a model for similar undertakings.

Furthermore, our bachelor's and master's programs were the first to be accredited at Saarland University within the Bologna process. With its research and the exemplayry role the Center plays for the university and beyond, it has made a valuable contribution to overcoming the monolithic self-image of many research subjects. This is all the more important as we are observing that the increasing complex innovations occur where the established research disciplines converge.

 

Impact nationally and internationally

Beyond the regional borders, the Center for Bioinformatics has made important contributions to the development of the national and international bioinformatics scene. Here we list the most important of these:

• Thomas Lengauer is founding member and vice president of the International Society for Computational Biology, which organizes, among other things, the largest annual bioinformatics conference in the world.

• In the year 2002, the Center, represented by Thomas Lengauer and Hans-Peter Lenhof, founded at the largest annual European bioinformatics conference series, the European Conference on Computational Biology (ECCB). The first meeting was held in Saarbrücken and attracted 450 participants. Today, the number of participants in the meetings ranges from 900 to 1200 scientists.

• Jörn Walter coordinates the German Epigenome Program (DEEP) which is funded by the German Federal Ministry of Education and Research (BMBF) and which has been formative for the development of epigenetics in Germany. • From 2006 two 2015, Prof. Lengauer was the chair of the Section on Information Sciences of the German National Academy of Sciences Leopoldina. This section also comprises bioinformatics. Currently, Prof. Lengauer is a member of the Presidential Board of Leopoldina. Furthermore, Prof. Müller is a member of Leopoldina, and Prof. Lengauer and Prof. Müller are both members of the German Academy of Science and Technology acatech.

• Since 2001, Prof. Helms, together with Prof. Grubmüller (Max Planck Institute for Biophysical Chemistry, Göttingen, runs the annual Workshop on Computer Simulation and Theory of Macromolecules with approx. 120 participants. This conference acts formatively for this research area in Germany.

Members of the Center have received reputable scientific awards, such as the Phoenix-Pharmacy Science Award (R. Müller 2010, 2014), the Konrad Zuse Medal (T. Lengauer 2003), the Karl-Heinz Beckurts Award (T. Lengauer 2003), the Prize for Innovators Under 35 of the magazine Technology Review (V. Wolf 2013), the AIDS Research Award of the Heinz-Ansmann Foundation (T. Lengauer 2010), the Dechema Award of the Max Buchner Research Foundation (R. Müller 2010), the Order of Merit of the Federal Republic of Germany (N. Graf 2011), the Grant Fertility Innovation (A. Keller 2015), and the Hector Science Award (T. Lengauer 2015). C.-M. Lehr received research awards from the German Ministry for Nutrition, Agriculture and Consumer Protection (2011) and from of the Federal State of Rhineland-Palatinate (2011). Furthermore, Christoph Bock received an ERC Starting Grant (2016).

A detailed list of awards can be found here.

In summary, the Center for Bioinformatics are has opened doors to further interdisciplinary research. Its successful activities have sent important impulses into the region and beyond. Today, graduates of the Center populate the regional, natinal and international bioinformatics scene and, thus, are making their mark on the progress ofthis area. In this fashion, the Center for Bioinformatics has strengthened the reputation of the Saarland in the global scientific community. It is our aspiration to build on these achievements, to continue to make significant contributions for the region and the international scene, and to strengthen the scientific standing of our location in this manner.