New databases and bioinformatic tools provide the field of glycomics with a solid basis for dynamic development in molecular biology and medicine. Willi von der Lieth a researcher from Heidelberg was an important pioneer of glyco-bioinformatics. His sudden death is a great loss for this new scientific field.
Gene therapy approaches are increasingly being used for treating life-threatening diseases in humans. GeneWerk GmbH, a spin-off of the DKFZ and the NCT in Heidelberg, offers customised, high-resolution molecular and bioinformatic analyses that ensure the efficacy and safety of gene therapy and immunotherapy studies.
The combination of a newly developed bioinformatic model and experimental data provides new insights into the causes of Alzheimers disease. Researchers found that whilst the activity of a particular enzyme is reduced specific nerve cells are able to counteract this deficiency by rerouting the metabolic fluxes.
Bioinformatics methods are important tools for the classification of protein sequences. Prof. Dr. Tancred Frickey, Professor of Applied Bioinformatics at the University of Konstanz, has developed a programme that enabled him to classify the AAA ATPase protein family. CLANS software can also be used to visualise the similarities between film actors who have played roles in the same genre category.
Scientists of the Division of Theoretical Bioinformatics at the German Cancer Research Center DKFZ in Heidelberg have simulated on the computer how cells decide whether or not to migrate. The method forges new paths in cancer medicine.
Karlsruhe based quantiom bioinformatics has developed a software tool that enables the comparative analysis of chromosomes and that enables statements to be made on the correlation of genomic alterations and disease development.
In the next winter semester Freiburg University will offer a new masters course in Bioinformatics and Systems Biology. The objective of the two-year course is to train experts at the interface of the computer sciences and life sciences.
Baden-Württemberg is currently home to 151 biotech companies. In addition to dedicated biotechnology companies, this also includes bioinformatics, diagnostics and analytics companies that use modern biotechnology methods or focus on biotechnological production.
The new RNA Bioinformatics Center (RBC) is a joint project of the Universities of Freiburg and Leipzig as well as the Max-Delbrück Center Berlin. It is one of six performance centers selected for funding by the Federal Ministry of Education and Research (BMBF) and will receive 3.3 million euros in the next five years. It is part of the project “German Network for Bioinformatics Infrastructure,” which was launched on 1 March 2015.
The German Network for Bioinformatics Infrastructure, de.NBI for short, is a successful model for infrastructures in the life sciences and biomedicine that is currently being expanded. The network, which was established in 2015, will benefit from more hardware, more staff, more projects and its own cloud. It has also joined the European ELIXIR network.
Thanks to the latest generation of sequencing technology, the deciphering of the complete genome of organisms is becoming faster and cheaper. The challenge is to compile the book of life from millions of DNA fragments and unlock the secrets of the human and other organisms. The young bioinformatics company Computomics in Tübingen is doing just this for crops. In contrast to the human genome, the genome of the majority of plants is still a book with seven seals.
Bacteria have developed a versatile defence system to protect themselves against viral infections. One of these defence tools, known as CRISPR/Cas9 system, is currently hogging the headlines as it promises to revolutionise the way genetic material can be modified. Prof. Rolf Backofen from the Institute of Bioinformatics at the University of Freiburg has managed to classify the defence system of all bacterial species sequenced to date. This will certainly facilitate the search for a new generation of powerful genetic engineering tools.
Not that long ago it took six months or more to sequence a single gene. Nowadays modern genomics means that it takes less than a week to sequence an entire microorganism. This development means that scientists are more interested than ever in looking into biological systems as a whole. Professor Dr. Anke Becker from the University of Freiburg is investigating how groups of genes and molecules interact with each other. She is particularly interested in the signalling interactions between symbiotic bacteria and their host plants. Besides being a biologist she has also knowledge of the fields of bioinformatics and robotics indispensable for researchers investigating biological systems.
Prof. Dr. Jan G. Korvink, Director of the Laboratory for Simulation in the Department of Microsystems Engineering (IMTEK) and Director of the FRIAS School of Soft Matter Research at the University of Freiburg has been awarded an ERC (European Research Council) Advanced Grant for basic research. Together with the research group headed by Prof. Dr. Ralf Baumeister, professor of bioinformatics and molecular genetics at the Institute of Biology III and fellow of the FRIAS School of Life Sciences – LifeNet, Korvink will use the five-year funding to develop a microsystems platform which will open up entirely new possibilities for systems biology research.
Metabolism stress response and gene expression are all controlled by regulatory networks in living systems. Well-known regulators are proteins which function as enzymes chaperones or transcription factors to regulate numerous processes. Less well-known are RNA-molecules which also regulate a multitude of processes small RNAs or sRNAs. Dr. Jens Georg from the Department of Genetics and Experimental Bioinformatics at the University of Freiburg has made it his goal to identify these sRNAs and their interactions and physiological functions in bacteria. In order to do so along with colleague he has developed a new computer-assisted tool the online software CopraRNA which can be used to make extensive predictions about the small RNAs.
“Omics” is a current buzz word used to describe comprehensive investigations in many areas of the life sciences. In practice, omics refers to fields of scientific study that involve a huge number of experiments and even more data. Evaluating and managing all the data within a fixed period is a huge challenge for most researchers working on their own. It was to address these issues that the Quantitative Biology Center – QBiC for short – was established at the University of Tübingen in 2012. To date, the QBiC is the only bioinformatics core facility in Germany. It offers scientists from different disciplines support in carrying out all types of high-throughput analyses. The centre is also the only one that provides professional support from initial planning of experiments to final analysis.
Dr. Carsten Daub a German bioinformatician who first studied chemistry at the TU Berlin did his doctoral degree in 2004 at the MPI of Molecular Plant Physiology in Potsdam Germany and after a two years post-doctoral training at the Karolinska Institutets Center or Genomics and Bioinformation in Stockholm Sweden joined the Genome Sciences Center at RIKEN in April 2006 on a five years contract.
In recent years, the University of Tübingen has developed a tightly integrated service structure for the computer-based management of life sciences data. This structure is the point of contact for all those that produce or work with “omics” data – in Tübingen and beyond.
Heidelberg bioinformaticians have developed a novel method for the automated prediction of regulatory interactions. The regulatory interaction predictor, a machine-learning based approach for predicting interactions between DNA-binding transcription factors and their target genes and obtaining important insights into the gene regulatory networks in complex cells.
There is a well-known saying: travel broadens the mind. This is not the only consequence of travel – the biochemist Dr. Dirk Linke from Tübingen travelled to India on holiday and brought back an idea for a new scientific project. Since his return, his idea, the possibility of developing a vaccine with a wide-ranging effect against some of the most frequent diarrhoea pathogens, has even generated financial backing from prominent supporters.
Targeted substance design using an advanced platform technology that takes into account the natural dynamics of pharmaceutical substances and targets early on during the discovery process – this is what the Ulm-based biopharmaceutical company Acrovis biostructures GmbH offers. Acrovis has all the instruments needed to be able to optimally determine the structure of pharmaceutical substances.
Since January 2015, Tübingen has been home to a Centre for Personalised Medicine (ZPM). Twenty-three institutes and hospitals have joined forces to improve diagnosis of disease and develop individualised treatments for patients with a variety of diseases. In parallel, the centre also develops new diagnostic strategies. This means, for example, that data derived from the analysis of the entire genetic material of cells, proteins and metabolic processes are taken into account when stratifying patient therapy.
Since 2012, a DFG-funded research group called FOR1680 has been studying CRISPR-Cas, an immune system that unicellular bacteria and arachaea use to protect themselves against attacks from viruses and plasmids. Prof. Dr. Anita Marchfelder, a molecular biologist at Ulm University and coordinator of the FOR1680 research group, and many other researchers were surprised to find that prokaryotes incorporate the genetic material of enemies as a kind of self-vaccination and even pass this protection on to their progeny.
Seven European research institutions and GATC Biotech have formed a consortium providing cutting-edge training in the scientific study of the human past. The BEAN (Bridging the European and Anatolian Neolithic) Initial Training Network has been awarded four years of funding from the European Commission through the Marie Curie Actions program. It is a new multinational and multidisciplinary Marie Curie Research initiative exploring the origins of European agriculture.