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Humboldt-Universität zu Berlin - Mathematisch-Naturwissenschaftliche Fakultät - Wissensmanagement in der Bioinformatik

Finished Projects

  • Prositu: Genotoxic stress-induced signaling pathways in tumor cells, BMBF, 2012-2015
  • EU-Med: Assessing phenotypic impact of human mutation profiles, BMWi, 2012-2015
  • Virtual Liver: Modeling human liver physiology, morphology, and function, BMBF, 2010-2015
  • Graduate School METRIK: Model-Based Development of Self-Organizing Networks for Disaster Management, DFG, 2006-2015
  • BioGraph:Querying and analyzing biological networks, internal, 2003-2015
  • CellFinder: A Cell Data Repository, DFG, 2010-2012
  • Transregio 54: Growth and Survival, Plasticity and Cellular Interactivity of Lymphatic Malignancies, DFG, 2009-2012
  • ColoNET: A Systems Biology Approach for Integrating Molecular Diagnostics, BMBF, 2009-2012
  • Ali Baba: PubMed as a graph, internal, 2002-2012
  • Aladin: Almost Hands-Off Data Integration for the Life Sciences, within BCB, 2005-2013
  • Columba: An integrated database of protein structures, sequences, and annotations, within BCB, 2002-2007
  • BCB: Berliner Centre for Genome-Based Bioinformatics, BMBF, 2002-2006
  • Interdisciplinary Network for Bioinformatic and Linguistics, Berlin, 2003-2007
  • DDD: Deutsch.Diachron.Digital, internal, 2004-2006




Prositu: Genotoxic stress-induced signalling pathways in tumor cells



Funding: BMBF

Period: 2012 - 2015

Project partner: MDC Berlin, Charite Berlin

The aim of this project is the development of a quantitative model and the identification of biomarkers for the description and detection of the activation state of genotoxic stress-induced signalling pathways in tumor cells, using a combination of mathematical modelling and targeted proteomics.

Virtual Liver: Modeling human liver physiology morphology and function


Virtual Liver NetworkHomepage

Funding: BMBF

Period: 2010 - 2015

Project partner: 70 partners all over Germany

The Virtual Liver will be a dynamic model that represents, rather than fully replicates, human liver physiology morphology and function, integrating quantitative data from all levels of organization. Our part in the project is concerned with curator support for building the Virtual Liver Knowledge Base.

Graduate School GRK 1324 METRIK: Model-Based Development of Self-Organizing Networks for Catastrophy Management


graduate school logoHomepage: METRIK

Funding: Deutsche Forschungsgemeinschaft

Period: 2006-2010, 2010 - 2015

Project partner: See this list

Recent progress in basic research has lead to visions how to use new self-organizing networks for advanced information systems. These networks function without central administration – all nodes are able to adapt themselves to new environments autonomously and independently. The addition of new nodes or failure of individual nodes does not significantly impact the network’s ability to function properly. Information systems and underlying technologies for self-organizing networks, in the context of a specific application domain, are the central topic of research for this graduate school. The research focuses on the important technologies needed at each individual node of a self-organizing network. Research challenges within this graduate school include: finding a path through a network with the help of new routing protocols and forwarding techniques, replication of decentralized data, automated deployment and update of software components at runtime as well as work-load balancing among terminal devices with limited resources. Furthermore, non-functional aspects such as reliability, latency and robustness will be studied.

BioGraph:Querying and Analyzing Biological Networks



Funding: Bundesministerium für Bildung und Forschung (BCB)

Period: 2005 -

Project partner:

Graphs are playing an increasingly important role in many areas of biology. Examples are metabolic networks, networks of gene regulation, graphs formed of protein-protein interactions and complexes, and cascades in signal transduction. The size of the graphs under study have, due to improved experimental techniques, considerably grown in size, with many networks today reaching tens of thousands of nodes. In our project, we develop algorithms and systems for efficiently handling graphs of such sizes. In particular, we study graph-based query languages, indexing, cluster-based analysis and visualization.

CellFinder: A Cell Data Repository



Funding: Deutsche Forschungsgemeinschaft

Period: 2010 - 2012

Project partner: Charité Berlin

CellFinder will develop an advanced information system for managing diverse data on stem cell lines. Our part in this project is the adaptation and development of methods for extracting relevant information from biomedical publications.

Transregio 54: Growth and Survival, Plasticity and Cellular Interactivity of Lymphatic Malignancies, project Z3


Transregio 54Homepage: TRR-54

Funding: Deutsche Forschungsgemeinschaft

Period: 2009 - 2012

Project partner: See this list

A short description of the overall goals of the Transregio can be found here (in German)

The goal of subproject Z3 is to develop and maintain a comprehensive data management and analysis platform for the Transregio. The platform will be based on a central database for storing experimental data as produced in the other subprojects. All data will undergo a standardized preprocessing stage and will be reviewed with respect to defined quality criteria. We database will also link the experimental data with information that is integrated from external data sources. It will be accessible through an intuitive web interface that also includes customizable functionality for integrated data analysis and visualization. Thus, the project will help to build up a high-quality, comprehensive data set offering an optimal basis for subsequent studies.

ColoNET: A Systems Biology Approach for Integrating Molecular Diagnostics


Funding: Bundesministerium für Bildung und Forschung

Period: 2009 - 2012

Project partner: Charite Berlin, Institute for Theoretical Biology, HUB, MDC Berlin, DKFZ Heidelberg, Universität Potsdam, Universität Saarbrücken, Universität Halle, MicroDiscovery GmbH

Our project will develop a software for ranking potential biomarkers with respect to their diagnostic power for colorectal carcinoma. The ranking will be based on information extracted from scientific articles, models of the important pathways as created by other projects within ColoNet, experimental results and data integrated from public sources. All information will be filtered through a rigorous quality control and will be weighted based on the strength of their respective evidence.Furthermore, the project will provide support for searching and analyzing the relevant literature using text mining methods.

Ali Baba: PubMed as a graph


AliBaba logoHomepage: AliBaba (Java Web Start Application)

Funding: Bundesministerium für Bildung und Forschung (BCB), Max Planck Society

Period: 2002 - 2013

Project partner:

The extraction of interactions taking place between various biological objects from text has become a major point of research for text mining during the last years. Our group focuses on the collection of interaction networks, both to provide quick overviews over specified subparts of domains, and to build complete interaction graphs that can be queried afterwards. We put our current emphasis on mining protein-protein interactions from scientific publications.

Aladin: Almost Hands-Off Data Integration for the Life Sciences


aladin logo 

Funding: Bundesministerium für Bildung und Forschung (Leser), Deutsche Forschungsgemeinschaft (Naumann)

Period: 2005 - 2013

Project partner: Felix Naumann, Hasso-Plattner Institute Potsdam

Aladin aims - as Columba - on integration of databases in the life sciences. But opposed to Columba, Aladin's challenge is to integrate the data sources automatically. The fundamental idea is to work data-centric instead of schema-centric, which is besides its known disadvantages especially unsuitable for life science databases. Another major point for Aladin is to use domain-specific knowledge for integration strategies, e.g. common properties and structures of life science databases.

BCB: Berliner Centre for Genome-Based Bioinformatics


BCB logo 

Funding: Bundesministerium für Bildung und Forschung

Period: 2002 - 2006

Project partner: Charite, Max-Planck-Institute for Molecular Genetics, Freie Universität Berlin, Technische Fachhochschule Berlin, Max-Delbrück-Zentrum, Zuse Institut Berlin

The promise of Bioinformatics is to bridge the gap between genome research and medicine. It is the goal of the Berlin Center for Genome Based Bioinformatics (BCB) to realize this vision. The cooperating groups of BCB will attack the major problems in the informational synthesis of genome data

  • genomic annotation and knowledge management,
  • prediction of structure and function of gene products,
  • cellular and disease modelling.

Scientific efforts will be closely integrated with and complemented by educational efforts specifically promoting short-term education of bioinformatics specialists through a 1.5 year curriculum at Technische Fachhochschule Berlin (TFH), and a MSc course in bioinformatics at Freie Universität Berlin (FUB) in close collaboration with Humboldt Universität zu Berlin (HUB).

Columba: An integrated database of protein structures, sequences, and annotations


columba logo 

Funding: Bundesministerium für Bildung und Forschung

Period: 2004 - 2007

Project partner: Kristian Rother, Robert Preissner (Charitè); Prof. Freytag (HUB Informatik), Thomas Steinke (ZIB), Ina Koch (TFH Berlin)

Researchers interested in the analysis of protein structures often require not only the actual structure, but also textual annotation that is spread over different datasources.

In the project Columba we integrate many resources on proteins. Columba is centered around protein structures obtained from the Protein Data Bank (PDB). We add as much annotations as possible to the structures by describing their properties. These annotation include folding classification from SCOP and CATH, secondary structures calculated with DSSP, enzyme annotation from the ENZYME database, participation in metabolic pathways from KEGG, taxonomic classification from the NCBI Taxonomy, and function characterisation from Gene Ontology.

Interdisciplinary Network for Bioinformatic and Linguistics


biolinguistics logo 

Funding: Berliner Senat

Period: 2003 - 2007

Project partner: Prof. Lüdeling, Prof. Donhauser (Institut für Deutsche Sprache, HUB)

The project studies the two areas where linguistics and bioinformatics try to solve common problems. First, evolutionary biology tries to uncover the ancestral relationships between species. Similarly, historical linguistics is interested in the relationships of languages and dialects. Both use phylogenetic methods for this analysis. Second, biological databases annotate their objects with controlled vocabularies, ontologies, and thesauri, to denote gene function and structure. In a similar fashion, corpora in linguistic research are annotated with multiple and possible structured layers of knowledge describing morphology, syntax, and semantics of words and sentences. Both rely on efficient methods for dealing with large amounts of complex and structured annotation. In the project, we exploit and further develop synergies between these independent, yet highly related branches of research.

DDD: Deutsch.Diachron.Digital


DDD logo 


Period: 2004 - 2006

Project partner: Prof. Lüdeling, Prof. Donhauser (Institut für Deutsche Sprache, HUB), plus 16 further partners throughout Germany

The project Deutsch.Diachron.Digital is a German-wide and interdisciplinary initiative for the development of a digital reference corpus of German, starting from the very first manuscripts of predecessors of the German language to current time. Within this consortium, our group is responsible for the development of the central corpus database.