Recent Research News

December 2011: Research highlights in the press.
Recently, our research work has been highlighted in the international Magazine Germany (Magazin Deutschland) on Europe's Silicon Valley in Southwest Germany as well as in a press article (English and German) on systems medicine in the magazine systembiologie.de.
September 2011: Poster Award for novel disease gene prioritization approach at GCB 2011.
Tim Kacprowski and his co-authors received one of three Poster Awards at the German Conference on Bioinformatics (GCB), Munich, 2011. The poster introduced new network-based prioritization methods for candidate diesease genes as resulting from genome-wide association studies (GWAS) and RNA interference (RNAi) screens.
July 2011: Three talks at the worldwide largest bioinformatics conference ISMB/ECCB 2011.
Sven-Eric Schelhorn, Fidel Ramírez, and Nadezhda Doncheva presented our recent research results on protein complex modeling, biological database searching, and residue interaction networks, respectively, in different conference sessions. This international bioinformatics conference took place in Vienna, Austria, from 15 to 19 July 2011.
June 2011: Novel approach to assess the quality of molecular interaction data.
Our new PSISCORE technique is now published in the leading journal Nature Methods and complements the PSICQUIC protocol to exchange molecular interaction data with confidence scores. PSISCORE is a distributed scoring approach based on a decentralized client-server architecture, that is, multiple scoring servers can be used to compute the quality of individual interactions. This comprehensive scoring framework was developed by Hagen Blankenburg at the Max Planck Institute for Informatics with cooperation partners at the well-known European Bioinformatics Institute (EBI), Hinxton, United Kingdom.
May 2011: Associate Editor of the well-known journal Bioinformatics.
Dr. Mario Albrecht became Associate Editor of the scientific standard journal Bioinformatics published by Oxford University Press. He has been a member of its Editorial Board since 2010.
April 2011: New method for modeling protein complexes.
In the recent issue of the important proteomics journal Molecular & Cellular Proteomics, Sven-Eric Schelhorn introduces a new method how to determine high-confidence physical protein contacts within protein complexes. This method particularly outperforms other modeling approaches if the involved proteins have been screened multiple times in affinity purification experiments.
March 2011: New software for visualizing residue interaction networks of 3D protein structures (Press release).
The new Cytoscape plugin RINalyzer developed by Nadezhda Doncheva and her colleagues allows the simultaneous 2D visualization and interactive analysis of residue interaction networks (RINs) together with the corresponding 3D protein structures displayed in UCSF Chimera. This innovative software tool is presented in the recent issue of the journal Trends in Biochemical Sciences. It also provides a comprehensive set of topological centrality measures to gain additional insights into the structural and functional role of interacting residues.
February 2011: Comprehensive analysis of the tissue specificity of human genes and proteins.
Tissue-specific gene expression can result in the presence or absence of certain protein interactions and complexes, leading to profound functional differences of biological processes between the tissues. In our recent study published in the established Journal of Proteome Research, Dorothea Emig integrated human gene expression data based on RNA-sequencing with protein interactions, domains and complexes to analyze the functional implications of their tissue specificity.
January 2011: Discovery of new disease targets for the hepatitis C virus (Press release).
The hepatitis C virus affects more than 200 million people worldwide and is a frequent cause of liver cancer and transplants. In close collaboration with expert virologists led by Prof. Dr. Ralf Bartenschlager at the University Hospital Heidelberg, our bioinformatics network analysis by Hagen Blankenburg at the Max Planck Institute for Informatics contributed to the identification of potential human drug targets of this virus. Our joint results were published in the important journal Cell Host & Microbe.
November 2010: New gene associated with psoriasis susceptibility (Press release).
Psoriasis is a frequent inflammatory skin disease. The functional consequences of novel sequence variants found with patients were studied in silico by Dr. Gabriele Mayr and her colleagues at the Max Planck Institute for Informatics. The corresponding genome-wide association study conducted by an international consortium were published together with our important results on affected immunological pathways in the renowned journal Nature Genetics.
September 2010: HUPO Early Career Investigator Award at HUPO World Congress 2010.
Dr. Mario Albrecht received the HUPO Young Gun Award by the international Human Proteome Organization (HUPO) for outstanding early career investigators. This prize was handed over at the HUPO World Congress 2010 in Sydney, Australia.
July 2010: New software for analyzing and visualizing the functional impact of alternative splicing (Press release).
A major update of the software pipeline consisting of AltAnalyze and DomainGraph is now freely available and described in a special issue of the journal Nucleic Acids Research. This comprehensive software suite is the result of joint work by Dorothea Emig at the Max Planck Institute for Informatics with collaboration partners at the renowned Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA.
June 2010: Comprehensive study on the tissue specificity of human genes and proteins at WCSB 2010.
Dorothea Emig gave an important talk on the tissue specificity of human genes and proteins at the international Workshop on Computation Systems Biology (WCSB) in Luxembourg. The presented study compared microarray expression data with next-generation RNA-sequencing results to identify tissue-specific genes and proteins. This showed that the detection performance of RNA-sequencing is much better.
May 2010: New prioritization method for candidate disease genes presented at HUGO Meeting 2010.
Andreas Schlicker developed a novel prioritization MedSim method for candidate disease genes obtained by genome-wide association studies (GWAS) or large-scale RNA interference (RNAi) screens. This method introduced at the HUGO Meeting 2010 in Montpellier, France, is based on functional similarity measures using the Gene Ontology and network information. It is available free of charge via our web server FunSimMat. Update: In September 2010, the new disease gene prioritization method was presented in more detail at the European bioinformatics conference ECCB, Ghent, Belgium, and published in the well-known journal Bioinformatics.
April 2010: Workshop on signaling scaffolds at EMBO Meeting 2011.
Signaling enzymes and receptors are frequently organized into macromolecular complexes by scaffold proteins. Therefore, their study is of great interest from biochemical, structural, evolutionary, medical, systems and synthetic biology perspectives. The successful workshop proposal by Dr. Attila Reményi and Dr. Mario Albrecht for the EMBO Meeting 2011, Vienna, Austria, addresses these different biological perspectives. Invited speakers include Prof. Dr. Rune Linding, Prof. Dr. Walter Kolch, and Prof. Dr. Giulio Superti-Furga.
March 2010: New gene associated with ulcerative colitis (Press release).
Ulcerative colitis is an important inflammatory bowel disease. The evolutionary conservation and functional impact of new sequence variants identified by an international consortium were studied in silico by Dr. Gabriele Mayr and her colleagues at the Max Planck Institute for Informatics. The corresponding genome-wide association study together with our results were published in the renowned journal Nature Genetics.
January 2010: New computational approach for finding scaffold proteins in interactomes.
Scaffold proteins play an important functional role in many signaling pathways, mediating the assembly of signal-processing protein complexes. In a recently published letter to Trends in Cell Biology, Fidel Ramírez and Dr. Mario Albrecht showed how to automatically identify dozens of human scaffold proteins in protein interaction data. To this end, our novel, freely accessible, integrated data search engine BioMyn was used successfully.
December 2009: First SaarLorLux Workshop on Systems Biology.
This first joint workshop was a great success, gathering many leading scientists from the SaarLorLux region in Nancy, France, on 14-15 December. The common topics presented at the meeting covered computational, structural and medical approaches of systems biology.
August 2009: New integrative workflow for understanding the functional impact of alternative splicing.
A tutorial on the newly developed software pipeline of AltAnalyze and DomainGraph was presented at CSB 2009, Stanford University, CA, USA. The pipeline is primarily joint work by Dorothea Emig with Nathan Salomonis from the renowned Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA.
July 2009: Outstanding Poster Award for disease gene prioritization at ISMB/ECCB 2009.
Andreas Schlicker and his co-authors received one of three Outstanding Poster Awards selected from over 700 scientific posters presented at this worldwide largest bioinformatics conference in Stockholm, Sweden. The poster introduced the novel MedSim method for prioritizing potential disease genes as obtained from genome-wide association studies (GWAS). The method is implemented in our new web server FunSimMat for Gene Ontology-based functional similarity computation.
May 2009: New Internet-based DASMI system for molecular interaction data (Press release).
This system based on the Distributed Annotation System (DAS) and our new DASMIweb server, both of which mainly developed by Hagen Blankenburg and Fidel Ramírez, support exchanging, annotating and assessing protein interaction data. The project was performed together with members of the European BioSapiens Network of Excellence, particularly, from the Wellcome Trust Sanger Institute and the European Bioinformatics Institute, Hinxton/Cambridge, UK.
January 2009: New bioinformatics book Modern Genome Annotation: The Biosapiens Network available.
This book is the result of joint work among members of the European BioSapiens Network of Excellence.
December 2008: Travel Grant from the Boehringer Ingelheim Fonds for new research cooperations with the University of California.
Dorothea Emig received the travel grant from this Boehringer Ingelheim Foundation for Basic Research in Medicine for funding her research internship on alternative splicing and protein networks with our collaboration partners in Berkeley/San Francisco, CA, USA, from February to May 2009.
October 2008: New sequence variants associated with ulcerative colitis (Press release).
Ulcerative colitis is an important inflammatory bowel disease particularly in industrialized countries. The functional and structural consequences of the new protein sequence variants discovered by an international consortium were studied in silico by Dr. Gabriele Mayr and her colleagues at the Max Planck Institute for Informatics. The corresponding genome-wide association study together with our bioinformatics results was published in the renowned journal Nature Genetics.
September 2008: New integrative approach for predicting protein region interactions at ECCB 2008.
The novel prediction approach and the corresponding peer-reviewed conference paper published in the journal Bioinformatics was presented by Sven-Eric Schelhorn in an invited talk at this largest European bioinformatics conference in Cagliari, Italy.
July 2008: New national genome research network on chronic inflammatory barrier diseases (NGFNplus).
The bioinformatics project directed by Dr. Mario Albrecht within this NGFNplus network is the continuation of the successful analysis support provided for NGFN projects since 2004.
June 2008: New membership in the recently established MMCI Cluster of Excellence.
Dr. Mario Albrecht and his group joined this new local research cluster for developing novel computational methods for systems biology applications.

Contact: Dr. Mario Albrecht (E-mail: mario.albrecht@mpi-inf.mpg.de)