BIOTEC - Biotechnology Center TU Dresden

With the advent of high-throughput technologies biomedical research produces an avalanche of data. Thousands of public databases store millions of sequences, hundred thousands of protein interactions, ten thousands of protein structures, and ten millions of scientific articles. Bioinformatics develops algorithms to interpret these masses of data to solve biomedical problems such as the identification of cancer biomarkers or key regulators for differentiating stem cells. To address such problems, the group focuses on two areas: protein interactions and functional annotation with text-mining and ontologies.

Protein interactions are fundamental to all processes in the cell. Protein interactions have been shown to be useful to predict disease genes and in particular for the identification of cancer biomarkers. In collaboration with medical groups, we reconstruct disease pathways in pancreas cancer and identify important interactions such as the inhibition of TMPRSS4. To develop such applications in disease an understanding of the structure of protein interaction networks is fundamental. The group develops novel methods, which identify modules in networks. Such modules are suitable to predict the function of uncharacterized proteins using the principle of guilt-by-association. Often these modules correspond to stable complexes of multiple interacting proteins. It is an open problem to model such large complexes at atomic resolution. Understanding how proteins interact and characterizing the interaction interfaces is an important step towards a solution of this problem. In this context, we systematically characterized protein binding-sites giving insights into the evolution of interactions. In particular, we identified interfaces, which are mimicked by viruses to interfere with native host pathways. 3D models of complexes also form the core of an ambitious visualization project: The Zoomable Cell aims to implement a Google Earth for a cell. It will integrate microscopy images, models of complexes and 3D structures of proteins in a 3D environment that supports the seamless navigation across many orders of magnitude of size.

Text-mining and ontologies. To facilitate the interpretation of genomic data, biologists develop controlled vocabularies/ontologies and annotate gene products. While manual annotation is of high quality, it cannot keep pace with the tremendous growth in sequences. Text-mining aims to automatically identify gene products and ontology terms in text. To this end, the group develops knowledge-based algorithms, which performed best at an international competition in the area. They form the basis for a novel semantic search engine, GoPubMed, which has led to the spin-off Transinsight.

For a complete list of papers click here

• Gene mention normalization and interaction extraction with context models and sentence motifs. Jörg Hakenberg, Conrad Plake, Loic Royer, Hendrik Strobelt, Ulf Leser, and Michael Schroeder. Genome Biology, 9(2):S14, 2008 [Full Text]
• Unraveling Protein Networks with Power Graph Analysis. Loic Royer, Matthias Reimann, William Andreopoulos, and Michael Schroeder. PLoS Computational Biology, 4(7):e1000108, 2008 [Full Text]
• The Many Faces of Protein-protein Interactions: A Compendium of Interface Geometry. Wan Kyu Kim, Andreas Henschel, Christof Winter, and Michael Schroeder. PLoS Computational Biology, 2:e124, 2006 [Full Text]

Prof. Michael Schroeder, michael.schroeder(at)biotec.tu-dresden.de,
Tel: 0049 351 463 400 62
Assistant: Mandy Glässer, mandy.glaesser(at)biotec.tu-dresden.de,
Tel: 0049 351 463 400 60
Address: BIOTEC, TU Dresden, Tatzberg 47-51, 01307 Dresden, Germany Map

We are always looking for excellent people. Please send your CV and why you want to join us.

GoPubMed

GoPubMed is a novel semantic search engine, which helps answering questions using ontologies. This type of semantic search is also available for web search (GoWeb), gene annotation (GoGene) and search for alternatives to animal experiments (Go3R).

SCOPPI

SCOPPI is a database of structural protein interactions.

PowerGraphs

PowerGraphs is a software to find modules in graphs.

OBOedit plugin

OBOedit plugin for ontology generation allows users to automatically generate ontology terms, definitions and parent-child relationships.

META-PPI

META-PPI is a meta server to predict protein interction interfaces.

Ligsite^csc

Ligsite^csc predicts ligand binding sites based on pocket size and conservation.

Transinsight is a spin-off founded in late 2005, which markets and develops GoPubMed and related software.

Nanometis is a spin-off to be founded in 2009. It develops software to analyse atomic force microscopy data.

• Nanometis wins 2nd prize Science4Life businessplan competition, Frankfurt, 7.2009
• Nanometis wins 1st prize FutureSax businessplan competition, Leipzig, 7.2009
• Dr. Andreas Doms wins Georg Helms prize of TU Dresden. 10.2009
• Nanometis wins Science4Life concept competition, Berlin, 3.2009
• Nomination of Dr. Andreas Henschel for PhD thesis award of German Society of Computing (GI Dissertationspreis). 2.2009
• Lohmann-Medal for diploma thesis of Steffen Jensch. 12.12.2008
• Transinsight named among top 5 biotec start ups at European Venture Summit, Düsseldorf, 2.12.2008
• Output-Award of computer science faculty of TU Dresden for GoPubMed. Dresden, 18.4.2008
• BioCreative textmining challenge 2007. Best group in gene name identification task. Madrid, 23.4.2007
• 1st prize for presentation of Transinsight at futureSax 'Durchstarten mit Riskikokapital'. Dresden, 17.10.2007
• Award "Leuchtturmprojekt des High-Tech Gründerfonds" by national ministry for economic affairs and technology for Transinsight.com. Berlin, 16.2.2006
• IBM-prize of computing faculty of TU Dresden for diploma thesis of Andreas Doms, 2005

We organised the national bioinformatics conference GCB2008

Current Group

Alex Mestiashvili, Annalisa Marsico, Anne Tuukanen, Bill Andreopolou, Christof Winter, Conrad Plake, Dimitra Alexopolou, Frank Dressel, Heiko Dietze, Janine Roy, Joachim Haupt, Joscha Köllner, Loic Royer, Mandy Glässer, Matthias Reimann, Michael Schroeder, Rainer Winnenburg, Simone Daminelli, Thomas Wächter.

You can find their contact details on the Staff page

Former Group Members

• Andreas Doms, 2004-2009, now SAP Research, Dresden
• Gihan Dawelbait, 2004-2009, now Masdar, Abu Dhabi
• Andreas Henschel, 2004-2009, now Masdar, Abu Dhabi
• Dirk Labudde, 2006-2009, now Professor, FH Mittweida
• Adrian Paschke, 2007/8, now Junior Professor, HU Berlin
• Bingding Huang, 2004-2007, now group leader Zhejiang University, China
• Jörg Hakenberg, 2006-2007, now Arizona State University, Tempe, Arizona, USA
• Wan Kim, 2004-2006, now Professor, Ewha Womans University, Seoul, Korea
• Nataraj Dongre, 2004/5, now Virginia Tech

Visitors

Marta Altrichter (2007, Uni Budapest) Sebastian Kelm (2006, Imperial College), Baghat Christ (2006, Uni Lubeck), Tobias Kuhn (2005/6, Uni Zurich), Vasco Pedro (2005/6, Uni Lisbon), Robert Henschel (2004/5, ZIH, TUD), Samatha Kottha (2004-, ZIH, TUD), Lars Feuerbach (2004/5, Uni Berlin), Sabine Werner (2004/5, Uni Halle), Edda Happ (2004, Uni Freiburg), Michael Kuehn (2004, Caltech), Kerstin Scheubert (2009, Jena) .

Master Students (local)

Alexander Rojas (2010), Natalia Macari (2010), Denica Zheleva (2010), Eva Wagner (2009), Ivan Popov (2007/8), Atif Iqbal (2007/8), Hendrik Strobelt (2007, now PhD Uni Konstanz), Steffen Jaensch (2007, now PhD at MPI-CBG), Matthias Riemann (2006, now PhD at Biotec), Andre Wobst (2006), Stephan Preibisch (2006, now PhD at MPI-CBG), Michael Held (2005, now PhD at Uni Zurich), Wenhan Wang (2005), Yanju Yhang (2005, now PhD Uni Leiden), Andreas Doms (2004, now PhD Biotec), Atanas Tsvetkov (2004), Lee Cheung (2004)

Funding by BMBF, BMWi, EU, DFG is kindly acknowledged.

• PONTE, EU, 2010-2012
• PPI-Marker, EU, 2010-2012
• GoOn, BMBF, 2009-2011
• Go3R, BMBF, 2009-2012
• CLSD Computational life science lab, BMBF, 2008-2011
• Zoomable Cell, DFG, 2008-2011
• Nanobrain, BMBF, 2008
• Sealife, EU, 2006-2009
• GoEverywhere, EFRE, 2005-2007
• FoldUnfold, EFRE, 2005-2007
• CODI, EFRE, 2004-2006
• REWERSE, EU, 2004-2008
• BioGrid, EU, 2002-2004
• GeneStream, EU, 2002-2003

You can find information about the bioinformatics classes here.