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 other research in computational biology, please see compbio-dresden.de

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. 

DOG4DAG

DOG4DAG is an ontology generation plugin for Protégé and OBO-Edit that 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. 

Memotif

 Memotif MeMotif is a database of linear motifs in alpha-helical membrane proteins 

 

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

• Transinsight wins German Innovation Prize at Cebit (43 winners out of 2000 submissions) , 3/2011
• Nomination of Dr. Loic Royer for PhD thesis award of German Society of Computing (GI Dissertationspreis). 2.2011
• Christof Winter wins Klaus Tschira prize, Dresden, 10.2010
• GoPubMed wins Deutschen Industriepreis 2010 in category research and development, Hannover. 19.4.2010
• Dr. Andreas Doms wins Georg Helms prize of TU Dresden. 10.2009
• Nanometis wins 2nd prize Science4Life businessplan competition, Frankfurt, 7.2009
• Nanometis wins 1st prize FutureSax businessplan competition, Leipzig, 7.2009 
• 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
• 1st prize for presentation of Transinsight at futureSax 'Durchstarten mit Riskikokapital'. Dresden, 17.10.2007 
• BioCreative textmining challenge 2007. Best group in gene name identification task. Madrid, 23.4.2007 
•  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

Current Group

Oberwiesentahl Group retreat 2011

 Alex Mestiashvili, Daniel Eisinger, George Tsatsaronis, Janine Roy, Jan Mönnich, Joachim Haupt, Mandy Glässer, Maria Kissa, Matthias Reimann, Michael Schroeder, Simone Daminelli, Sainitin Donakonda, Thomas Wächter, Zerrin Isik.

You can find their contact details on the Staff page

Former Group Members

 
• Joscha Köllner, 2009-2011, now T-Systems/TU Dresden 
• Conrad Plake , 2008-20011, now ID Information und Dokumentation im Gesundheitsewsen, Berlin
• Rainer Winnenburg, 2007-2011, now NLM, Washington, USA
• Anne Tuukkanen, 2006-2011, now EMBL, Hamburg
• Dimitra Alexopoulou, 2006-2011, now Biotec, TU Dresden
• Loic Royer, 2005-2011, now Janelia Farms, Washington, USA
• Frank Dressel, 2005-2011, now Plastic Logic, Dresden
• Christof Winter, 2004-2010, now Postdoc in Lund, Sweden
• Heiko Dietze, 2005-2010, now UC Berkeley, USA 
• Annalisa Marsico, 2006-2010, now Vingron group, MPI for molecular genetics, Berlin
• Bill Andreopoulos, 2006-2010, now Columbia University, New York, USA
• Andreas Doms, 2004-2009, now SAP Research, Dresden 
•  Gihan Dawelbait, 2004-2009, now Masdar, Abu Dhabi and MIT, Boston, USA
•  Andreas Henschel, 2004-2009, now Masdar, Abu Dhabi and MIT, Boston, USA  
•  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 Hoffmann-La Roche's Disease Translational Informatics, NJ, USA 
•  Wan Kim, 2004-2006, now Professor, Ewha Womans University, Seoul, Korea 
•  Nataraj Dongre, 2004/5, now Virginia Tech 

Visitors

Kerstin Scheubert (2009, Jena), 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).
 

Master Students (local)

Xiaofeng Yu (2011), Götz Fabian (2011), 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) 

 
We organised the national bioinformatics conference GCB2008

 
 2006 - group retreat in saxonia-switzerland 

 
 2007 - summer excursion 
 

 
 2008 - group retreat in Eibenstock 

 
 2011 - Bowling

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

• GeneCloud, BMWi, 2011-2014
• PONTE, EU, 2010-2013 
• 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

We take part in the international Bachelor and Master Courses hold at the TU Dresden and BIOTEC. 
Information about the Bioinformatic classes can be found here.

 Conrad Plake, Gene annotation by automated literature analysis with an application to drug-target interaction prediction. 2010 

Loic Royer. Unravelling the structure and assessing the quality of protein networks with power graphs. Summa cum laude. 2010 

Thomas Wächter. Semi-automated ontology generation for biocuration and semantic search. Summa cum laude. 2010 

Heiko Dietze. GoWeb: Semantic search and browsing for the life sciences. 2010 

Dimitra Alexopoulou. Word-sense disambiguation in biomedical ontologies. 2010 

Annalisa Marsico. Discovery and characterization of new structure and function motifs in alpha-helical transmembrane proteins with an application to interpret Single Molecule Force Spectroscopy data. Summa cum laude. 2009 

Christof Winter. Protein interactions in disease: Using structural protein interaction and regulatory networks to predict disease-related mechanisms. Summa cum laude. 2009 

Gihan Dawelbait. From cancer gene expression to protein interaction: Interaction prediction, network reasoning and applications in pancreatic cancer. 2009 

Andreas Doms. GoPubMed:ontology-based literature search for life sciences. Summa cum laude. 2008

 Andreas Henschel. A structural classification of protein-protein interactions for deteection Protein interactions. Summa cum laude. 2008

Frank Dressel. Sequenz, Energie, Struktur - Untersuchungen zur Beziehung zwischen Primär- und  Tertiärstruktur in globulären und Membran-Proteinen. 2008 

Bingding Huang. Improving protein docking with binding site prediction. 2008