Michael Schroeder - Bioinformatics
- 1997 PhD University of Hanover and Lisbon
- 1998-2003 Lecturer and Senior Lecturer at Dept. of Computing, City University, London, UK
- since 2003 Professor in Bioinformatics, BIOTEC and Dept. of Computing, TU Dresden
- 2006 - 2015 CSO Transinsight.com
- 2012 - 2014 Director, Biotechnology Center, TU Dresden
Research
Drug repositioning applies known drugs to new indications. The most prominent example is Viagra, originally tested against heart disease. Less known, but equally striking, is the antiviral herpes treatment BVDU, which has a positive effect in cancer. In the past, we established that BVDU exerts its anti-cancer effect by inhibiting the chaperone heat shock protein 27, which is over expressed in many cancers and involved in apoptosis. HSP27 is an attractive anti-cancer target, as its inhibition suppresses resistance development against chemotherapy.
To identify novel HSP27 inhibitors, we developed screening algorithms, which identify remotely similar binding sites across evolutionary unrelated target proteins. We screen the entire known structural proteome and predicted and experimentally validated novel HSP27 inhibitors. We are currently testing the compounds in vivo.
Generally, the avalanche of publicly available data on compounds, genes, proteins, and diseases and their relationships creates a tremendous need for computational approaches to organize and analyze this data. In my group we are specifically focusing on developing algorithms and analysis pipelines using protein structures and sequencing data. We currently focus on cancer as application, where we have a wealth of experimental data from collaborations with medical groups.
Publications
For a complete list of papers click here
- New HSP27 inhibitors efficiently down-regulate resistance development in cancer cells
Heinrich, J.-C., Donakonda, S., Haupt, V. J., Lennig, P., Zhang, Y. and Schroeder, M.
OncoTarget, 7, 68156-68169, 2016
- Systematic drug perturbations on cancer cells reveal diverse exit paths from proliferative state
Zhou, J. X., Isik, Z., Xiao, C., Rubin, I., Kauffman, S. A., Schroeder, M. and Huang, S.
OncoTarget, 7, 2016
- Drug target prioritization by perturbed gene expression and network information
Isik, Z., Baldow, C., Cannistraci, C. V. and Schroeder, M.
Scientific Reports, 5, 2015
- PLIP: fully automated protein-ligand interaction profiler
Salentin, S., Schreiber, S., Haupt, V. J., Adasme, M. F. and Schroeder, M.
Nucleic Acids Research, 43, 2015
- An overview of the BIOASQ large-scale biomedical semantic indexing and question answering competition
Tsatsaronis, G., et al.
BMC Bioinformatics, 16, 2015
Software
PLIP
The Protein-Ligand Interaction Profiler (PLIP) is a web service and command line tool for fully automated characterization of non-covalent interactions between proteins and ligands in 3D structures.
GoPubMed
GoPubMed is a novel semantic search engine, which helps answering questions using ontologies.
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 for ontology terms, definitions and parent-child relationships.
metaPocket 2.0
MetaPocket 2.0 is a meta server to identify ligand binding sites on protein surface.
Ligsitecsc
Ligsitecsc predicts ligand binding sites based on pocket size and conservation.
Memotif
Memotif MeMotif is a database of linear motifs in alpha-helical membrane proteins.
META-PPI
META-PPI is a meta server to predict protein interction interfaces.
Spin-off
Transinsight is a spin-off founded in late 2005, which markets and develops GoPubMed and related software.
Awards
- 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
- Transinsight wins Red Dot Design Award, Wuppertal, Germany, 8.2009
- 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
People
Current Group
Alex Mestiashvili, Jörg Heinrich, Mandy Glässer, Melissa Adasme, Michael Schroeder, Norhan Mahfouz, Sebastian Salentin.
You can find their contact details on the Staff page
Former PhDs and PostDocs
- Janine Roy, 2010-2016, now Staburo, Munich
- Joachim Haupt, 2010-2016, now T-Systems, Dresden
- Simone Daminelli, 2010-2016, now at Fios Genomics, Edinburgh
- George Tsatsaronis, 2010-2015, now Elsevier, Amsterdam
- Daniel Eisinger, 2010-2015, now Zencap, Berlin
- Maria Kissa, 2011-2015, now PopSugar, San Francisco, USA
- Eleni Christodoulou, 2011-2015, now National Cancer Center, Singapore
- Zerrin Isik, 2011-2014, now assistant professor at Dokuz Eylül Üniversitesi, Izmir, Turkey
- Thomas Wächter, 2005-2012, now T-Systems, Dresden
- Joscha Köllner, 2009-2011, now KiwiGrid, Dresden
- Conrad Plake , 2008-20011, now ID Information und Dokumentation im Gesundheitsewsen, Berlin
- Rainer Winnenburg, 2007-2011, now PostDoc, Stanford, USA
- Anne Tuukkanen, 2006-2011, now EMBL, Hamburg
- Dimitra Alexopoulou, 2006-2011, now Biotec, TU Dresden
- Loic Royer, 2005-2011, now PostDoc, MPI-CBG, Dresden
- Frank Dressel, 2005-2011, now Plastic Logic, Dresden
- Christof Winter, 2004-2010, now Groupleader, Munich
- Heiko Dietze, 2005-2010, now Lawrence Berkeley National Laboratory, Berkeley, USA
- Annalisa Marsico, 2006-2010, now Professor, FU Berlin and MPI Molecular Genetics, Berlin
- Bill Andreopoulos, 2006-2010, now Lawrence Berkeley National Laboratory, Berkeley, USA
- Andreas Doms, 2004-2009, now SAP Research, Dresden
- Gihan Dawelbait, 2004-2009, now Masdar, Abu Dhabi
- Andreas Henschel, 2004-2009, now Professor, Masdar, Abu Dhabi
- Dirk Labudde, 2006-2009, now Professor, FH Mittweida
- Adrian Paschke, 2007/8, now Professor, FU Berlin
- Bingding Huang, 2004-2007, now Bioinformatics scientist at Computational Oncology Group, German Cancer Research Center, Heidelberg
- Jörg Hakenberg, 2006-2007, now Senior Bioinformatics Scientist, now Illumina, Santa Clara, California, USA
- Wan Kim, 2004-2006, now Professor, Ewha Womans University, Seoul, Korea
- Nataraj Dongre, 2004/5, now Virginia Tech
Oberwiesentahl Group retreat 2011
We organized the national bioinformatics conference GCB2008
2006 - group retreat in saxonia-switzerland
2007 - summer excursion
2008 - group retreat in Eibenstock
2011 - Bowling
2013 - Group retreat in Czech Republic
Projects
Funding by BMBF, BMWi, EU, DFG is kindly acknowledged.
- Redivia, BMWi, 2017-2019
- Fortissimo, EU, 2014-2016
- SigSax, Saxony, 2015-2016
- OpenScienceLink, EU, 2013-2016
- Hybris, DFG, 2012-2015
- 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
Teaching
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.
Completed PhD theses
24. Sebastian Salentin. In Silico Identification of Novel Cancer Drugs with 3D Interaction Profiling. Summa cum laude. 2017
23. Norhan Mahfouz. Quantifying the antibiotic resistance potential of wastewater E. coli. 2017
22. Sainitin Donakonda. Prediction and validation of novel compounds binding the cancer target HSPB1. 2015
21. Maria Kissa. Cassandra: drug gene association prediction via text mining and ontologies. 2015
20. Eleni Christodoulou. Detection of KRAS Synthetic Lethal Partners through Integration of existing RNAi Screens. 2015
19. Simone Daminelli. Drug repositioning with incomplete bi-cliques and structural bioinformatics. 2014
18. Joachim Haupt. Protein binding site similarity as driver for drug repositioning. 2014
17. Janine Roy. From correlation to causality: Outcome prediction in cancer. Summa cum laude. 2014
16. Daniel Eisinger. Automated Patent Categorisation and Guided Patent Search using IPC as inspired by MeSH and PubMed. 2013
15. Rainer Winnenburg. Mutations and their role in protein interactions and diseases: Computational methods for automated retrieval, analysis, and application. 2011
14. Conrad Plake. Gene annotation by automated literature analysis with an application to drug-target interaction prediction. 2010
13. Loic Royer. Unravelling the structure and assessing the quality of protein networks with power graphs. Summa cum laude. 2010
12. Thomas Wächter. Semi-automated ontology generation for biocuration and semantic search. Summa cum laude. 2010
11. Heiko Dietze. GoWeb: Semantic search and browsing for the life sciences. 2010
10. Dimitra Alexopoulou. Word-sense disambiguation in biomedical ontologies. 2010
9. 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
8. Christof Winter. Protein interactions in disease: Using structural protein interaction and regulatory networks to predict disease-related mechanisms. Summa cum laude. 2009
7. Gihan Dawelbait. From cancer gene expression to protein interaction: Interaction prediction, network reasoning and applications in pancreatic cancer. 2009
6. Andreas Doms. GoPubMed:ontology-based literature search for life sciences. Summa cum laude. 2008
5. Andreas Henschel. A structural classification of protein-protein interactions for deteection Protein interactions. Summa cum laude. 2008
4. Frank Dressel. Sequenz, Energie, Struktur - Untersuchungen zur Beziehung zwischen Primär- und Tertiärstruktur in globulären und Membran-Proteinen. 2008
3. Bingding Huang. Improving protein docking with binding site prediction. 2008
2. Penny Noy. Enhancing comprehension of Complex Data Visualizations: Framework and Techniques Based on Signature Exploration. 2004.
1. Jacek Gomoluch. Market Protocols for Resource Allocation in Computational Clusters and Grids. 2003
