Edgar Wingender

Summary

Affiliation: Dept. of Bioinformatics, University Medical Center Goettingen
Location: Goettingen, Germany
URL: http://www.edgar-wingender.de

Publications

  1. ncbi Evaluating phylogenetic footprinting for human-rodent comparisons
    Tilman Sauer
    Department of Bioinformatics, UKG, Georg August University of Goettingen Goldschmidtstrasse 1, 37077 Goettingen, Germany
    Bioinformatics 22:430-7. 2006
  2. ncbi Systematic DNA-binding domain classification of transcription factors
    Philip Stegmaier
    BIOBASE GmbH, Halchtersche Str 33, D 38304 Wolfenbuttel, Germany
    Genome Inform 15:276-86. 2004
  3. ncbi Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database
    Claudia Choi
    BIOBASE GmbH, Halchtersche Str 33, D 38304 Wolfenbuttel, Germany
    Genome Inform 15:244-54. 2004
  4. ncbi Construction of predictive promoter models on the example of antibacterial response of human epithelial cells
    Ekaterina Shelest
    Dept of Bioinformatics, UKG, University of Gottingen, Goldschmidtstr, 1, D 37077 Gottingen, Germany
    Theor Biol Med Model 2:2. 2005
  5. ncbi Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods
    A Kel
    Institute of Cytology and Genetics SB RAN, Lavrentyev pr, 10, 630090, Novosibirsk, Russia
    Bioinformatics 20:1512-6. 2004
  6. ncbi TRANSFAC, TRANSPATH and CYTOMER as starting points for an ontology of regulatory networks
    Edgar Wingender
    Department of Bioinformatics, UKG, University of Goettingen, Goldschmidtstr 1, D 37077 Goettingen, Germany
    In Silico Biol 4:55-61. 2004
  7. ncbi Composition-sensitive analysis of the human genome for regulatory signals
    Olga V Kel-Margoulis
    BIOBASE GmbH, Halchtersche Str 33, D 38304 Wolfenbuettel, Germany
    In Silico Biol 3:145-71. 2003
  8. ncbi MATCH: A tool for searching transcription factor binding sites in DNA sequences
    A E Kel
    BIOBASE GmbH, Halchtersche Str 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 31:3576-9. 2003
  9. ncbi TRANSPATH: an integrated database on signal transduction and a tool for array analysis
    Mathias Krull
    BIOBASE Biological Databases GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 31:97-100. 2003
  10. ncbi The TRANSPATH signal transduction database: a knowledge base on signal transduction networks
    F Schacherer
    GBF German Research Centre for Biotechnology Biobase Biological Databases GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Bioinformatics 17:1053-7. 2001

Collaborators

Detail Information

Publications62

  1. ncbi Evaluating phylogenetic footprinting for human-rodent comparisons
    Tilman Sauer
    Department of Bioinformatics, UKG, Georg August University of Goettingen Goldschmidtstrasse 1, 37077 Goettingen, Germany
    Bioinformatics 22:430-7. 2006
    ..A systematic evaluation of its validity and usability based on known TFBSs is needed to use phylogenetic footprinting most effectively in the identification of unknown TFBSs...
  2. ncbi Systematic DNA-binding domain classification of transcription factors
    Philip Stegmaier
    BIOBASE GmbH, Halchtersche Str 33, D 38304 Wolfenbuttel, Germany
    Genome Inform 15:276-86. 2004
    ..The HMM library obtained can be used to classify any newly discovered transcription factor according to its DNA-binding domain and, thus, to generate hypotheses about its DNA-binding specificity...
  3. ncbi Consistent re-modeling of signaling pathways and its implementation in the TRANSPATH database
    Claudia Choi
    BIOBASE GmbH, Halchtersche Str 33, D 38304 Wolfenbuttel, Germany
    Genome Inform 15:244-54. 2004
    ..The new model makes the data better suitable for reconstructing signaling pathways and networks and mapping expression data, for instance from microarray experiments, onto regulatory networks...
  4. ncbi Construction of predictive promoter models on the example of antibacterial response of human epithelial cells
    Ekaterina Shelest
    Dept of Bioinformatics, UKG, University of Gottingen, Goldschmidtstr, 1, D 37077 Gottingen, Germany
    Theor Biol Med Model 2:2. 2005
    ..We use this example for examining the ways of triggering the response of the eukaryotic cell(s), leading us to a better understanding of the details of the inflammatory process in general...
  5. ncbi Recognition of multiple patterns in unaligned sets of sequences: comparison of kernel clustering method with other methods
    A Kel
    Institute of Cytology and Genetics SB RAN, Lavrentyev pr, 10, 630090, Novosibirsk, Russia
    Bioinformatics 20:1512-6. 2004
    ..Often one set of sites can contain several subsets of sequences that follow not just one but several different patterns. There is a need for sensitive methods to reveal multiple patterns in unaligned sets of sequences...
  6. ncbi TRANSFAC, TRANSPATH and CYTOMER as starting points for an ontology of regulatory networks
    Edgar Wingender
    Department of Bioinformatics, UKG, University of Goettingen, Goldschmidtstr 1, D 37077 Goettingen, Germany
    In Silico Biol 4:55-61. 2004
    ....
  7. ncbi Composition-sensitive analysis of the human genome for regulatory signals
    Olga V Kel-Margoulis
    BIOBASE GmbH, Halchtersche Str 33, D 38304 Wolfenbuettel, Germany
    In Silico Biol 3:145-71. 2003
    ....
  8. ncbi MATCH: A tool for searching transcription factor binding sites in DNA sequences
    A E Kel
    BIOBASE GmbH, Halchtersche Str 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 31:3576-9. 2003
    ..com/pub/programs.html#match. The same program with a different web interface can be found at http://compel.bionet.nsc.ru/Match/Match.html. An advanced version of the tool called Match Professional is available at http://www.biobase.de...
  9. ncbi TRANSPATH: an integrated database on signal transduction and a tool for array analysis
    Mathias Krull
    BIOBASE Biological Databases GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 31:97-100. 2003
    ..More information on TRANSPATH is available at http://www.biobase.de/pages/products/databases.html...
  10. ncbi The TRANSPATH signal transduction database: a knowledge base on signal transduction networks
    F Schacherer
    GBF German Research Centre for Biotechnology Biobase Biological Databases GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Bioinformatics 17:1053-7. 2001
    ..All information is validated with references to the original publications. Also, references to other databases are provided (TRANSFAC, SWISS-PROT, EMBL, PubMed and others)...
  11. ncbi Computer-assisted identification of cell cycle-related genes: new targets for E2F transcription factors
    A E Kel
    Institute of Cytology and Genetics, Novosibirsk, Russia
    J Mol Biol 309:99-120. 2001
    ..The tools described are available at http://compel.bionet.nsc.ru/FunSite/SiteScan.html...
  12. ncbi Database-assisted promoter analysis
    R Hehl
    Institut fur Genetik, Technische Universitat Braunschweig, Spielmannstr 7, D 38106, Braunschweig, Germany
    Trends Plant Sci 6:251-5. 2001
    ..The binding transcription factors and interacting factors might already be present in the database...
  13. ncbi TiProD: the Tissue-specific Promoter Database
    Xin Chen
    Centre of Bioinformatics, College of Life Sciences, National Laboratory of Protein Engineering and Plant Genetic Engineering, Peking University, Beijing 100871, China
    Nucleic Acids Res 34:D104-7. 2006
    ..We have defined a measure for tissue-specificity that allows the user to discriminate between ubiquitously and specifically expressed genes. The database is accessible at http://tiprod.cbi.pku.edu.cn:8080/index.html...
  14. ncbi TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes
    V Matys
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 34:D108-10. 2006
    ..The here described public releases, TRANSFAC 7.0 and TRANSCompel 7.0, are accessible under http://www.gene-regulation.com/pub/databases.html...
  15. ncbi EndoNet: an information resource about endocrine networks
    Anatolij Potapov
    Department of Bioinformatics, University of Gottingen Medical School, Goldschmidtstrasse 1, D 37077 Gottingen, Germany
    Nucleic Acids Res 34:D540-5. 2006
    ..These sets can be used as a starting point for a more complex query or for obtaining a quick overview. The EndoNet database is accessible at http://endonet.bioinf.med.uni-goettingen.de/...
  16. ncbi Integration of gene expression data with prior knowledge for network analysis and validation
    Michael Ante
    Department of Bioinformatics, Medical School, Georg August University Goettingen, Goldschmidtstr, 1, 37077 Goettingen, Germany
    BMC Res Notes 4:520. 2011
    ..abstract:..
  17. ncbi Advanced computational biology methods identify molecular switches for malignancy in an EGF mouse model of liver cancer
    Philip Stegmaier
    BIOBASE GmbH, Wolfenbuettel, Germany
    PLoS ONE 6:e17738. 2011
    ..Together, we propose a switch in autocrine signaling to foster tumor growth that was initially triggered by EGF and demonstrate the knowledge gain form promoter analysis combined with upstream key node identification...
  18. ncbi Comparative analysis of topological patterns in different mammalian networks
    Bjoern Goemann
    Department of Bioinformatics, University Medical Center Goettingen, Georg August University Goettingen, Goldschmidtstr 1, D 37077 Goettingen, Germany
    Genome Inform 23:32-45. 2009
    ..Interestingly, some of the most important 3-node patterns of both the transcription and the signaling network can be concatenated to subnetworks comprising many genes that play a particular role in the regulation of cell proliferation...
  19. ncbi An approach to evaluate the topological significance of motifs and other patterns in regulatory networks
    Björn Goemann
    Department of Bioinformatics, Medical School, Georg August University of Gottingen, Gottingen, Germany
    BMC Syst Biol 3:53. 2009
    ..Here, we show how a recently proposed metric, the pairwise disconnectivity index, can be adapted to survey if and which kind of topological patterns and their instances are most important for sustaining the connectivity within a network...
  20. ncbi Building a knowledge base for systems pathology
    Holger Michael
    Department of Bioinformatics, Goldschmidtstr 1, D 37077 Gottingen, Germany
    Brief Bioinform 9:518-31. 2008
    ....
  21. ncbi ExPlain: finding upstream drug targets in disease gene regulatory networks
    A Kel
    BIOBASE GmbH, Wolfenbüttel, Germany
    SAR QSAR Environ Res 19:481-94. 2008
    ..ExPlain system was applied to microarray data on inflammatory bowel diseases (IBD). The results obtained suggest a number of highly interesting biological hypotheses about molecular mechanisms of pathological genetic disregulation...
  22. ncbi The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation
    Edgar Wingender
    Department of Bioinformatics, Medical School, University of Gottingen, Goldschmidtstr 1, D 37077 Gottingen, Germany
    Brief Bioinform 9:326-32. 2008
    ..In the following, I describe what the original concepts were, what their present status is and how they may be expected to contribute to future system biology approaches...
  23. ncbi EndoNet: an information resource about regulatory networks of cell-to-cell communication
    Jürgen Dönitz
    Department of Bioinformatics, University of Gottingen Medical School, D 37077 Gottingen
    Nucleic Acids Res 36:D689-94. 2008
    ..A newly implemented hormone classification enables to browse the database and may be used as alternative entry point. EndoNet is accessible at: http://endonet.bioinf.med.uni-goettingen.de/...
  24. ncbi Integrating pathway data for systems pathology
    Edgar Wingender
    BIOBASE GmbH, Wolfenbüttel, Germany
    In Silico Biol 7:S17-25. 2007
    ..The overall aim is to come up with a platform that is suitable to provide knowledge for systems pathology, i. e. a system-wide modeling of pathological states and their development...
  25. ncbi Beyond microarrays: find key transcription factors controlling signal transduction pathways
    Alexdander Kel
    BIOBASE GmbH, Halchtersche Str, 33, D 38304 Wolfenbuttel, Germany
    BMC Bioinformatics 7:S13. 2006
    ..Therefore, such important functional changes of transcription factors are not directly visible in the microarray experiments...
  26. ncbi Composite Module Analyst: identification of transcription factor binding site combinations using genetic algorithm
    T Waleev
    A.P. Ershov's Institute of Informatics Systems 6, Lavrentiev Avenue, 630090 Novosibirsk, Russia
    Nucleic Acids Res 34:W541-5. 2006
    ..gene-regulation.com/pub/programs/cma/CMA.html. An advanced version of CMA is also a part of the commercial system ExPlaintrade mark (www.biobase.de) designed for causal analysis of gene expression data...
  27. ncbi Composite Module Analyst: a fitness-based tool for identification of transcription factor binding site combinations
    A Kel
    BIOBASE GmbH Halchtersche Str 33, D 38304 Wolfenbuttel, Germany
    Bioinformatics 22:1190-7. 2006
    ..Cis-element combinations provide a structural basis for the generation of unique patterns of gene expression...
  28. ncbi TRANSPATH: an information resource for storing and visualizing signaling pathways and their pathological aberrations
    Mathias Krull
    BIOBASE GmbH, Halchtersche Strasse 33, D 38304 Wolfenbuttel, Germany
    Nucleic Acids Res 34:D546-51. 2006
    ..TRANSPATH Public 6.0 is freely accessible for users from non-profit organizations under http://www.gene-regulation.com/pub/databases.html...
  29. ncbi The TRANSFAC system on gene expression regulation
    E Wingender
    Gesellschaft fur Biotechnologische Forschung mbH, Mascheroder Weg 1, D 38124 Braunschweig, Germany
    Nucleic Acids Res 29:281-3. 2001
    ..They are accompanied by a number of program routines for identifying potential transcription factor binding sites or for localizing individual components in the regulatory network of a cell...
  30. ncbi TRANSFAC: an integrated system for gene expression regulation
    E Wingender
    Gesellschaft fur Biotechnologische Forschung mbH, Mascheroder Weg 1, D 38124 Braunschweig, Germany
    Nucleic Acids Res 28:316-9. 2000
    ..Additionally, the databases TRANSPATH, about signal transduction, and CYTOMER, about organs and cell types, have been extended and are increasingly integrated with the TRANSFAC data sources...
  31. ncbi Organization and sequence of the gene encoding the human acrosin-trypsin inhibitor (HUSI-II)
    A Moritz
    Department of Clinical Chemistry and Clinical Biochemistry, University of Munich, Germany
    Gene 123:277-81. 1993
    ..The localization of the gene to chromosome 4 was determined by hybridization of a 5' genomic fragment to the DNA of a panel of somatic hybrids between human and rodent cells...
  32. ncbi Purification of human transcription factor IIIA and its interaction with a chemically synthesized gene encoding human 5 S rRNA
    K H Seifart
    Institut fur Molekularbiologie and Tumorforschung, Marburg Lahnberge, Federal Republic of Germany
    J Biol Chem 264:1702-9. 1989
    ..These results, together with the difference in molecular mass of these functionally analogous proteins, reemphasize the importance of homologous systems for the analysis of mechanisms involved in gene regulation...
  33. ncbi Structure of the gene encoding the rat T cell ecto-ADP-ribosyltransferase RT6
    F A Haag
    Department of Immunology, University Hospital Hamburg Eppendorf, Germany
    J Immunol 157:2022-30. 1996
    ..Analysis of RT6 transcripts showed that this promoter is the major one in adult rat spleen cells. The 3' end of the gene does not display alternative splicing. However, two polyadenylation signals are found in the 3' untranslated region...
  34. ncbi Integrated databases and computer systems for studying eukaryotic gene expression
    N A Kolchanov
    Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, prosp Lavrentieva 10, Novosibirsk 630090, Russia
    Bioinformatics 15:669-86. 1999
    ....
  35. ncbi Recognition of NFATp/AP-1 composite elements within genes induced upon the activation of immune cells
    A Kel
    Institute of Cytology and Genetics, pr Lavrentyeva 10, 630090, Novosibirsk, Russia
    J Mol Biol 288:353-76. 1999
    ..The program for recognition NFAT composite elements is available through the World Wide Web (http://compel.bionet.nsc.ru/FunSite/CompelScan. html and http://transfac.gbf.de/dbsearch/funsitep/s _comp.html)...
  36. ncbi GeneExpress: a computer system for description, analysis, and recognition of regulatory sequences in eukaryotic genome
    N A Kolchanov
    Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
    Proc Int Conf Intell Syst Mol Biol 6:95-104. 1998
    ..Integration of the databases in the GeneExpress is based on the Sequence Retrieval System (SRS) created in the European Bioinformatics Institute...
  37. ncbi TRANSFAC, TRRD and COMPEL: towards a federated database system on transcriptional regulation
    E Wingender
    Gesellschaft fur Biotechnologische Forschung mbH, Mascheroder Weg 1, D 38124 Braunschweig, Germany
    Nucleic Acids Res 25:265-8. 1997
    ..COMPEL comprises specific information on composite regulatory elements. Here, we describe the present status of these databases and the first steps towards their federation...