Clemens Wrzodek

Summary

Country: Germany

Publications

  1. pmc Precise generation of systems biology models from KEGG pathways
    Clemens Wrzodek
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, Tubingen, Germany
    BMC Syst Biol 7:15. 2013
  2. pmc InCroMAP: integrated analysis of cross-platform microarray and pathway data
    Clemens Wrzodek
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, 72076 Tubingen, Germany
    Bioinformatics 29:506-8. 2013
  3. doi request reprint Pathway-based visualization of cross-platform microarray datasets
    Clemens Wrzodek
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, 72076 Tubingen, Germany
    Bioinformatics 28:3021-6. 2012
  4. pmc Linking the epigenome to the genome: correlation of different features to DNA methylation of CpG islands
    Clemens Wrzodek
    Center for Bioinformatics Tubingen, ZBIT, University of Tubingen, Tubingen, Germany
    PLoS ONE 7:e35327. 2012
  5. doi request reprint ModuleMaster: a new tool to decipher transcriptional regulatory networks
    Clemens Wrzodek
    Center for Bioinformatics Tübingen ZBIT, University of Tubingen, Sand 1, 72076 Tubingen, Germany
    Biosystems 99:79-81. 2010
  6. pmc KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
    Clemens Wrzodek
    Center for Bioinformatics Tuebingen, University of Tuebingen, 72076 Tubingen, Germany
    Bioinformatics 27:2314-5. 2011
  7. pmc Qualitative translation of relations from BioPAX to SBML qual
    Finja Büchel
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, 72076 Tubingen, Germany
    Bioinformatics 28:2648-53. 2012
  8. doi request reprint Inferring statin-induced gene regulatory relationships in primary human hepatocytes
    Adrian Schröder
    Center for Bioinformatics Tuebingen, University of Tuebingen, Tuebingen, Germany
    Bioinformatics 27:2473-7. 2011
  9. pmc JSBML: a flexible Java library for working with SBML
    Andreas Dräger
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, Tubingen, Germany
    Bioinformatics 27:2167-8. 2011
  10. pmc TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors
    Johannes Eichner
    Center of Bioinformatics Tuebingen ZBIT, University of Tuebingen, Tubingen, Germany
    PLoS ONE 8:e82238. 2013

Collaborators

Detail Information

Publications14

  1. pmc Precise generation of systems biology models from KEGG pathways
    Clemens Wrzodek
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, Tubingen, Germany
    BMC Syst Biol 7:15. 2013
    ..Thus, a direct conversion into systems biology models would produce incomplete and erroneous models...
  2. pmc InCroMAP: integrated analysis of cross-platform microarray and pathway data
    Clemens Wrzodek
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, 72076 Tubingen, Germany
    Bioinformatics 29:506-8. 2013
    ....
  3. doi request reprint Pathway-based visualization of cross-platform microarray datasets
    Clemens Wrzodek
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, 72076 Tubingen, Germany
    Bioinformatics 28:3021-6. 2012
    ..Above all, there is a demand for methods that can visualize genomic features that are not directly linked to protein-coding genes, such as regulatory RNAs (e.g. miRNAs) and epigenetic alterations (e.g. DNAm), in a pathway-centred manner...
  4. pmc Linking the epigenome to the genome: correlation of different features to DNA methylation of CpG islands
    Clemens Wrzodek
    Center for Bioinformatics Tubingen, ZBIT, University of Tubingen, Tubingen, Germany
    PLoS ONE 7:e35327. 2012
    ..The developed software, as well as the predicted datasets and a web-service to compare methylation states of CpG islands are available at http://www.cogsys.cs.uni-tuebingen.de/software/dna-methylation/...
  5. doi request reprint ModuleMaster: a new tool to decipher transcriptional regulatory networks
    Clemens Wrzodek
    Center for Bioinformatics Tübingen ZBIT, University of Tubingen, Sand 1, 72076 Tubingen, Germany
    Biosystems 99:79-81. 2010
    ..Availability: ModuleMaster is freely available to academics as a webstart application and for download at http://www.ra.cs.uni-tuebingen.de/software/ModuleMaster/, including comprehensive documentation...
  6. pmc KEGGtranslator: visualizing and converting the KEGG PATHWAY database to various formats
    Clemens Wrzodek
    Center for Bioinformatics Tuebingen, University of Tuebingen, 72076 Tubingen, Germany
    Bioinformatics 27:2314-5. 2011
    ..g. MIRIAM annotations) beyond the scope of the KGML document, and amends missing components to fragmentary reactions within the pathway to allow simulations on those...
  7. pmc Qualitative translation of relations from BioPAX to SBML qual
    Finja Büchel
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, 72076 Tubingen, Germany
    Bioinformatics 28:2648-53. 2012
    ..Before the development of SBML qual, relations could not be properly translated into SBML. Until now, there exists no BioPAX to SBML converter that is fully capable of translating both reactions and relations...
  8. doi request reprint Inferring statin-induced gene regulatory relationships in primary human hepatocytes
    Adrian Schröder
    Center for Bioinformatics Tuebingen, University of Tuebingen, Tuebingen, Germany
    Bioinformatics 27:2473-7. 2011
    ..However, statins elicit pleitropic responses including beneficial as well as adverse effects in the liver or other organs. Today, the regulatory mechanisms that cause these pleiotropic effects are not sufficiently understood...
  9. pmc JSBML: a flexible Java library for working with SBML
    Andreas Dräger
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, Tubingen, Germany
    Bioinformatics 27:2167-8. 2011
    ..JSBML also supports modules that can facilitate the development of plugins for end user applications, as well as ease migration from a libSBML-based backend...
  10. pmc TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors
    Johannes Eichner
    Center of Bioinformatics Tuebingen ZBIT, University of Tuebingen, Tubingen, Germany
    PLoS ONE 8:e82238. 2013
    ..The online and stand-alone versions of TFpredict and SABINE are freely available to academics at http://www.cogsys.cs.uni-tuebingen.de/software/TFpredict/ and http://www.cogsys.cs.uni-tuebingen.de/software/SABINE/. ..
  11. pmc A toxicogenomic approach for the prediction of murine hepatocarcinogenesis using ensemble feature selection
    Johannes Eichner
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, Tubingen, Germany
    PLoS ONE 8:e73938. 2013
    ..Based on the extracted mouse liver gene expression patterns, CPA would be predicted as a nongenotoxic compound. In contrast, both WY and TAA would be classified as genotoxic mouse hepatocarcinogens. ..
  12. pmc Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein
    Finja Büchel
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, 72076 Tubingen, Germany
    BMC Neurosci 14:136. 2013
    ..Therefore, mathematical or probabilistic models for the human disease are to be constructed in silico in order to predict specific processes within a cell, such as the dopamine metabolism and transport processes in a neuron...
  13. pmc Integrative pathway-based approach for genome-wide association studies: identification of new pathways for rheumatoid arthritis and type 1 diabetes
    Finja Büchel
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, Tubingen, Germany
    PLoS ONE 8:e78577. 2013
    ..These results provide new leads to understand the molecular underpinnings of these diseases. The developed software herein used is available at http://www.cogsys.cs.uni-tuebingen.de/software/GWASPathwayIdentifier/index.htm...
  14. ncbi request reprint Evaluation of toxicogenomics approaches for assessing the risk of nongenotoxic carcinogenicity in rat liver
    Johannes Eichner
    Center for Bioinformatics Tuebingen ZBIT, University of Tuebingen, Tubingen, Germany
    PLoS ONE 9:e97678. 2014
    ..Among the genes most frequently incorporated into prediction models were Phlda3, Cdkn1a, Akr7a3, Ccng1 and Abcb4. ..