Clemens Kreutz

Summary

Affiliation: University of Freiburg
Country: Germany

Publications

  1. doi request reprint Profile likelihood in systems biology
    Clemens Kreutz
    Physics Department, University of Freiburg, 79104 Freiburg, Germany
    FEBS J 280:2564-71. 2013
  2. pmc Likelihood based observability analysis and confidence intervals for predictions of dynamic models
    Clemens Kreutz
    Physics Department, University of Freiburg, Hermann Herder Straße 3, 79104 Freiburg, Germany
    BMC Syst Biol 6:120. 2012
  3. doi request reprint TSSi--an R package for transcription start site identification from 5' mRNA tag data
    C Kreutz
    Institute for Physics, University of Freiburg, Germany
    Bioinformatics 28:1641-2. 2012
  4. doi request reprint Systems biology: experimental design
    Clemens Kreutz
    Physics Department, University of Freiburg, Germany
    FEBS J 276:923-42. 2009
  5. ncbi request reprint An error model for protein quantification
    C Kreutz
    Freiburg Center for Data Analysis and Modeling FDM, Eckerstrasse 1, Freiburg, Germany
    Bioinformatics 23:2747-53. 2007
  6. ncbi request reprint Gene profiling of polycystic kidneys
    Gisela Schieren
    Renal Division, Department of Internal Medicine, Ruhr University Hospital Bochum at Marienhospital Herne, Freiburg, Germany
    Nephrol Dial Transplant 21:1816-24. 2006
  7. doi request reprint Combination of immunosuppressive drugs leaves specific "fingerprint" on gene expression in vitro
    Brigitta Rumberger
    Renal Division, Department of Internal Medicine, University Hospital, Freiburg, Germany
    Immunopharmacol Immunotoxicol 31:283-92. 2009
  8. ncbi request reprint cDNA microarray analysis of adaptive changes after renal ablation in a sclerosis-resistant mouse strain
    Brigitta Rumberger
    Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg, Germany
    Kidney Blood Press Res 30:377-87. 2007
  9. ncbi request reprint Dynamic pathway modeling: feasibility analysis and optimal experimental design
    Thomas Maiwald
    Freiburg Center for Data Analysis and Modeling, Freiburg University, Eckerstrasse 1, 79104 Freiburg, Germany
    Ann N Y Acad Sci 1115:212-20. 2007
  10. pmc Experimental design for parameter estimation of gene regulatory networks
    Bernhard Steiert
    Institute for Physics, University of Freiburg, Freiburg, Germany
    PLoS ONE 7:e40052. 2012

Collaborators

Detail Information

Publications23

  1. doi request reprint Profile likelihood in systems biology
    Clemens Kreutz
    Physics Department, University of Freiburg, 79104 Freiburg, Germany
    FEBS J 280:2564-71. 2013
    ..In this article, the profile likelihood concept is reviewed and the potential of the approach is demonstrated for a model of the erythropoietin (EPO) receptor...
  2. pmc Likelihood based observability analysis and confidence intervals for predictions of dynamic models
    Clemens Kreutz
    Physics Department, University of Freiburg, Hermann Herder Straße 3, 79104 Freiburg, Germany
    BMC Syst Biol 6:120. 2012
    ..For dynamic models of biochemical networks, the nonlinearity in combination with the large number of parameters hampers the calculation of prediction confidence intervals and renders classical approaches as hardly feasible...
  3. doi request reprint TSSi--an R package for transcription start site identification from 5' mRNA tag data
    C Kreutz
    Institute for Physics, University of Freiburg, Germany
    Bioinformatics 28:1641-2. 2012
    ..The framework also comprises a regularization procedure which can be applied as a preprocessing step to decrease the noise and thereby reduce the number of false predictions...
  4. doi request reprint Systems biology: experimental design
    Clemens Kreutz
    Physics Department, University of Freiburg, Germany
    FEBS J 276:923-42. 2009
    ..Furthermore, the relevant classical aspects of experimental design, such as randomization, replication and confounding, are reviewed...
  5. ncbi request reprint An error model for protein quantification
    C Kreutz
    Freiburg Center for Data Analysis and Modeling FDM, Eckerstrasse 1, Freiburg, Germany
    Bioinformatics 23:2747-53. 2007
    ..Here, we present statistical approaches improving reproducibility of protein quantification by immunoprecipitation and immunoblotting...
  6. ncbi request reprint Gene profiling of polycystic kidneys
    Gisela Schieren
    Renal Division, Department of Internal Medicine, Ruhr University Hospital Bochum at Marienhospital Herne, Freiburg, Germany
    Nephrol Dial Transplant 21:1816-24. 2006
    ..Fluid secretion with cyst expansion and reactive changes in the extracellular matrix composition combined with increased apoptosis and proliferation rates have been implicated in cystogenesis...
  7. doi request reprint Combination of immunosuppressive drugs leaves specific "fingerprint" on gene expression in vitro
    Brigitta Rumberger
    Renal Division, Department of Internal Medicine, University Hospital, Freiburg, Germany
    Immunopharmacol Immunotoxicol 31:283-92. 2009
    ..Furthermore, our approach may help to identify marker genes urgently needed to optimize and individualize immunosuppressive drug regimens after organ transplantation...
  8. ncbi request reprint cDNA microarray analysis of adaptive changes after renal ablation in a sclerosis-resistant mouse strain
    Brigitta Rumberger
    Renal Division, Department of Medicine, University Hospital Freiburg, Freiburg, Germany
    Kidney Blood Press Res 30:377-87. 2007
    ..Oxidative stress, transforming growth factor-beta (TGF-beta), and the de novo synthesis of collagen seem to contribute to this process. However, these factors might also be required for tissue repair without fibrosis...
  9. ncbi request reprint Dynamic pathway modeling: feasibility analysis and optimal experimental design
    Thomas Maiwald
    Freiburg Center for Data Analysis and Modeling, Freiburg University, Eckerstrasse 1, 79104 Freiburg, Germany
    Ann N Y Acad Sci 1115:212-20. 2007
    ..To be able to concentrate on feasible questions on account of inexpensive computational simulations yields not only enormous cost and time saving, but also helps to specify realizable, systematic research projects in advance...
  10. pmc Experimental design for parameter estimation of gene regulatory networks
    Bernhard Steiert
    Institute for Physics, University of Freiburg, Freiburg, Germany
    PLoS ONE 7:e40052. 2012
    ..Although presented in the context of the GRNs to be inferred for the DREAM6 challenge, the approach is generic and applicable to most types of quantitative models in systems biology and other disciplines...
  11. doi request reprint A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimens
    Silke Lassmann
    Institute of Pathology, University Hospital, Albert Ludwigs University, Breisacherstr 115a, 79106, Freiburg, Germany
    J Mol Med (Berl) 87:211-24. 2009
    ..In summary, our approach represents a major step towards integration of microarrays into retrospective studies and enables further investigation of the relevance of microarray analysis for clinico-pathological diagnostics...
  12. doi request reprint Joining forces of Bayesian and frequentist methodology: a study for inference in the presence of non-identifiability
    Andreas Raue
    Institute for Physics, University of Freiburg, Freiburg, Germany
    Philos Transact A Math Phys Eng Sci 371:20110544. 2013
    ..Using an application from cell biology, we compare both methods and show that a successive application of the two methods facilitates a realistic assessment of uncertainty in model predictions...
  13. ncbi request reprint Host cell responses induced by hepatitis C virus binding
    Xinhua Fang
    Department of Medicine II, University of Freiburg, Freiburg, Germany
    Hepatology 43:1326-36. 2006
    ..Reprogramming of cellular gene expression induced by HCV-cell surface interaction may be part of the viral strategy to condition viral entry and replication and escape from innate host cell responses...
  14. doi request reprint Estimation of gene induction enables a relevance-based ranking of gene sets
    Kilian Bartholomé
    Institute of Physics, University of Freiburg, Freiburg, Germany
    J Comput Biol 16:959-67. 2009
    ..An R-package is available...
  15. ncbi request reprint Data-based identifiability analysis of non-linear dynamical models
    S Hengl
    Physics Institute, University of Freiburg, Hermann Herder Strasse 3, 79104 Freiburg i Br, Germany
    Bioinformatics 23:2612-8. 2007
    ..We exemplify our approach on a realistic dynamical model and demonstrate that the variability of estimated parameter values decreases from 81 to 1% after detection and fixation of structural non-identifiabilities...
  16. doi request reprint Addressing parameter identifiability by model-based experimentation
    A Raue
    University of Freiburg, Physics Institute, Freiburg, Germany
    IET Syst Biol 5:120-30. 2011
    ..Both strategies enhance model predictability and will be elucidated by an example application. [Includes supplementary material]...
  17. pmc Subcellular mislocalization of the transcription factor NF-E2 in erythroid cells discriminates prefibrotic primary myelofibrosis from essential thrombocythemia
    Konrad Aumann
    Institute of Pathology, and
    Blood 122:93-9. 2013
    ..727), we propose that quantitative NF-E2 immunohistochemistry represents a diagnostic tool that can reliably support a differential diagnosis between ET and PMF. ..
  18. doi request reprint Caspase-3 feeds back on caspase-8, Bid and XIAP in type I Fas signaling in primary mouse hepatocytes
    Karine Sá Ferreira
    Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
    Apoptosis 17:503-15. 2012
    ..Thus, potent, selective caspase-3 inhibitors are useful tools to understand complex signaling circuitries in apoptosis...
  19. ncbi request reprint Gene expression profiling in polycythaemia vera: overexpression of transcription factor NF-E2
    Philipp S Goerttler
    Department of Experimental Anaesthesiology, University Hospital Freiburg, Center for Clinical Research, Freiburg, Germany
    Br J Haematol 129:138-50. 2005
    ..In this model, the level of NF-E2 overexpression determines both the severity of erythrocytosis and the concurrent presence or absence of thrombocytosis...
  20. doi request reprint Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood
    A Raue
    Physics Institute, University of Freiburg, 79104 Freiburg, Germany
    Bioinformatics 25:1923-9. 2009
    ..This knowledge is essential for further investigation of model predictions. For this reason a major topic in modeling is identifiability analysis...
  21. ncbi request reprint Microarray analysis reveals influence of the sesquiterpene lactone parthenolide on gene transcription profiles in human epithelial cells
    M T Lindenmeyer
    Institute for Pharmaceutical Sciences, Department of Pharmaceutical Biology and Biotechnology, Albert Ludwigs University, Freiburg, Germany
    Life Sci 80:1608-18. 2007
    ..Confirmatory analyses were carried out using quantitative real-time RT-PCR (TaqMan). Additional studies with selected genes revealed the concentration-dependent influence of parthenolide on the expression of these genes...
  22. ncbi request reprint Quantitative data generation for systems biology: the impact of randomisation, calibrators and normalisers
    M Schilling
    German Cancer Research Center, Heidelberg, Germany
    Syst Biol (Stevenage) 152:193-200. 2005
    ..This analysis showed that the procedure is robust and can significantly improve the quality of experimental data...
  23. ncbi request reprint Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways
    U Klingmuller
    Boveri Group, Systems Biology of Signal Transduction, German Cancer Research Center DKFZ, Heidelberg, Germany
    Syst Biol (Stevenage) 153:433-47. 2006
    ....