Genomes and Genes
Affiliation: University of Freiburg
- Profile likelihood in systems biologyClemens 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...
- Likelihood based observability analysis and confidence intervals for predictions of dynamic modelsClemens 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...
- TSSi--an R package for transcription start site identification from 5' mRNA tag dataC 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...
- Systems biology: experimental designClemens 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...
- An error model for protein quantificationC 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...
- Combination of immunosuppressive drugs leaves specific "fingerprint" on gene expression in vitroBrigitta 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...
- Dynamic pathway modeling: feasibility analysis and optimal experimental designThomas 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...
- cDNA microarray analysis of adaptive changes after renal ablation in a sclerosis-resistant mouse strainBrigitta 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...
- Lessons learned from quantitative dynamical modeling in systems biologyAndreas Raue
Institute of Physics, University of Freiburg, Freiburg, Germany Institute of Computational Biology, Helmholtz Center, Munich, Germany
PLoS ONE 8:e74335. 2013..We provide a freely available open source software package that implements the algorithms and examples compared here. ..
- Experimental design for parameter estimation of gene regulatory networksBernhard 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...
- A novel approach for reliable microarray analysis of microdissected tumor cells from formalin-fixed and paraffin-embedded colorectal cancer resection specimensSilke 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...
- Joining forces of Bayesian and frequentist methodology: a study for inference in the presence of non-identifiabilityAndreas Raue
Institute for Physics, University of Freiburg, Freiburg, Germany
Philos Trans 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...
- Estimation of gene induction enables a relevance-based ranking of gene setsKilian Bartholomé
Institute of Physics, University of Freiburg, Freiburg, Germany
J Comput Biol 16:959-67. 2009..An R-package is available...
- Data-based identifiability analysis of non-linear dynamical modelsS Hengl
Physics Institute, University of Freiburg, Hermann Herder Strasse 3, 79104 Freiburg i Br, Germany
Bioinformatics 23:2612-8. 2007..However, models may comprise non-identifiable parameters which cannot be unambiguously determined. Non-identifiability manifests itself in functionally related parameters, which are difficult to detect...
- Addressing parameter identifiability by model-based experimentationA 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]...
- Driving the Model to Its Limit: Profile Likelihood Based Model ReductionTim Maiwald
Institute of Physics, University of Freiburg, Freiburg im Breisgau, Germany
PLoS ONE 11:e0162366. 2016..data2dynamics.org/, as well as the R packages dMod/cOde available at https://github.com/dkaschek/. Moreover, the concept is generally applicable and can readily be used with any software capable of calculating the profile likelihood. ..
- Host cell responses induced by hepatitis C virus bindingXinhua 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...
- Subcellular mislocalization of the transcription factor NF-E2 in erythroid cells discriminates prefibrotic primary myelofibrosis from essential thrombocythemiaKonrad Aumann
Institute of Pathology, University Medical Center Freiburg, Freiburg, Germany
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. ..
- Cause and cure of sloppiness in ordinary differential equation modelsChristian Tönsing
Institute of Physics, University of Freiburg, 79104 Freiburg, Germany
Phys Rev E Stat Nonlin Soft Matter Phys 90:023303. 2014..Furthermore, we present strategies using optimal experimental design methods in order to circumvent the sloppiness issue and present nonsloppy designs for a benchmark model. ..
- PI3K-p110-alpha-subtype signalling mediates survival, proliferation and neurogenesis of cortical progenitor cells via activation of mTORC2Shalaka Dhanraj Wahane
Department of Molecular Embryology, Institute of Anatomy and Cell Biology, Albert Ludwigs University Freiburg, Freiburg, Germany Faculty of Biology, Albert Ludwigs University Freiburg, Freiburg, Germany
J Neurochem 130:255-67. 2014..PI3K-p110-beta-signalling activates a different mTORC2. Both PI3K/mTORC2-signalling pathways are required but not directly activated in TGFβ-mediated neuronal differentiation. ..
- Gene profiling of polycystic kidneysGisela 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...
- Caspase-3 feeds back on caspase-8, Bid and XIAP in type I Fas signaling in primary mouse hepatocytesKarine 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...
- Gene expression profiling in polycythaemia vera: overexpression of transcription factor NF-E2Philipp 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...
- Microarray analysis reveals influence of the sesquiterpene lactone parthenolide on gene transcription profiles in human epithelial cellsM 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...
- Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihoodA 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...
- Quantitative data generation for systems biology: the impact of randomisation, calibrators and normalisersM 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...
- Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathwaysU Klingmuller
Boveri Group, Systems Biology of Signal Transduction, German Cancer Research Center DKFZ, Heidelberg, Germany
Syst Biol (Stevenage) 153:433-47. 2006....