Fabian J Theis

Summary

Country: Germany

Publications

  1. ncbi Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine
    Katharine J Webb
    Department Zebrafish Neurogenetics, Institute of Developmental Genetics, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Ingolstaedter Landstrasse, Neuherberg, 85764 Germany
    Genome Biol 10:R81. 2009
  2. ncbi MicroRNAs coordinately regulate protein complexes
    Steffen Sass
    MIPS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstädter Landstraße 1, D 85764 Neuherberg, Germany
    BMC Syst Biol 5:136. 2011
  3. ncbi Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs
    Mara L Hartsperger
    Institute of Bioinformatics and Systems Biology MIPS, Helmholtz Zentrum Munchen German Research Center for Environmental Health, Ingolstadter Landstr 1, 85764 Neuherberg, Germany
    BMC Bioinformatics 11:522. 2010
  4. ncbi Odefy--from discrete to continuous models
    Jan Krumsiek
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Ingolstadter Landstrasse 1, 85764 Munich Neuherberg, Germany
    BMC Bioinformatics 11:233. 2010
  5. ncbi Theoretical analysis of time-to-peak responses in biological reaction networks
    Fabian J Theis
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    Bull Math Biol 73:978-1003. 2011
  6. ncbi Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network
    Jan Krumsiek
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Munchen, Germany
    PLoS ONE 6:e22649. 2011
  7. ncbi Effective parameters determining the information flow in hierarchical biological systems
    Florian Blöchl
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen German Research Center for Environmental Health, Neuherberg, Germany
    Bull Math Biol 73:706-25. 2011
  8. ncbi Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation
    Andreas Kowarsch
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    BMC Bioinformatics 11:585. 2010
  9. ncbi Tissue-specific target analysis of disease-associated microRNAs in human signaling pathways
    Andreas Kowarsch
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    PLoS ONE 5:e11154. 2010
  10. ncbi Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks
    Dominik M Wittmann
    Computational Modeling in Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen German Research Center for Environmental Health, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    J Theor Biol 266:436-48. 2010

Detail Information

Publications24

  1. ncbi Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine
    Katharine J Webb
    Department Zebrafish Neurogenetics, Institute of Developmental Genetics, Helmholtz Zentrum Muenchen, German Research Center for Environmental Health, Ingolstaedter Landstrasse, Neuherberg, 85764 Germany
    Genome Biol 10:R81. 2009
    ....
  2. ncbi MicroRNAs coordinately regulate protein complexes
    Steffen Sass
    MIPS, Institute for Bioinformatics and System Biology, Helmholtz Center Munich, German Research Center for Environmental Health, Ingolstädter Landstraße 1, D 85764 Neuherberg, Germany
    BMC Syst Biol 5:136. 2011
    ..Interactions between targets of co-expressed miRNAs (including miRNA clusters) have not yet been systematically investigated...
  3. ncbi Structuring heterogeneous biological information using fuzzy clustering of k-partite graphs
    Mara L Hartsperger
    Institute of Bioinformatics and Systems Biology MIPS, Helmholtz Zentrum Munchen German Research Center for Environmental Health, Ingolstadter Landstr 1, 85764 Neuherberg, Germany
    BMC Bioinformatics 11:522. 2010
    ..In order to reveal their structural organization and describe the contained information in a more coarse-grained fashion, we ask how to detect clusters within each node type...
  4. ncbi Odefy--from discrete to continuous models
    Jan Krumsiek
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Ingolstadter Landstrasse 1, 85764 Munich Neuherberg, Germany
    BMC Bioinformatics 11:233. 2010
    ..As biological interaction networks have steadily grown in size and complexity, a fully automated framework for the conversion process is desirable...
  5. ncbi Theoretical analysis of time-to-peak responses in biological reaction networks
    Fabian J Theis
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    Bull Math Biol 73:978-1003. 2011
    ....
  6. ncbi Hierarchical differentiation of myeloid progenitors is encoded in the transcription factor network
    Jan Krumsiek
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Munchen, Germany
    PLoS ONE 6:e22649. 2011
    ..We predict previously uncharacterized regulatory interactions and alterations of the differentiation process, and line out reprogramming strategies...
  7. ncbi Effective parameters determining the information flow in hierarchical biological systems
    Florian Blöchl
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen German Research Center for Environmental Health, Neuherberg, Germany
    Bull Math Biol 73:706-25. 2011
    ..We demonstrate that this fitting problem can be reformulated as the problem of fitting exponential sums, for which robust algorithms exist...
  8. ncbi Knowledge-based matrix factorization temporally resolves the cellular responses to IL-6 stimulation
    Andreas Kowarsch
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    BMC Bioinformatics 11:585. 2010
    ..However, such correlation-based methods have so far not be applied in bioinformatics, because large scale biological data rarely imply a natural order that allows the definition of a delayed correlation function...
  9. ncbi Tissue-specific target analysis of disease-associated microRNAs in human signaling pathways
    Andreas Kowarsch
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    PLoS ONE 5:e11154. 2010
    ..Our analysis provides systematic insights into the interaction of disease-associated microRNAs and signaling pathways and uncovers differences in cellular locations and process types of microRNA targets and disease-associated proteins...
  10. ncbi Biologically meaningful update rules increase the critical connectivity of generalized Kauffman networks
    Dominik M Wittmann
    Computational Modeling in Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen German Research Center for Environmental Health, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    J Theor Biol 266:436-48. 2010
    ..We analytically show that their usage indeed increases the critical connectivity. From a general point of view, our thermodynamic considerations link discrete and continuous models of gene regulatory networks...
  11. ncbi miTALOS: analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs
    Andreas Kowarsch
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    RNA 17:809-19. 2011
    ..miTALOS provides novel features that accomplish a substantial support to systematically infer regulation of signaling pathways mediated by miRNAs. The web-server is freely accessible at http://hmgu.de/cmb/mitalos...
  12. ncbi PhenomiR: a knowledgebase for microRNA expression in diseases and biological processes
    Andreas Ruepp
    Institute for Bioinformatics and Systems Biology MIPS, Helmholtz Center Munich German Research Center for Environmental Health GmbH, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Genome Biol 11:R6. 2010
    ..Using the PhenomiR dataset, we could demonstrate that, depending on disease type, independent information from cell culture studies contrasts with conclusions drawn from patient studies...
  13. ncbi Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling
    Dominik M Wittmann
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen German Research Center for Environmental Health, Neuherberg, Germany
    BMC Syst Biol 3:98. 2009
    ..Nowadays however, experiments yield more and more quantitative data. An obvious question therefore is how qualitative models can be used to explain and predict the outcome of these experiments...
  14. ncbi Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli
    Carsten Marr
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen German Research Center for Environmental Health, Neuherberg, Germany
    PLoS Comput Biol 6:e1000836. 2010
    ....
  15. ncbi Spatial analysis of expression patterns predicts genetic interactions at the mid-hindbrain boundary
    Dominik M Wittmann
    Computational Modeling in Biology, Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, German Research Centre for Environmental Health, Munich Neuherberg, Germany
    PLoS Comput Biol 5:e1000569. 2009
    ..We show, in particular, that the spatial gene expression patterns around the MHB help us to understand the maintenance of this boundary on a systems level...
  16. ncbi Gaussian graphical modeling reconstructs pathway reactions from high-throughput metabolomics data
    Jan Krumsiek
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Germany
    BMC Syst Biol 5:21. 2011
    ..Previous studies in this area mainly focused on Pearson correlation coefficients, which however are generally incapable of distinguishing between direct and indirect metabolic interactions...
  17. ncbi Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects
    Dominik Lutter
    Institute of Bioinformatics and Systems Biology, CMB, Helmholtz Zentrum Munchen, Germany
    BMC Genomics 11:224. 2010
    ..In our study we investigate this linkage towards a relationship beyond transcriptional co-regulation...
  18. ncbi An ensemble approach for inferring semi-quantitative regulatory dynamics for the differentiation of mouse embryonic stem cells using prior knowledge
    Dominik Lutter
    Institute of Bioinformatics and Systems Biology, CMB, Helmholtz Zentrum Munchen, Munich, Germany
    Adv Exp Med Biol 736:247-60. 2012
    ..Applied to data from differentiating mouse ESCs reveals new regulatory interactions, in particular we confirm the activation of Foxh1 through Oct4, mediating Nodal signaling...
  19. ncbi Complex principal component and correlation structure of 16 yeast genomic variables
    Fabian J Theis
    Helmholtz Center Munich German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, Neuherberg, Germany
    Mol Biol Evol 28:2501-12. 2011
    ..cerevisiae, and Homo sapiens (http://webclu.bio.wzw.tum.de:18080/quagmire)...
  20. ncbi An evolutionary and structural characterization of mammalian protein complex organization
    Philip Wong
    Helmholtz Center Munich German Research Center for Environmental Health GmbH, Institute of Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, Neuherberg, Germany
    BMC Genomics 9:629. 2008
    ..Combining CORUM with other resources, we assembled a dataset of over 2700 mammalian complexes. The availability of a rich information resource allows us to search for organizational properties concerning these complexes...
  21. ncbi Vertex centralities in input-output networks reveal the structure of modern economies
    Florian Blöchl
    Helmholtz Zentrum Munchen, Ingolstädter Landstraße 1, D 85764 Neuherberg, Germany
    Phys Rev E Stat Nonlin Soft Matter Phys 83:046127. 2011
    ..We further validate our indices by clustering according to sectors' centralities. This analysis reveals geographical proximity and similar developmental status...
  22. ncbi Discovery of sexual dimorphisms in metabolic and genetic biomarkers
    Kirstin Mittelstrass
    Unit of Molecular Epidemiology, Helmholtz Center Munich, German Research Center for Environmental Health, Neuherberg, Germany
    PLoS Genet 7:e1002215. 2011
    ..Our study provides new important insights into sex-specific differences of cell regulatory processes and underscores that studies should consider sex-specific effects in design and interpretation...
  23. ncbi Huge splicing frequency in human Y chromosomal UTY gene
    Ingeborg Laaser
    Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Institute of Experimental Genetics, Genome Analysis Center, Neuherberg, Germany
    OMICS 15:141-54. 2011
    ..Our study provides new insights into the complexity of human alternative splicing and its potential contribution to the transcript diversity of the transcriptome...
  24. ncbi Stability and multiattractor dynamics of a toggle switch based on a two-stage model of stochastic gene expression
    Michael Strasser
    Institute for Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
    Biophys J 102:19-29. 2012
    ..Notably, we present a system with high protein abundance that nevertheless requires a probabilistic description to exhibit multistability, complex switching dynamics, and lineage priming...