Fabian J Theis

Summary

Country: Germany

Publications

  1. pmc An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy
    Felix Buggenthin
    Institute of Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
    BMC Bioinformatics 14:297. 2013
  2. pmc Effects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study
    Tao Xu
    Research Unit of Molecular Epidemiology, Helmholtz Zentrum Munchen, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
    BMC Med 11:60. 2013
  3. pmc 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
  4. pmc 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. doi request reprint 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. doi request reprint Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation
    Sabrina Hock
    Institute of Computational Biology, Helmholtz Center Munich, Ingolstadter Landstr 1, Neuherberg 85764, Germany
    BMC Syst Biol 7:48. 2013
  7. pmc 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
  8. doi request reprint Bayesian independent component analysis recovers pathway signatures from blood metabolomics data
    Jan Krumsiek
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Germany
    J Proteome Res 11:4120-31. 2012
  9. pmc A modular framework for gene set analysis integrating multilevel omics data
    Steffen Sass
    Institute of Computational Biology, Helmholtz Zentrum Munchen, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany and Department of Mathematics, Technische Universitat Munchen, Boltzmannstraße 3, 85747 Garching, Germany
    Nucleic Acids Res 41:9622-33. 2013
  10. doi request reprint Multi-scale modeling of GMP differentiation based on single-cell genealogies
    Carsten Marr
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen German Research Center for Environmental Health, Neuherberg Munich, Germany
    FEBS J 279:3488-500. 2012

Collaborators

Detail Information

Publications38

  1. pmc An automatic method for robust and fast cell detection in bright field images from high-throughput microscopy
    Felix Buggenthin
    Institute of Computational Biology, Helmholtz Center Munich, 85764 Neuherberg, Germany
    BMC Bioinformatics 14:297. 2013
    ....
  2. pmc Effects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study
    Tao Xu
    Research Unit of Molecular Epidemiology, Helmholtz Zentrum Munchen, Ingolstädter Landstraße 1, Neuherberg 85764, Germany
    BMC Med 11:60. 2013
    ..Here, we extend our metabolomics study with a large prospective study including female smokers and quitters...
  3. pmc 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
    ....
  4. pmc 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. doi request reprint 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. doi request reprint Sharpening of expression domains induced by transcription and microRNA regulation within a spatio-temporal model of mid-hindbrain boundary formation
    Sabrina Hock
    Institute of Computational Biology, Helmholtz Center Munich, Ingolstadter Landstr 1, Neuherberg 85764, Germany
    BMC Syst Biol 7:48. 2013
    ..Because the secreted Wnt1 protein plays a prominent role in isthmic organizer function, we focused in particular on the refinement of Wnt1 gene expression in this context...
  7. pmc 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...
  8. doi request reprint Bayesian independent component analysis recovers pathway signatures from blood metabolomics data
    Jan Krumsiek
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Germany
    J Proteome Res 11:4120-31. 2012
    ..We conclude that the Bayesian ICA methodology has the power and flexibility to replace many of the nowadays common PCA and clustering-based analyses common in the research field...
  9. pmc A modular framework for gene set analysis integrating multilevel omics data
    Steffen Sass
    Institute of Computational Biology, Helmholtz Zentrum Munchen, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany and Department of Mathematics, Technische Universitat Munchen, Boltzmannstraße 3, 85747 Garching, Germany
    Nucleic Acids Res 41:9622-33. 2013
    ..The MONA framework is flexible enough to allow for different underlying regulatory motifs or ontologies. It is ready-to-use for applied researchers and is available as a standalone application from http://icb.helmholtz-muenchen.de/mona. ..
  10. doi request reprint Multi-scale modeling of GMP differentiation based on single-cell genealogies
    Carsten Marr
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen German Research Center for Environmental Health, Neuherberg Munich, Germany
    FEBS J 279:3488-500. 2012
    ..Thus we provide a multi-scale picture of cell differentiation in murine GMPs, and illustrate the need for single-cell time-resolved observations of cellular decisions...
  11. doi request reprint 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...
  12. pmc On the hypothesis-free testing of metabolite ratios in genome-wide and metabolome-wide association studies
    Ann Kristin Petersen
    Institute of Genetic Epidemiology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    BMC Bioinformatics 13:120. 2012
    ..So far, only a rule of thumb was applied to determine the significance of the p-gain...
  13. doi request reprint 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...
  14. pmc 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...
  15. pmc A novel approach for resolving differences in single-cell gene expression patterns from zygote to blastocyst
    Florian Buettner
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, 85764 Neuherberg, Germany
    Bioinformatics 28:i626-i632. 2012
    ..Furthermore, to date, no approach taking the temporal structure of the data into account has been presented...
  16. pmc 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...
  17. pmc 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...
  18. pmc Bayesian model selection validates a biokinetic model for zirconium processing in humans
    Daniel Schmidl
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen German Research Center for Environmental Health, Neuherberg, Germany
    BMC Syst Biol 6:95. 2012
    ..In the context of observing the dynamics of multiple compartments, Bayesian methods provide efficient tools for model inference and selection...
  19. pmc 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
    ....
  20. pmc Mining the unknown: a systems approach to metabolite identification combining genetic and metabolic information
    Jan Krumsiek
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    PLoS Genet 8:e1003005. 2012
    ..Our approach is generic in nature and can be directly transferred to metabolomics data from different experimental platforms...
  21. pmc Body fat free mass is associated with the serum metabolite profile in a population-based study
    Carolin Jourdan
    Institute of Epidemiology I, Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
    PLoS ONE 7:e40009. 2012
    ..To characterise the influence of the fat free mass on the metabolite profile in serum samples from participants of the population-based KORA (Cooperative Health Research in the Region of Augsburg) S4 study...
  22. pmc 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...
  23. doi request reprint miR-335 promotes mesendodermal lineage segregation and shapes a transcription factor gradient in the endoderm
    Dapeng Yang
    Institute of Stem Cell Research, Helmholtz Zentrum Munchen, D 85764 Neuherberg, Germany
    Development 141:514-25. 2014
    ..Taken together, our results suggest that miR-335 targets endoderm TFs for spatio-temporal gradient formation in the endoderm and to stabilize lineage decisions during mesendoderm formation. ..
  24. pmc 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...
  25. doi request reprint 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...
  26. ncbi request reprint A unilateral negative feedback loop between miR-200 microRNAs and Sox2/E2F3 controls neural progenitor cell-cycle exit and differentiation
    Changgeng Peng
    Institute of Developmental Genetics, Helmholtz Zentrum Munchen, Deutsches Forschungszentrum für Umwelt und Gesundheit, and Technische Universität München Weihenstephan, D 85764 Neuherberg, Germany
    J Neurosci 32:13292-308. 2012
    ....
  27. doi request reprint The Sox17-mCherry fusion mouse line allows visualization of endoderm and vascular endothelial development
    Ingo Burtscher
    Institute of Diabetes and Regeneration, Helmholtz Zentrum Munchen, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Genesis 50:496-505. 2012
    ..In summary, the generation of the Sox17-mCherry reporter mouse line allows direct visualization of endoderm and vascular development in culture and the mouse embryo...
  28. pmc 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...
  29. pmc 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...
  30. pmc 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...
  31. doi request reprint 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)...
  32. pmc 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...
  33. pmc 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...
  34. pmc 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...
  35. pmc 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...
  36. ncbi request reprint 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...
  37. doi request reprint 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...
  38. pmc 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...