computational
modeling in biology

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Carsten Marr

Postdoctoral fellow


Tel.: +49 89 (0) 3187 3642
Room: 152


Research

  • Single-cell analysis and models of stem cell dynamics
  • Gene regulatory networks in cellular differentiation
  • Topological properties of biological networks
  • Cellular automata on graphs

 

Publications

  • Social Transfer of Pathogenic Fungus Promotes Active Immunisation in Ant Colonies.
    M. Konrad, M. L. Vyleta, F. J. Theis, M. Stock, S. Tragust, M. Klatt, V. Drescher, C. Marr, L. V. Ugelvig, and S. Cremer.
    PLoS Biol, 10(4):e1001300, 2012 [DOI].
  • Stability and multiattractor dynamics of a toggle switch based on a two-stage model of stochastic gene expression.
    M. Strasser, F. J. Theis, and C. Marr.
    Biophysical Journal, 102(1):19–29, 2012 [arXiv, DOI].
  • Efficient fluorescence image normalization for time lapse movies.
    M. Schwarzfischer*, C. Marr*, J. Krumsiek, P. S. Hoppe, T. Schroeder, and F. J. Theis.
    ICSB 2011 workshop: Microscopic Image Analysis with Applications in Biology, 2011  [ PDF ]
  • Hierarchical Differentiation of Myeloid Progenitors Is Encoded in the Transcription Factor Network.
    J. Krumsiek*, C. Marr*, T. Schroeder, and F. J. Theis.
    PLoS ONE, 6:e22649, 2011  [ PDF, DOI, PubMed ]
  • miTALOS: Analyzing the tissue-specific regulation of signaling pathways by human and mouse microRNAs.
    A. Kowarsch, M. Preusse, C. Marr, and F.J. Theis.
    RNA, 17(5), 2011 [DOI].
  • Biologically meaningful update rules increase the critical connectivity of generalized kauffman networks.
    D. M. Wittmann, C. Marr, and F. J. Theis.
    Journal of Theoretical Biololgy, 266(3):436–448, 2010 [DOI].
  • Tissue-specific target analysis of disease-associated microRNAs in human signaling pathways.
    A. Kowarsch*, C. Marr*, D. Schmidl, A. Ruepp, and F. Theis.
    PLoS ONE, 5(6):e11154, 2010 [DOI].
  • Intronic microRNAs support their host genes by mediating synergistic and antagonistic regulatory effects.
    D. Lutter, C. Marr, J. Krumsiek, E. W. Lang, and F. J. Theis. 
    BMC Genomics, 11(1):224, 2010 [DOI].

  • Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli. 
    C. Marr, F.J. Theis, L. Liebovitch, and M.-T. Hütt.
    PLoS Computational Biology, 6(7): e1000836, 2010 [arXiv, DOI].

  • Zebrafish reward mutants reveal novel transcripts mediating the behavioral effects of amphetamine.
    K. J. Webb, W. H. Norton, D. Trumbach, A. H. Meijer, J. Ninkovic, S. Topp, D. Heck, C. Marr, W. Wurst, F. J. Theis, H. P. Spaink, and L. Bally-Cuif.
    Genome Biology, 10(7):R81, 2009 [DOI].

  • Handbook of Research on Computational Methodologies in Gene Regulatory Networks,
    ch. Determining the Properties of Gene Regulatory Networks from Expression Data.
    L. S. Liebovitch, L. A. Shehadeh, V. K. Jirsa, M.-T. Hütt, and C. Marr.
    Medical Information Science Reference (IBI Global), 2009 [DOI].

  • Dissecting the logical types of network control in gene expression profiles.
    C. Marr*, M. Geertz*, M.-T. Hütt, G. Muskhelishvili.
    BMC Systems Biology, 2(1):18, 2008 [PubMed, PDF].
  • Regularizing capacity of metabolic networks.
    C. Marr, M. Müller-Linow, M.-T. Hütt.
    Physical Review E, 75:041917, 2007 [DOI, PDF].
  • Similar impact of topological and dynamic noise on complex patterns.
    C. Marr, M.-T. Hütt.
    Physics Letters A, 349:302–305, 2006 [DOI, PDF].
  • Topology regulates pattern formation capacity of binary cellular automata on graphs.
    C. Marr, M.-T. Hütt.
    Physica A, 354:641–662, 2005 [DOI, PDF].
  • Speeding up gate operations through dissipation.
    A. Beige, H. Cable, C. Marr, and P. L. Knight.
    Laser physics, 15(1):162–169, 2005 [arXiv].
  • Entangled-state preparation via dissipation-assisted adiabatic passages.
    C. Marr, A. Beige, and G. Rempe. 
    Physical Review A, 68(3):33817, 2003 [arXiv, DOI].

 

Curriculum Vitae

Carsten Marr received his diploma in general physics from Technical University Munich in 2002. He wrote his diploma thesis at the Max-Planck-Institute for Quantum Optics (Garching, Germany) and visited the Quantum Information and Quantum Optics Theory Group at Imperial College (London, UK). In 2003, he worked as a research associate for Die Junge Akademie, an institution of the Berlin-Brandenburgische Akademie der Wissenschaften. In 2004, he received a PhD fellowship from the Technische Universität Darmstadt and joined the Bioinformatcs Group there, working on dynamical processes on graphs and biological networks. He visited the Center for Complex Systems and Brain Sciences (Florida Atlantic University, USA) and Jacobs University Bremen (Germany) during his PhD. In June 2007 he joined Jacobs University as a postdoctoral fellow, focusing on gene regulatory networks. Since January 2008, he is a member of the CMB Group, where he works on the quantification, analysis, and modeling of murine stem cell data. In 2011, he visited the University of Edinburgh for six months to learn about pluripotency and stochastic descriptions of gene expression.