@article{BaslerEbenhoehSelbigetal.2011,
  author    = {Basler, Georg and Ebenhoeh, Oliver and Selbig, Joachim and Nikoloski, Zoran},
  title     = {Mass-balanced randomization of metabolic networks},
  series = {Bioinformatics},
  volume    = {27},
  journal   = {Bioinformatics},
  number    = {10},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {1367-4803},
  doi       = {10.1093/bioinformatics/btr145},
  pages     = {1397 -- 1403},
  year      = {2011},
  abstract  = {Motivation: Network-centered studies in systems biology attempt to integrate the topological properties of biological networks with experimental data in order to make predictions and posit hypotheses. For any topology-based prediction, it is necessary to first assess the significance of the analyzed property in a biologically meaningful context. Therefore, devising network null models, carefully tailored to the topological and biochemical constraints imposed on the network, remains an important computational problem. Results: We first review the shortcomings of the existing generic sampling scheme-switch randomization-and explain its unsuitability for application to metabolic networks. We then devise a novel polynomial-time algorithm for randomizing metabolic networks under the (bio)chemical constraint of mass balance. The tractability of our method follows from the concept of mass equivalence classes, defined on the representation of compounds in the vector space over chemical elements. We finally demonstrate the uniformity of the proposed method on seven genome-scale metabolic networks, and empirically validate the theoretical findings. The proposed method allows a biologically meaningful estimation of significance for metabolic network properties.},
  language  = {en}
}
@article{EbenhoehHouwaartLoksteinetal.2011,
  author    = {Ebenhoeh, Oliver and Houwaart, Torsten and Lokstein, Heiko and Schlede, Stephanie and Tirok, Katrin},
  title     = {A minimal mathematical model of nonphotochemical quenching of chlorophyll fluorescence},
  series = {Biosystems : journal of biological and information processing sciences},
  volume    = {103},
  journal   = {Biosystems : journal of biological and information processing sciences},
  number    = {2},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0303-2647},
  doi       = {10.1016/j.biosystems.2010.10.011},
  pages     = {196 -- 204},
  year      = {2011},
  abstract  = {Under natural conditions, plants are exposed to rapidly changing light intensities. To acclimate to such fluctuations, plants have evolved adaptive mechanisms that optimally exploit available light energy and simultaneously minimise damage of the photosynthetic apparatus through excess light. An important mechanism is the dissipation of excess excitation energy as heat which can be measured as nonphotochemical quenching of chlorophyll fluorescence (NPQ). In this paper, we present a highly simplified mathematical model that captures essential experimentally observed features of the short term adaptive quenching dynamics. We investigate the stationary and dynamic behaviour of the model and systematically analyse the dependence of characteristic system properties on key parameters such as rate constants and pool sizes. Comparing simulations with experimental data allows to derive conclusions about the validity of the simplifying assumptions and we further propose hypotheses regarding the role of the xanthophyll cycle in NPQ. We envisage that the presented theoretical description of the light reactions in conjunction with short term adaptive processes serves as a basis for the development of more detailed mechanistic models by which the molecular mechanisms of NPQ can be theoretically studied.},
  language  = {en}
}
@article{KartalMahlowSkupinetal.2011,
  author    = {Kartal, Oender and Mahlow, Sebastian and Skupin, Alexander and Ebenhoeh, Oliver},
  title     = {Carbohydrate-active enzymes exemplify entropic principles in metabolism},
  series = {Molecular systems biology},
  volume    = {7},
  journal   = {Molecular systems biology},
  number    = {10},
  publisher = {Nature Publ. Group},
  address   = {New York},
  issn      = {1744-4292},
  doi       = {10.1038/msb.2011.76},
  pages     = {11},
  year      = {2011},
  abstract  = {Glycans comprise ubiquitous and essential biopolymers, which usually occur as highly diverse mixtures. The myriad different structures are generated by a limited number of carbohydrate-active enzymes (CAZymes), which are unusual in that they catalyze multiple reactions by being relatively unspecific with respect to substrate size. Existing experimental and theoretical descriptions of CAZyme-mediated reaction systems neither comprehensively explain observed action patterns nor suggest biological functions of polydisperse pools in metabolism. Here, we overcome these limitations with a novel theoretical description of this important class of biological systems in which the mixing entropy of polydisperse pools emerges as an important system variable. In vitro assays of three CAZymes essential for central carbon metabolism confirm the power of our approach to predict equilibrium distributions and non-equilibrium dynamics. A computational study of the turnover of the soluble heteroglycan pool exemplifies how entropy-driven reactions establish a metabolic buffer in vivo that attenuates fluctuations in carbohydrate availability. We argue that this interplay between energy- and entropy-driven processes represents an important regulatory design principle of metabolic systems.},
  language  = {en}
}