abstract bibtex

Feedback loops play an important role in determining the dynamics of biological networks. In order to study the role of negative feedback loops, this paper introduces the notion of "distance to positive feedback (PF-distance)" which in essence captures the number of "independent" negative feedback loops in the network, a property inherent in the network topology. Through a computational study using Boolean networks it is shown that PF-distance has a strong influence on network dynamics and correlates very well with the number and length of limit cycles in the phase space of the network. To be precise, it is shown that, as the number of independent negative feedback loops increases, the number (length) of limit cycles tends to decrease (increase). These conclusions are consistent with the fact that certain natural biological networks exhibit generally regular behavior and have fewer negative feedback loops than randomized networks with the same numbers of nodes and connectivity.

@ARTICLE{sontag_laubenbacher_jarrah07, AUTHOR = {E.D. Sontag and A. Veliz-Cuba and R. Laubenbacher and A.S. Jarrah}, JOURNAL = {Biophysical Journal}, TITLE = {The effect of negative feedback loops on the dynamics of Boolean networks}, YEAR = {2008}, OPTMONTH = {}, OPTNOTE = {}, OPTNUMBER = {}, PAGES = {518-526}, VOLUME = {95}, KEYWORDS = {monotone systems, positive feedback systems, Boolean networks, limit cycles}, PDF = {../../FTPDIR/sontag_cuba_laubenbacher_jarrah_biophysical_journal_2008.pdf}, ABSTRACT = {Feedback loops play an important role in determining the dynamics of biological networks. In order to study the role of negative feedback loops, this paper introduces the notion of "distance to positive feedback (PF-distance)" which in essence captures the number of "independent" negative feedback loops in the network, a property inherent in the network topology. Through a computational study using Boolean networks it is shown that PF-distance has a strong influence on network dynamics and correlates very well with the number and length of limit cycles in the phase space of the network. To be precise, it is shown that, as the number of independent negative feedback loops increases, the number (length) of limit cycles tends to decrease (increase). These conclusions are consistent with the fact that certain natural biological networks exhibit generally regular behavior and have fewer negative feedback loops than randomized networks with the same numbers of nodes and connectivity. } }

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