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Identifying Discrete States of a Biological System Using a Novel Step Detection Algorithm

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  • Jan Opfer
  • Kay-Eberhard Gottschalk

Abstract

Identification of discrete states is a common task when studying biological systems on microscopic scales. Here, we present a novel step detection algorithm that is ideally suited to locate steplike features separating adjacent plateaus, even if they are smooth and hidden by noise. It can be adjusted to detect very low or narrow steps that cannot be recognized by conventional methods. We demonstrate the applicability of the technique on various experimental data and show strong evidence of sub-10-pN steps in atomic force spectroscopy measurements performed with living lymphocytes.

Suggested Citation

  • Jan Opfer & Kay-Eberhard Gottschalk, 2012. "Identifying Discrete States of a Biological System Using a Novel Step Detection Algorithm," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-10, November.
    • Handle: RePEc:plo:pone00:0045896
    DOI: 10.1371/journal.pone.0045896
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    References listed on IDEAS

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    1. Jacob W. J. Kerssemakers & E. Laura Munteanu & Liedewij Laan & Tim L. Noetzel & Marcel E. Janson & Marileen Dogterom, 2006. "Assembly dynamics of microtubules at molecular resolution," Nature, Nature, vol. 442(7103), pages 709-712, August.
    2. Elio A. Abbondanzieri & William J. Greenleaf & Joshua W. Shaevitz & Robert Landick & Steven M. Block, 2005. "Direct observation of base-pair stepping by RNA polymerase," Nature, Nature, vol. 438(7067), pages 460-465, November.
    3. Roop Mallik & Brian C. Carter & Stephanie A. Lex & Stephen J. King & Steven P. Gross, 2004. "Cytoplasmic dynein functions as a gear in response to load," Nature, Nature, vol. 427(6975), pages 649-652, February.
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