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Silence on the relevant literature and errors in implementation

Nature Biotechnology volume 33, pages 336–339 (2015)Cite this article

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To the Editor:

In the August 2013 issue of this journal, Barzel & Barabási reported a method for reconstructing network topologies1. Here we show that the Barzel & Barabási method is a variant of a previously published method, modular response analysis (MRA)2. We also demonstrate that the implementation of their algorithm using statistical similarity measures as a proxy for global network responses to perturbations is erroneous and its performance is overestimated.

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Figure 1: The DREAM5 challenge performances of the Barzel & Barabási 'silencer' method (dark blue) and the raw statistical similarity measures, the Pearson (red) and Spearman (light blue) correlations and mutual information (MI, green).

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Author information

Authors and Affiliations

  1. Department of Systemic Cell Biology, Max Planck Institute of Molecular Physiology, Dortmund, Germany

    Philippe Bastiaens

  2. Icahn School of Medicine at Mount Sinai, Dept. of Pharmacology and Systems Therapeutics, New York, New York, USA

    Marc R Birtwistle

  3. Institut für Pathologie Charite, Universitätsmedizin Berlin, Campus Mitte, Berlin, Germany

    Nils Blüthgen

  4. Integrative Research Institute for the Life Sciences, Humboldt University Berlin, Berlin, Germany

    Nils Blüthgen

  5. Systems Bioinformatics, VU University, Amsterdam, The Netherlands

    Frank J Bruggeman

  6. Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Yuseong-gu, Daejeon, Republic of Korea

    Kwang-Hyun Cho

  7. Department of Experimental and Clinical Medicine, Magna Graecia University of Catanzaro, Campus Salvatore Venuta, Catanzaro, Italy

    Carlo Cosentino

  8. Department of Biomathematics and Bioinformatics, Institute for Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Mecklenburg-Vorpommern, Germany

    Alberto de la Fuente

  9. Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania, USA

    Jan B Hoek

  10. Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA

    Anatoly Kiyatkin

  11. Max Planck Institute for Dynamics of Complex Technical Systems, Magdeburg, Germany

    Steffen Klamt

  12. Systems Biology Ireland, University College Dublin, Belfield, Dublin, Ireland

    Walter Kolch, Tapesh Santra & Boris N Kholodenko

  13. Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin, Ireland

    Walter Kolch & Boris N Kholodenko

  14. School of Medicine and Medical Science, University College Dublin, Belfield, Dublin, Ireland

    Walter Kolch & Boris N Kholodenko

  15. Institute of Molecular Biology (IMB), Mainz, Germany

    Stefan Legewie

  16. Manchester Centre for Integrative Systems Biology, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK

    Pedro Mendes & Hans V Westerhoff

  17. School of Computer Science, Manchester Institute of Biotechnology, The University of Manchester, Manchester, UK

    Pedro Mendes

  18. Center for Quantitative Medicine, University of Connecticut Health Center, Farmington, Connecticut, USA

    Pedro Mendes

  19. Faculty of Information Science, Kyushu Sangyo University, Higashi-ku, Fukuoka, Japan

    Takashi Naka

  20. Department of Mathematics and Cancer Institute of New Jersey, Rutgers University, Piscataway, New Jersey, USA

    Eduardo Sontag

  21. Molecular Cell Physiology, VU University, Amsterdam, The Netherlands

    Hans V Westerhoff

  22. Synthetic Systems Biology, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam, The Netherlands

    Hans V Westerhoff

Authors
  1. Philippe Bastiaens
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  2. Marc R Birtwistle
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  3. Nils Blüthgen
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  4. Frank J Bruggeman
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  6. Carlo Cosentino
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  7. Alberto de la Fuente
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  8. Jan B Hoek
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  9. Anatoly Kiyatkin
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  10. Steffen Klamt
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  11. Walter Kolch
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  12. Stefan Legewie
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  13. Pedro Mendes
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  14. Takashi Naka
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  15. Tapesh Santra
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  16. Eduardo Sontag
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  17. Hans V Westerhoff
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  18. Boris N Kholodenko
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Corresponding author

Correspondence to Boris N Kholodenko.

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The authors declare no competing financial interests.

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Bastiaens, P., Birtwistle, M., Blüthgen, N. et al. Silence on the relevant literature and errors in implementation. Nat Biotechnol 33, 336–339 (2015). https://doi.org/10.1038/nbt.3185

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