Silence on the relevant literature and errors in implementation. Bastiaens, P., Birtwistle, M. R., Bluthgen, N., Bruggeman, F. J., Cho, K., Cosentino, C., de la Fuente, A., Hoek, J. B., Kiyatkin, A., Klamt, S., Kolch, W., Legewie, S., Mendes, P., Naka, T., Santra, T., Sontag, E., Westerhoff, H. V., & Kholodenko, B. N. Nature Biotech, 33:336-339, 2015. abstract bibtex This letter discusses a paper in the same journal which reported a method for reconstructing network topologies. Here we show that the method is a variant of a previously published method, modular response analysis. We also demonstrate that the implementation of the algorithm in that paper using statistical similarity measures as a proxy for global network responses to perturbations is erroneous and its performance is overestimated.
@ARTICLE{kholodenko_naturebiotech_2015_letter,
AUTHOR = {P. Bastiaens and M. R. Birtwistle and N. Bluthgen and
F. J. Bruggeman and K.-H. Cho and C. Cosentino and de la Fuente, A. and
J. B. Hoek and A. Kiyatkin and S. Klamt and W. Kolch and S. Legewie and
P. Mendes and T. Naka and T. Santra and E.D. Sontag and
H. V. Westerhoff and B. N. Kholodenko},
JOURNAL = {Nature Biotech},
TITLE = {Silence on the relevant literature and errors in
implementation},
YEAR = {2015},
OPTMONTH = {},
OPTNOTE = {},
OPTNUMBER = {},
PAGES = {336-339},
VOLUME = {33},
KEYWORDS = {reverse engineering, systems biology,
systems identification},
PDF = {../../FTPDIR/bastiaens_et_al_kholodenko_about_barabasi_nature_biotech2015.pdf},
ABSTRACT = {This letter discusses a paper in the same journal which
reported a method for reconstructing network topologies. Here we show
that the method is a variant of a previously published method,
modular response analysis. We also demonstrate that the
implementation of the algorithm in that paper using statistical
similarity measures as a proxy for global network responses to
perturbations is erroneous and its performance is overestimated.}
}
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