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Silence on the relevant literature and errors in implementation

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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).

References

  1. Barzel, B. & Barabási, A.L. Nat. Biotechnol. 31, 720–725 (2013).

    Article  CAS  Google Scholar 

  2. Kholodenko, B.N. et al. Proc. Natl. Acad. Sci. USA 99, 12841–12846 (2002).

    Article  CAS  Google Scholar 

  3. Stark, J., Callard, R. & Hubank, M. Trends Biotechnol. 21, 290–293 (2003).

    Article  CAS  Google Scholar 

  4. Kholodenko, B.N. Nat. Cell Biol. 9, 247–249 (2007).

    Article  CAS  Google Scholar 

  5. Sontag, E.D. Essays Biochem. 45, 161–176 (2008).

    Article  CAS  Google Scholar 

  6. Selvarajoo, K., Tomita, M. & Tsuchiya, M. J. Bioinform. Comput. Biol. 7, 243–268 (2009).

    Article  CAS  Google Scholar 

  7. Kholodenko, B., Yaffe, M.B. & Kolch, W. Sci. Signal. 5, re1 (2012).

    Article  Google Scholar 

  8. de la Fuente, A., Brazhnik, P. & Mendes, P. in Metabolic Engineering in the Post Genomic Era (eds. Kholodenko, B.N. & Westerhoff, H.V.) (Horizon Bioscience, 2004).

    Google Scholar 

  9. Stelniec-Klotz, I. et al. Mol. Syst. Biol. 8, 601 (2012).

    Article  Google Scholar 

  10. Klinger, B. et al. Mol. Syst. Biol. 9, 673 (2013).

    Article  Google Scholar 

  11. de la Fuente, A., Brazhnik, P. & Mendes, P. Trends Genet. 18, 395–398 (2002).

    Article  CAS  Google Scholar 

  12. Gardner, T.S., di Bernardo, D., Lorenz, D. & Collins, J.J. Science 301, 102–105 (2003).

    Article  CAS  Google Scholar 

  13. de la Fuente, A. & Makhecha, D.P. Syst. Biol. (Stevenage) 153, 257–262 (2006).

    Article  CAS  Google Scholar 

  14. Bansal, M., Belcastro, V., Ambesi-Impiombato, A. & di Bernardo, D. Mol. Syst. Biol. 3, 78 (2007).

    Article  Google Scholar 

  15. Scheinine, A. et al. Ann. NY Acad. Sci. 1158, 287–301 (2009).

    Article  Google Scholar 

  16. Shimoni, Y., Fink, M.Y., Choi, S.G. & Sealfon, S.C. PLoS Comput. Biol. 6, e1000828 (2010).

    Article  Google Scholar 

  17. Kholodenko, B.N. & Sontag, E.D. Determination of functional network structure from local parameter dependence data. arXiv: physics/0205003 (2002).

    Google Scholar 

  18. Sontag, E., Kiyatkin, A. & Kholodenko, B.N. Bioinformatics 20, 1877–1886 (2004).

    Article  CAS  Google Scholar 

  19. Andrec, M., Kholodenko, B.N., Levy, R.M. & Sontag, E. J. Theor. Biol. 232, 427–441 (2005).

    Article  CAS  Google Scholar 

  20. Brown, G.C., Hoek, J.B. & Kholodenko, B.N. Trends Biochem. Sci. 22, 288 (1997).

    Article  CAS  Google Scholar 

  21. Ferrell, J.E. Jr. Trends Biochem. Sci. 22, 288–289 (1997).

    Article  CAS  Google Scholar 

  22. Kholodenko, B.N., Hoek, J.B., Westerhoff, H.V. & Brown, G.C. FEBS Lett. 414, 430–434 (1997).

    Article  CAS  Google Scholar 

  23. Soucek, T., Pusch, O., Hengstschlager-Ottnad, E., Adams, P.D. & Hengstschlager, M. Oncogene 14, 2251–2257 (1997).

    Article  CAS  Google Scholar 

  24. Pomerening, J.R., Sontag, E.D. & Ferrell, J.E. Nat. Cell Biol. 5, 346–351 (2003).

    Article  CAS  Google Scholar 

  25. Holt, L.J., Krutchinsky, A.N. & Morgan, D.O. Nature 454, 353–357 (2008).

    Article  CAS  Google Scholar 

  26. Trunnell, N.B., Poon, A.C., Kim, S.Y. & Ferrell, J.E. Jr. Mol. Cell 41, 263–274 (2011).

    Article  CAS  Google Scholar 

  27. Bagowski, C.P., Besser, J., Frey, C.R. & Ferrell, J.E. Curr. Biol. 13, 315–320 (2003).

    Article  CAS  Google Scholar 

  28. Schachter, K.A., Du, Y., Lin, A. & Gallo, K.A. J. Biol. Chem. 281, 19134–19144 (2006).

    Article  CAS  Google Scholar 

  29. Alon, U. Nat. Rev. Genet. 8, 450–461 (2007).

    Article  CAS  Google Scholar 

  30. Kholodenko, B.N. Nat. Rev. Mol. Cell Biol. 7, 165–176 (2006).

    Article  CAS  Google Scholar 

  31. Santos, S.D., Verveer, P.J. & Bastiaens, P.I. Nat. Cell Biol. 9, 324–330 (2007).

    Article  CAS  Google Scholar 

  32. Tibshirani, R. J. R. Stat. Soc. Series B Stat. Methodol. 58, 267–288 (1996).

    Google Scholar 

  33. Shimamura, T., Imoto, S., Yamaguchi, R. & Miyano, S. Genome Inform. 19, 142–153 (2007).

    CAS  PubMed  Google Scholar 

  34. Friedman, J., Hastie, T. & Tibshirani, R. Biostatistics 9, 432–441 (2008).

    Article  Google Scholar 

  35. de la Fuente, A., Bing, N., Hoeschele, I. & Mendes, P. Bioinformatics 20, 3565–3574 (2004).

    Article  CAS  Google Scholar 

  36. Veiga, D.F., Vicente, F.F., Grivet, M., de la Fuente, A. & Vasconcelos, A.T. Genet. Mol. Res. 6, 730–742 (2007).

    CAS  PubMed  Google Scholar 

  37. Friedman, N. Science 303, 799–805 (2004).

    Article  CAS  Google Scholar 

  38. Zou, H. & Hastie, T. J. R. Stat. Soc. Series B Stat. Methodol. 67, 301–320 (2005).

    Article  Google Scholar 

  39. Santra, T., Kolch, W. & Kholodenko, B.N. BMC Syst. Biol. 7, 57 (2013).

    Article  Google Scholar 

  40. Davis, J. & Goadrich, M. in Proceedings of the 23rd International Conference on Machine Learning, 233–240 (ACM, Pittsburgh, Pennsylvania, 2006).

    Google Scholar 

Download references

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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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