Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Silence on the relevant literature and errors in implementation

This is a preview of subscription content

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

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. 1

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

    CAS  Article  Google Scholar 

  2. 2

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

    CAS  Article  Google Scholar 

  3. 3

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

    CAS  Article  Google Scholar 

  4. 4

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

    CAS  Article  Google Scholar 

  5. 5

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

    CAS  Article  Google Scholar 

  6. 6

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

    CAS  Article  Google Scholar 

  7. 7

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

    Article  Google Scholar 

  8. 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. 9

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

    Article  Google Scholar 

  10. 10

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

    Article  Google Scholar 

  11. 11

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

    CAS  Article  Google Scholar 

  12. 12

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

    CAS  Article  Google Scholar 

  13. 13

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

    CAS  Article  Google Scholar 

  14. 14

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

    Article  Google Scholar 

  15. 15

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

    Article  Google Scholar 

  16. 16

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

    Article  Google Scholar 

  17. 17

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

    Google Scholar 

  18. 18

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

    CAS  Article  Google Scholar 

  19. 19

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

    CAS  Article  Google Scholar 

  20. 20

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

    CAS  Article  Google Scholar 

  21. 21

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

    CAS  Article  Google Scholar 

  22. 22

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

    CAS  Article  Google Scholar 

  23. 23

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

    CAS  Article  Google Scholar 

  24. 24

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

    CAS  Article  Google Scholar 

  25. 25

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

    CAS  Article  Google Scholar 

  26. 26

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

    CAS  Article  Google Scholar 

  27. 27

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

    CAS  Article  Google Scholar 

  28. 28

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

    CAS  Article  Google Scholar 

  29. 29

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

    CAS  Article  Google Scholar 

  30. 30

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

    CAS  Article  Google Scholar 

  31. 31

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

    CAS  Article  Google Scholar 

  32. 32

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

    Google Scholar 

  33. 33

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

    CAS  PubMed  Google Scholar 

  34. 34

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

    Article  Google Scholar 

  35. 35

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

    CAS  Article  Google Scholar 

  36. 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. 37

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

    CAS  Article  Google Scholar 

  38. 38

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

    Article  Google Scholar 

  39. 39

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

    Article  Google Scholar 

  40. 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

Author information

Affiliations

Authors

Corresponding author

Correspondence to Boris N Kholodenko.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

Supplementary information

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

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

Download citation

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing