Silence on the relevant literature and errors in implementation

Nature Biotechnology

Volumn 33, Issue 4, 2015, Pages 336-339

  Bastiaens, Philippe ^a   Birtwistle, Marc R ^b   Blüthgen, Nils ^c,d   Bruggeman, Frank J ^e   Cho, Kwang Hyun ^f   Cosentino, Carlo ^g   De La Fuente, Alberto ^h   Hoek, Jan B ⁱ   Kiyatkin, Anatoly ^j   Klamt, Steffen ^k   Kolch, Walter ^l   Legewie, Stefan ^m   Mendes, Pedro ^n,o   Naka, Takashi ^p   Santra, Tapesh ^l   Sontag, Eduardo ^q   Westerhoff, Hans V ^e,n,r   Kholodenko, Boris N ^l  

^a MAX PLANCK INSTITUTE OF MOLECULAR PHYSIOLOGY   (Germany)

^b MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^c CHARITÉ UNIVERSITÄTSMEDIZIN BERLIN   (Germany)

^d HUMBOLDT UNIVERSITY   (Germany)

^e VU UNIVERSITY AMSTERDAM   (Netherlands)

^f Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^g UNIVERSITY MAGNA GRAECIA OF CATANZARO   (Italy)

^h LEIBNIZ INSTITUTE FOR FARM ANIMAL BIOLOGY FBN   (Germany)

ⁱ THOMAS JEFFERSON UNIVERSITY   (United States)

^j UNIVERSITY OF PENNSYLVANIA   (United States)

^k MAX PLANCK INSTITUTE FOR DYNAMICS OF COMPLEX TECHNICAL SYSTEMS   (Germany)

^l UNIVERSITY COLLEGE DUBLIN   (Ireland)

^m Conway Institute of Biomolecular and Biomedical Research University College Dublin ^*  (Germany)

ⁿ UNIVERSITY OF MANCHESTER   (United Kingdom)

^o UNIVERSITY OF CONNECTICUT HEALTH CENTER   (United States)

^p KYUSHU SANGYO UNIVERSITY   (Japan)

^q RUTGERS CANCER INSTITUTE OF NEW JERSEY   (United States)

^r UNIVERSITY OF AMSTERDAM   (Netherlands)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ERROR; GLOBAL CHANGE; LETTER; MAXIMUM LIKELIHOOD METHOD; PRIORITY JOURNAL; PROTEIN MODIFICATION; SCIENTIFIC LITERATURE; STEADY STATE; GENE REGULATORY NETWORK; THEORETICAL MODEL;

GENE REGULATORY NETWORKS; MODELS, THEORETICAL;

EID: 84926611831     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.3185     Document Type: Letter

References (40)

1. Barzel, B. & Barabási, A.L. Nat. Biotechnol. 31, 720-725 (2013).
2. Kholodenko, B.N. et al. Proc. Natl. Acad. Sci. USA 99, 12841-12846 (2002).
3. Stark, J., Callard, R. & Hubank, M. Trends Biotechnol. 21, 290-293 (2003).
4. Kholodenko, B.N. Nat. Cell Biol. 9, 247-249 (2007).
5. Sontag, E.D. Essays Biochem. 45, 161-176 (2008).
6. Selvarajoo, K., Tomita, M. & Tsuchiya, M. J. Bioinform. Comput. Biol. 7, 243-268 (2009).
7. Kholodenko, B., Yaffe, M.B. & Kolch, W. Sci. Signal. 5, re1 (2012).
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).
9. Stelniec-Klotz, I. et al. Mol. Syst. Biol. 8, 601 (2012).
10. Klinger, B. et al. Mol. Syst. Biol. 9, 673 (2013).
11. de la Fuente, A., Brazhnik, P. & Mendes, P. Trends Genet. 18, 395-398 (2002).
12. Gardner, T.S., di Bernardo, D., Lorenz, D. & Collins, J.J. Science 301, 102-105 (2003).
13. de la Fuente, A. & Makhecha, D.P. Syst. Biol. (Stevenage) 153, 257-262 (2006).
14. Bansal, M., Belcastro, V., Ambesi-Impiombato, A. & di Bernardo, D. Mol. Syst. Biol. 3, 78 (2007).
15. Scheinine, A. et al. Ann. NY Acad. Sci. 1158, 287-301 (2009).
16. Shimoni, Y., Fink, M.Y., Choi, S.G. & Sealfon, S.C. PLoS Comput. Biol. 6, e1000828 (2010).
17. Kholodenko, B.N. & Sontag, E.D. Determination of functional network structure from local parameter dependence data. arXiv: physics/0205003 (2002).
18. Sontag, E., Kiyatkin, A. & Kholodenko, B.N. Bioinformatics 20, 1877-1886 (2004).
19. Andrec, M., Kholodenko, B.N., Levy, R.M. & Sontag, E. J. Theor. Biol. 232, 427-441 (2005).
20. Brown, G.C., Hoek, J.B. & Kholodenko, B.N. Trends Biochem. Sci. 22, 288 (1997).
21. Ferrell, J.E. Jr. Trends Biochem. Sci. 22, 288-289 (1997).
22. Kholodenko, B.N., Hoek, J.B., Westerhoff, H.V. & Brown, G.C. FEBS Lett. 414, 430-434 (1997).
23. Soucek, T., Pusch, O., Hengstschlager-Ottnad, E., Adams, P.D. & Hengstschlager, M. Oncogene 14, 2251-2257 (1997).
24. Pomerening, J.R., Sontag, E.D. & Ferrell, J.E. Nat. Cell Biol. 5, 346-351 (2003).
25. Holt, L.J., Krutchinsky, A.N. & Morgan, D.O. Nature 454, 353-357 (2008).
26. Trunnell, N.B., Poon, A.C., Kim, S.Y. & Ferrell, J.E. Jr. Mol. Cell 41, 263-274 (2011).
27. Bagowski, C.P., Besser, J., Frey, C.R. & Ferrell, J.E. Curr. Biol. 13, 315-320 (2003).
28. Schachter, K.A., Du, Y., Lin, A. & Gallo, K.A. J. Biol. Chem. 281, 19134-19144 (2006).
29. Alon, U. Nat. Rev. Genet. 8, 450-461 (2007).
30. Kholodenko, B.N. Nat. Rev. Mol. Cell Biol. 7, 165-176 (2006).
31. Santos, S.D., Verveer, P.J. & Bastiaens, P.I. Nat. Cell Biol. 9, 324-330 (2007).
32. Tibshirani, R. J. R. Stat. Soc. Series B Stat. Methodol. 58, 267-288 (1996).
33. Shimamura, T., Imoto, S., Yamaguchi, R. & Miyano, S. Genome Inform. 19, 142-153 (2007).
34. Friedman, J., Hastie, T. & Tibshirani, R. Biostatistics 9, 432-441 (2008).
35. de la Fuente, A., Bing, N., Hoeschele, I. & Mendes, P. Bioinformatics 20, 3565-3574 (2004).
36. Veiga, D.F., Vicente, F.F., Grivet, M., de la Fuente, A. & Vasconcelos, A.T. Genet. Mol. Res. 6, 730-742 (2007).
37. Friedman, N. Science 303, 799-805 (2004).
38. Zou, H. & Hastie, T. J. R. Stat. Soc. Series B Stat. Methodol. 67, 301-320 (2005).
39. Santra, T., Kolch, W. & Kholodenko, B.N. BMC Syst. Biol. 7, 57 (2013).
40. Davis, J. & Goadrich, M. in Proceedings of the 23rd International Conference on Machine Learning, 233-240 (ACM, Pittsburgh, Pennsylvania, 2006).