Table of contents
    1. 1. Reading
    2. 2. Bibliography

    The study of biological networks has become widespread over the last ten years, to the point that Systems Biology or Network Science have been touted as new scientific disciplines.  Some of the concepts of systems biology, such as the idea that biological networks are scale-free networks, or that hubs and bottlenecks in networks play critical roles in disease, have been widely, and rather uncritically, are frequently presented as facts.  At the same time, Systems Biology has been held to a somewhat lower standard than other fields insofar as the kinds of controls that are required in other fields are often omitted.  We can ask some basic questions

    • To what extent do the concepts of Systems Biology improve our understanding of biology?
    • Does systems biology give us insights into biological complexity?
    • How well are the conclusions of systems biological analysis supported by positive and negative controls?
    • How much does the incompleteness of our current knowledge affect the picture?

    Reading

    • Albert R. Scale-free networks in cell biology. J Cell Sci. 2005 Nov 1;118(Pt21):4947-57. PubMed PMID: 16254242. PDF
    • Weitz JS, Benfey PN, Wingreen NS. Evolution, interactions, and biological networks. PLoS Biol. 2007 Jan;5(1):e11. PubMed PMID: 17227140; PubMed Central PMCID: PMC1769436. PDF
    • Almaas E. Biological impacts and context of network theory. J Exp Biol. 2007 May;210(Pt 9):1548-58. PubMed PMID: 17449819. PDF

       

    Bibliography

    • Aittokallio T, Schwikowski B. Graph-based methods for analysing networks incell biology. Brief Bioinform. 2006 Sep;7(3):243-55. Epub 2006 Jul 30. Review. PubMed PMID: 16880171.
      Gives a high-level introductions to some of the computational analyses used with biological networks.
    • Hecker M, Lambeck S, Toepfer S, van Someren E, Guthke R. Gene regulatory network inference: data integration in dynamic models-a review. Biosystems. 2009 Apr;96(1):86-103. Epub 2008 Dec 27. Review. PubMed PMID: 19150482.
      This relatively recent review gives a high level summary of the main computational approaches to discovering gene regualtory networks.  It includes a wealth of more detailed references.

    • Ideker T, Ozier O, Schwikowski B, Siegel AF. Discovering regulatory and signalling circuits in molecular interaction networks. Bioinformatics. 2002;18 Suppl 1:S233-40. PubMed PMID: 12169552.
      This relatively early paper is better than many in the field

    • H. Kitano, Foundations of Systems Biology (MIT Press, Cambridge, MA, 2001).

      Kitano H. Systems biology: a brief overview. Science. 2002 Mar 1;295(5560):1662-4. Review. PubMed PMID: 11872829.

      This brief review now has over 2000 citations and, together with Kitano's book, above, can be largely credited with setting off the boom in systems biology


       

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