Systems biology/Bibliography

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Books

• Boogerd FC, Bruggeman FJ, Hofmeyr J-HS, Westerhoff HV (eds) (2007) Systems Biology: Philosophical Foundations. 360 pages; 14 chapters; Elsevier ISBN 0444520856 maintarget=&isbn=9780444520852&country=United+States&srccode=&ref=goog&subcode=&head=&pdf=&basiccode=&txtSearch=&SearchField=&operator=&order=&community=pharmatox Book description
• Alon U (2007) An Introduction to Systems Biology: Design Principles of Biological Circuits. Boca Raton: Chapman and Hall/CRC ISBN 1-58488-642-0

Table of Contents

• Ashby R (1947) Principles of the self-organizing dynamic system. J Gen Psychol 37:125.
• Banathy BH (1992) A Systems View of Education; Concepts and Principles for effective Practice. Eductional Techology Publications, New Jersey. ISBN 0-87778-245-8
• Bock G, Goode JA (eds). (2002) "In Silico" Simulation of Biological Processes, Novartis Foundation Symposium 247. Wiley, ISBN 0-470-84480-9
• Boulding K (1985) The World as a Total System, Thousand Oaks, CA, Sage Publications.
• Ellner SP, Guckenheimer J (2006) Dynamic Models In Biology. Princeton: Princeton University Press. PMID 13-978-0-691-12589-3
• Emery F. E., (ed.) (1969) Systems Thinking: Selected Readings Penguin, New York
• Flood R, Carson E (1988) Dealing with Complexity. An Introduction to the Theory and Application of Systems Science. Plenum Press, New York
• Kaneko K (2006) Life: An Introduction to Complex Systems Biology. Berlin: Springer ISBN 3-540-32666-9 (Table of Contents)
• Kitano H (editor) (2001) Foundations of Systems Biology. MIT Press ISBN 0-262-11266-3
• Klipp E, Herwig R, Kowald A, Wierling C, Lehrach H. (2005) Systems Biology in Practice. Wiley-VCH: ISBN 3-527-31078-9
• Klir G (ed.) (1991), Facets of Systems Science, New York, Plenum Press
• Miller JG (1978), Living Systems, New York, McGraw Hill Book Company.
• Palsson B (2006) Systems Biology - Properties of Reconstructed Networks. Cambridge University Press ISBN 9780521859035
• Rapoport A (1968), General System Theory. In David L. Sills (Ed.). The International Encyclopedia of Social Sciences. Volume 15. New York: Macmillan & The Free Press, 452-8.
• Rosen R (1970) Dynamical Systems Theory in Biology. Vol. 1: Stability Theory and its Applications. Wiley, New York.
• Skyttner L (2005) General Systems Theory: Problems, Perspectives, Practice. New Jersey: World Scientific. ISBN 981-256-467-5
• Szallasi Z, Stelling J, Periwal V (eds). (2006) System Modelling in Cellular Biology: From Concept to Nuts and Bolt. A Bradford Book, The MIT Press ISBN 0-262-19548-8 (Table of Contents and Full-Texts: Preface; Sample Chapter; Contributors; References)
• Schneider ED, Sagan D (2005) Into the Cool: Energy Flow, Thermodynamics, and Life. Chicago: The University of Chicago Press ISBN 0-226-73937-6
• von Foerster H, Zopf GW (eds.) (1962) Principles of Self-Organization. Pergamon, New York
• Weiss PA (1970) Life, Order and Understanding. The Graduate Journal, University of Texas, VolVIII, Supplement.

Articles

• Tyson JJ. 2007 Bringing cartoons to life. Nature 445:823

Essay: Gives several examples illustrating goal stated in preface: “To understand cells as dynamic systems, mathematical tools are needed to fill the gap between molecular interactions and physiological consequences.”

• Pettinen A et al. (2005) Simulation tools for biochemical networks: evaluation of performance and usability. Bioinformatics 21:357-63

Examples of computational tools systems biologists use for simulation of living systems: "Simulation of dynamic biochemical systems is receiving considerable attention due to increasing availability of experimental data of complex cellular functions."

• Mandel J et al. (2004) Representing bioinformatics causality. Briefings in Bioinformatics 5:270-83 PMID 15383213

”.. the central concern of bioinformatics becomes the study of dynamical effects in biological systems.” Authors review the advantages and disadvantages of mathematical/computational/graphical/biostatistical tools to study dynamical biological systems: ODE = ordinary differential equations; HFPN = hybrid functional Petrinets; BN = Bayesian networks; DBN = dynamic Bayesian networks; SD = Forrester-type system dynamics

• de Jong H (2002) Modeling and simulation of genetic regulatory systems: a literature review. J Comp Biol 9:67-103 PMID 11911796

Indicates tools used to model gene regulatory networks, but applicable to modeling other biological systems. From Abstract: ”This paper reviews formalisms that have been employed in mathematical biology and bioinformatics to describe genetic regulatory systems, in particular directed graphs, Bayesian networks, Boolean networks and their generalizations, ordinary and partial differential equations, qualitative differential equations, stochastic equations, and rule-based formalisms. In addition, the paper discusses how these formalisms have been used in the simulation of the behavior of actual regulatory systems.”

• Nature Focus on Systems Biology, 2006

”Welcome to the Nature Cell Biology and Nature Reviews Molecular Cell Biology joint Focus on Systems Biology: a User's Guide. This collection of Review-type articles are designed as highly accessible and practical guides to some of the most important approaches and challenges in systems biology.”