Systems biology/Bibliography

Recommended reading, notes, and links

Boogerd FC, Bruggeman FJ, Hofmeyr J-HS, Westerhoff HV (eds) (2007) Systems Biology: Philosophical Foundations. Elsevier ISBN 0444520856

360 pages; 14 chapters; 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

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

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

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.

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.”

For 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.”

”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.”