Systems Biology Books
From Symbiopedia
Systems Biology: Properties of Reconstructed Networks - Bernhard O. Palsson
Palsson gives a broad overview and introduction to Systems Biology, particularly the constraint-based approach to reconstructed networks. This text primarily focuses on metabolic networks. The literature has advanced quite a bit since this book was published, so some of the concepts emphasized in this book haven't turned out to be widely applied. In attempting to be a catch-all beginner intro text, the book glosses over mathematical details, and so the examples are hard to follow, the math uses nonstandard notation and is confusing. However, investing more time in working through examples (and the use of supplemental texts) allows better understanding of Palsson's notation and general approach to Constraint-Based Modeling.
We've put together some tutorials that describe examples from this book and software used by the Palsson group.
System Modeling in Cellular Biology: From Concepts to Nuts and Bolts - Zoltan Szallasi, Jörg Stelling, Vipul Periwal (Eds)
Amazon Link - by Zoltan Szallasi (Editor), Jörg Stelling (Editor), Vipul Periwal (Editor)
A very good intro from MIT press. Better mathematical explanations, a bigger overview of various approaches, and a very good discussion of the philosophic underpinnings of various modeling approaches. Worth Buying
Systems Biology in Practice: Concepts, Implementation and Application - by Edda Klipp, Ralf Herwig, Axel Kowald, Christoph Wierling, Hans Lehrach
A pretty high level overview of everything. Chapters include things like "Biology in a Nutshell", "Mathematics in a Nuthshell", and "Experimental Techniques in a Nutshell" which consist of a list of common techniques and approaches with very little depth. A good quick reference for looking up the right terminology and make sure people are speaking the same language, but not a lot of depth to any particular section. A first intro book.
Principles of Computational Cell Biology: From Protein Complexes to Cellular Networks - by Volkhard Helms
To be reviewed more thoroughly, but chapter 6 is a very good overview of mathematical approaches to constraint-based analysis of metabolic networks (though section 6.5 is pretty mathematically challenging). The clearest explanation of eigenvalues and vectors I've read, and very clear examples are worked. As with most books, I want more examples.
An Introduction to Systems Biology: Design Principles of Biological Circuits - by Uri Alon
To be reviewed.
Uri Alon was referenced by Chris Myers
