System biology and evolution: Book-recommendations
Here there are a couple that I own:

The "classic" from Uri Alon touches many of the topics you mention. It is easy to read and goes relatively deep into the methods. There seems to be a new edition (if you search it in Amazon it will pop up), but it was planned for last year's April and then delayed so no so clear when will be actually published. For the original one: Amazon link

Title: An Introduction to Systems Biology: Design Principles of Biological Circuits
Year: 2006
Author: Uri Alon
Publisher: Chapman &amp; Hall/CRC Mathematical and Computational Biology


The other book is this textbook "Systems biology" by  Edda Klipp and others. I attended a talk by Edda Klipp two years ago and she seems to be doing interesting things. This book is more general, covering, somewhat superficially, many topics. It can be good to get a general idea on the field. Amazon link.

Title: Systems Biology Paperback
Year: 2009
Author: Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig
Publisher: Wiley-Blackwell


There are many others (see Amazon results here). Maybe other members can comment on some of the other titles.