There are several types of biological networks that include(but not limited to) Gene Regulatory Networks, Protein-Protein Interaction(PPI) Networks, Metabolic Networks and Signal Transduction Networks.
Uri Alon's book focuses on Regulatory and Transcriptional Networks. Network Motif is a powerful concept that was first introduced by Uri Alon to understand the design principles of biological networks. You can find Alon's motif finder software here.
I am not aware of any book on Network Biology but Barbasi's this Nature Review article is a very good introduction to the topic and all the terminology that you might come across in Network Biology papers.
This review paper by Yang and Su not only covers Network Biology concepts but also lists a set of algorithms for module discovery. The paper also has nice a "Application" section which discusses how the framework of networks and modules helps in understanding cellular behavior under different biological contexts.
Biological Networks can be built based on several types of data...:
- PPI from -Two Hybrid Assays, Mass Spec(protein complexes)
- Regulatory and Transcriptional from - ChIP-on-Chip, ChIP-Seq
- Metabolic Networks - eg KEGG PATHWAY database - from manual collection of metabolic reactions
- Human Disease Networks - based on known disease-gene associations