Chapter 3: Structure of networks #
Network Biology
Barabasi and Oltvai (2004) Nature Reviews GeneticsA classic review on network biology capturing a very good breadth of topics, ranging from network parameters all the way up to network perturbations.
A very nice article by Duncan Watts, the proponent of the small-world network hypothesis.
Using graph theory to analyze biological networks
Pavlopoulos et al. (2011) BioData MiningA nice review on graph theory applications in network biology.
Star Wars Social Network! (by Evelina Gabasova)
A fun exercise, studying the social networks in Star Wars movies!
Collective dynamics of ‘small-world’ networks
Watts and Strogatz (1998) NatureThe original paper on small world networks.
Complex networks: Structure and dynamics
Boccaletti et al. (2006) Physics ReportsExtremely detailed paper on networks (a mini book/reference!)
Complex Networks: Small-World, Scale-Free and Beyond
Wang and Chen (2003) IEEE Circuits and Systems MagazineA lucid easy-to-read paper discussing network models.
How Network Theory Is Revealing Previously Unknown Patterns in Sports
An interesting read on the use of network science in sports.
Emergence of Scaling in Random Networks
Barabasi and Albert (1999) ScienceThe original paper on scale-free networks.
Structure and Function of Complex Networks
Newman (2003) SIAM ReviewAnother excellent review/mini-book on networks, covering a wide gamut of topics.
Network motifs in the transcriptional regulation network of Escherichia coli
Shen-Orr et al. (2002) Nature GeneticsThe classic paper defining the concept of network motifs.
Network motifs: Simple building blocks of complex networks
Milo et al. (2002) ScienceAnother excellent paper building on the concept of network motifs.
FANMOD: a tool for fast network motif detection
An easy-to-use software tool for motif detection.
Aggregation of topological motifs in the Escherichia coli transcriptional regulatory network
Dobrin et al. (2004) BMC BioinformaticsAn insightful analysis of the organisation of E. coli transcriptional regulatory networks: motifs, clusters and superclusters.
Motifs, themes and thematic maps of an integrated Saccharomyces cerevisiae interaction network
Zhang et al. (2005) Journal of BiologyDiscusses the concept of ‘network themes’—classes of higher-order recurring interconnection patterns encompassing multiple occurrences of network motifs.
Error and attack tolerance of complex networks
Barabasi and Albert (2000) NatureThe classic paper illustrating the robustness of scale-free networks to random failures, and susceptibility to targeted attacks.
Attack vulnerability of complex networks
Holme et al. (2002) Physical Review EAn elaborate analysis of four different attack strategies on a variety of complex networks, based on degree/betweenness centrality.