We will pick readings according to the interests of students in the class. Some example readings are listed here:

Websites:

Check out Wikipedia: Complex systems, The different -omics, 'complex networks', self-organization

Books:
•      Camazine S, Deneubourg J-L, Franks NR, Sneyd J, Theraulaz G, Bonabeau E (2003). Self-Organization in Biological Systems (Princeton Studies in Complexity). Publisher: Princeton University Press. Check it out on google.
This is a fairly detailed and extensive treatment of the topic of self-organization, i.e. the emergence of collective behavior without a central leader or template. Most examples are from social insects, but there are also some from microbes etc. Written by the world experts in the field. A great resource.

•      Bar-Yam: "Dynamics of complex systems", Westview Press. Check it out on google.
•      Ball: "The Self-Made Tapestry: Pattern Formation in Nature" Check it out on google.
•      Watts: "Six degrees: the science of a connected age" WW Norton & Co. Check it out on google.
•      Stonier & Yu: "Complex systems: mechanisms of adaptation" IOS Press. Check it out on google.
•      Watts: "Small Worlds: The Dynamics of Networks Between Order and Randomness" Princeton Univ Press. Check it out on google.
•      Bossomaier & Green: "Complex systems" Cambridge Univ Press. Check it out on google.
•      Stocker: "Complex Systems: From Local Interactions to Global Phenomena" IOS Press. Check it out on google.
•      Kelso: "Dynamic Patterns: The Self-Organization of Brain and Behavior" MIT Press. Check it out on google.
•      Kauffman: "At Home in the Universe: The Search for Laws of Self-organization and Complexity" Oxford Univ Press. Check it out on google.


Papers (reviews):
•      Barabasi & Oltvai "Network biology: understanding the cell's functional organization" Nature Reviews Genetics 5: 101ff PDF
•      Kell et al. "Metabolic footprinting and systems biology: the medium is the message" Nature Reviews Microbiology 3: 557ff PDF
•      Lemberger: "Systems biology in human health and disease" Molecular Systems Biology 3:136
•      Nedelec et al. "Self-organisation and forces in the microtubule cytoskeleton" Current Opinion in Cell Biology 15: 118-124 PDF
•      Trianni & Dorigo: "Self-organisation and communication in groups of simulated and physical robots" Biol Cybern 95: 213-231 PDF
•      Bonabeau et al.: "Self-organization in social insects" TREE 12: 188ff PDF
•      Boomsma & Franks: "Social insects: from selfish genes to self organisation and beyond" TREE 21: 303ff PDF
•      Kitano: "Computational systems biology" Nature 420: 206ff PDF
•      Stumpf et al. "Evolution at the system level: the natural history of protein interaction networks" TREE 22: 366ff PDF
•      Proulx et al. "Network thinking in ecology and evolution" TREE 20: 345ff PDF
•      Sweetlove & Fernie "Regulation of metabolic networks: understanding metabolic complexity in the systems biology era" New Phytologist 168: 9-24 PDF
•      May: "Network structure and the biology of populations" TREE 21: 394ff PDF
•      Sporns et al.: "Organization, development and function of complex brain networks" Trends in Cognitive Sciences 8: 418ff PDF
•      Van der Meer: "Metabolic theories in ecology" TREE 21: 136ff PDF
•      Woodward et al.: "Body size in ecological networks" TREE 20: 402ff PDF


Papers (original studies):
Molecular:
•      Ma et al.: "The Edinburgh human metabolic network reconstruction and its functional analysis" Molecular Systems Biology 3:135
•      Carlson: "Metabolic systems cost-benefit analysis for interpreting network structure and regulation" Bioinformatics 23: 1258-1264

Cellular:
•      Glade et al. "Microtubule self-organisation by reaction-diffusion processes causes collective transport and organisation of cellular particles" BMC Cell Biology 5: 23 PDF
•      Van Orden et al. "Self-Organization of Cognitive Performance" J Exp Psych 132: 331-350 PDF
•      Turrigiano & Nelson "Homeostatic plasticity in the developing nervous system" Nature Reviews Neuroscience 5: 97ff PDF
•      Sole & Valverde: "Are network motifs the spandrels of cellular complexity?" TREE 21: 419ff PDF

Organismal:
•      Hemelrijk & Wantia "Individual variation by self-organisation" Neuroscience and behavioral reviews 29: 125-136 PDF

Ecosystem:
•      Green et al.: "Connectivity and catastrophe - towards a general theory of evolution" PDF

Modelling:
•      Barabasi & Albert: "Emergence of Scaling in Random Networks" Science 286: 509-512 PDF
•      May: "Will a large complex system be stable?" Nature 238: 413-414
•      Sales-Pardo et al.: "Extracting the hierarchical organization of complex systems" PNAS 104 (39): 15224. (2007) PDF
•      Boccaletti et al.: "Complex networks: structure and dynamics" Physics reports PDF

Engineering & robotics:
•      Dobson et al. "Complex systems analysis of series of blackouts: Cascading failure, critical points, and self-organization" Chaos 17 PDF
•      Prehofer & Bettstetter "Self-Organization in Communication Networks: Principles and Design Paradigms" Advances in self-organizing networks PDF