|Professor: William Bechtel||Office Hours: Wednesday, 3:30-4:50|
|Office: HSS 8076||Email: email@example.com|
|Telephone: 822-4461||Wiki site: http://mechanism.ucsd.edu:8080/Networks|
Network theorizing is playing a major role in a wide range of disciplines, from cell and molecular biology to the social sciences. This course will explore the various roles network theorizing is playing across this range of disciplines, with the goals of discovering whether there are common principles and how different disciplines might gain from the insights developed in the others.
Cog Sci. 200 is structured around a series of lectures. These lectures are open to the entire UCSD communiity, but they are invited for the course and students in the course are encouraged to be active in the discussions at the lectures. As preparation for the lectures, we will meet for an hour before the lecture and discuss papers relevant to the topic of the lecture.
Topic of Talk
No lecture: Class goes until 4:30
|William Bechtel, Philosophy, UCSD||Basics of network analysis||1. Watts, D., & Strogratz, S. (1998). Collective dynamics of small worlds. Nature, 393, 440-442.
2. Barabási, A.-L., & Bonabeau, E. (2003). Scale-free networks. Scientific American, 50-59.
3. Alon, U. (2007). Network motifs: Theory and experimental approaches. Nature Reviews Genetics, 8, 450-461.
|January 15||Trey Ideker, UCSD Department of Medicine and||Biomolecular networks||1. Hofree, M., Shen, J. P., Carter, H., Gross, A., & Ideker, T. (2013). Network-based stratification of tumor mutations. Nature Methods, 10, 1108-1115.
2. Dutkowski, J., Kramer, M., Surma, M. A., Balakrishnan, R., Cherry, J. M., Krogan, N. J., & Ideker, T. (2013). A gene ontology inferred from molecular networks. Nat Biotechnol, 31, 38-45.
|January 22||Hannah Carter, UCSD, Department of Medicine||Disease networks||1. Engin, H. B., Hofree, M., & Carter, H. (2015). Identifying mutation specific cancer pathways using a structurally resolved protein interaction network. Pac Symp Biocomput, 84-95.
|January 29||Gary Cottrell, Computer Science and Engineering, UCSD||Artificial neural networks||
1. McClelland, J. L., & Rumelhart, D. E. (1981). An Interactive Activation Model of Context Effects in Letter Perception: Part I. An Account of Basic Findings. Psychological Review, 88, 375-407.
|February 5||Lev Tsimring, BioCircuits Institute, UCSD||Synthetic gene networks||1. Ahmad S. Khalil & James J. Collins. Synthetic biology: applications come of age. Nature Reviews Genetics 11, 367-379 (May 2010).
2. Adrian L. Slusarczyk, Allen Lin & Ron Weiss. Foundations for the design and implementation of synthetic genetic circuits. Nature Reviews Genetics 13, 406-420 (June 2012).
3. Tal Danino, Octavio Mondragón-Palomino, Lev Tsimring & Jeff Hasty. A synchronized quorum of genetic clocks. Nature 463, 326-330 (21 January 2010).
|February 12||Andrea Chiba, Cognitive Science and Neurosciences, UCSD||Brain networks||1. Chiba, A. A., & Quinn, K. L. (2008). Basal forebrain and memory. In H. Eichenbaum (Ed.), Memory systems (Vol. 3 of Learning and memory: A comprehensive reference, pp. 281-302). Oxford: Elsevier.|
|February 19||Bradley Voytek, Cognitive Science, UCSD||Coordinated oscillations in brain networks||
1. Buzsaki, G., & Draguhn, A. (2004). Neuronal Oscillations in Cortical Networks. Science, 304, 1926-1929.
|February 26||No meeting|
|March 4||Noa Pinter-Wollman, BioCircuits Institute, UCSD||Agent networks||1. Pinter-Wollman, N., Wollman, R., Guetz, A., Holmes, S., & Gordon, D. M. (2011). The effect of individual variation on the structure and function of interaction networks in harvester ants. J R Soc Interface, 8, 1562-1573.
2. Pinter-Wollman, N., Hobson, E. A., Smith, J. E., Edelman, A. J., Shizuka, D., de Silva, S., Waters, J. S., Prager, S. D., Sasaki, T., Wittemyer, G., Fewell, J., & McDonald, D. B. (2014). The dynamics of animal social networks: analytical, conceptual, and theoretical advances. Behavioral Ecology, 25, 242-255.
3. Pinter-Wollman, N. (2015). Nest architecture shapes the collective behaviour of harvester ants. Biol Lett, 11.
|March 11||Massimo Franceschetti, Electrical and Computer Engineering, UCSD||Social networks||
1. Coviello, L., Fowler, J. H., & Franceschetti, M. (2014). Words on the Web: Noninvasive Detection of Emotional Contagion in Online Social Networks. Proceedings of the Ieee, 102, 1911-1921.
This course should be taken for S/U grade only. If there is some reason you need a letter grade, you must tell me at the outset and get my approval. Note: If you are taking the course for a letter grade, the research paper is not optional.
Students are required to: