| Date | Topic | Assignments/Further reading | HWs/Notes |
| Jan 7 | Intro to course and to networks. (Lecture 1) | Newman 1-19 | |
| Jan 9 | Random graphs and phase transitions. (Lecture 2) | Newman 20-25, Durrett Ch 1 & 2 | |
| Jan 14 | Power laws and preferential attachment. (Lecture 3) | -BA (1999) Science, Newman 30-35, Durrett Ch 4 | |
| Jan 16 | Exploring Robustness of Networks. (Lecture 4) Online reference materials (Including Rcode and sample Graphviz input files). | -AJB (2000) Nature -Doyle, et al (2005) PNAS | HW 1 assigned |
| Jan 21 | MLK Holiday (no class) | ||
| Jan 23 | Optimization and network growth. (Lecture 5) | -D'Souza, et al (2007) PNAS -Gastner and Newman, (2006) Phys Rev E | Bibliography (for starting on class project) |
| Jan 28 | Percolation and spreading on networks (SIR and SIS models) (Lecture 6) In-class open discussion. | -Callaway, etal (2000) Phys Rev Lett -Pastor-Satorras and Vespignani (2001) Phys Rev Lett | HW 1 due, HW 2 assigned |
| Jan 30 | Epidemiology (final details), Social Network Analysis and Mixing (Lecture 7) In-class discussion of project. | -Hanneman and Riddle Intro to social network methods -Netdraw, network visualization | |
| Feb 4 | Web search (Lecture 8) | ||
| Feb 6 | Decentralized search on small-worlds (Lecture 9)
"Network Theory for Biologists" | -Watts and Strogatz (1998) Nature -Kleinberg (2000) Nature -Milo, et al (2002) Science (Network motifs) | |
| Feb 11 | Community structure in networks (Lecture 10) | Dr. Soumen Roy UCD Comp Sci & Eng | |
| Feb 13 | In-class discussion of project (hand-in) | HW2 due (date change) HW3 assigned | |
| Feb 18 | President's Holiday (no class) | ||
| Feb 20 | Flows on spatial networks (Lecture 11) Gastner.pdf | worldmapper.org | HW1 soln |
| Feb 25 | Flows on networks II (Lecture 12) Zhang.ppt | -M. Kurant and P. Thiran (2006)
Phys Rev Lett -David Aldous page | |
| Feb 27 | 2 views of Biological Networks (and sign-up for presentation) (Almaas ppt), (Nuzhdin doc) | HW3 due | |
| Mar 3 | Spectral methods and applications to self-organizing networks (Lecture 14) Online reference materials (Including Rcode). | -Dan Spielman's Spectral Graph Theory Course | |
| Mar 5 | Prof. Julin Maloof Microarrays and Genetic Regulatory Networks (Lecture 15) | ||
| Mar 10 | Model selection (Lecture 16) Student presentations |
-Middendorf, et al (2005) PNAS -SCHEDULE of presentations | |
| Mar 12 | Student presentations | ||
| Mar 17 | Student presentations | Class Project Due! | Basic template for final project |