| Date | Topic | Assignments/Further reading | HWs/Notes |
| March 28 | Intro to course and to networks. (Lecture 1) | Newman 1-19 | |
| April 2 | Random graphs and phase transitions. (Lecture 2) | Newman 20-25, Durrett Ch 1 & 2 | |
| April 4 | Power laws and preferential attachment. (Lecture 3) | BA (1999) Science article, Newman 30-35, Durrett Ch 4 | |
| April 9 | Exploring Robustness of Networks. (Lecture 4) Online reference materials (Including Rcode and sample Graphviz input files). | AJB (2000) Nature article Doyle, et al (2005) PNAS article | |
| April 11 | Optimization and network growth. (Lecture 5) | D'Souza, et al (2007) PNAS article | HW 1 assigned |
| April 16 | Software tools for network analysis. (Lecture 6) | bioconductor.org, help: Rgraphviz on Mac OSX, Documentation for package `Rgraphviz', Tutorial (if you actually get Rgraphviz working) | Bibliography to get you started with class project |
| April 18 | No Lecture |  | |
| April 23 | Social Network Analysis and Paritioning of Networks (Spectral methods) (Lecture 7) | (See refs in notes) | |
| April 25 | Spectral methods (cont), and mixing (Lecture 8) Online reference materials (Including Rcode). | (See refs in notes) | HW1 due |
| April 30 | Web search and decentralized search on small-worlds (Lecture 9) | (See refs in notes) | HW 2 assigned |
| May 2 | Percolation and spreading on networks (SIR and SIS models) (Lecture 10) | In-class discussion of project | |
| May 7 | 2 views of Biological Networks: (Almaas ppt), (Nuzhdin doc) | Eivind Almaas Sergey Nuzhdin | |
| May 9 | No lecture | ||
| May 14 | Flows on real-world networks (Lecture 12) Gastner.pdf, Zhang.ppt | ||
| May 16 | Genetic networks in plants: co-expression, regulation, oscillation networks kazu.ppt, jose.ppt | Kazunari Nozue (Rhythmic growth) and Jose Jimenez-Gomez (Light response) | HW2 due |
| May 21 | Guest Lecture yuan.ppt | Lihua Yuan, DNS Hierarchy structure and attack vulnerabilities | |
| May 23 | Community structure in networks | Dr. Soumen Roy UCD Comp Sci & Eng | RD at NetSci2007 |
| May 28 | Holiday (no class) | ||
| May 30 | Microarray data and statistical inference pollard.pdf (13 MB) | Prof. Katie Pollard UCD Dept of Statistics | |
| June 4 | Class review and student presentations (Lecture 17) | ||
| June 6 | Student presentations | Class Project Due! (Mon June, 11) | Basic template for final project |