| . | Name | Email address | Office hours |
| Instructor | Luay K. Nakhleh | nakhleh@cs.rice.edu | by appointment, DH 3119 |
| Teaching Assistant | Yun Yu | yy9@cs.rice.edu | by appointment, DH 3117 |
| Slides Set # | Topic | Slides | Additional material |
| 1 | Introduction to the course | Network Analysis Resources | |
| 2 | Sequence alignment and phylogenetic trees: A (very) brief overview | ||
| 3 | Introduction to systems biology | ||
| 4 | Graphical models: Graphs, Boolean, and Bayesian networks | Bayesian Networks Primer, GRN Modeling Review | |
| 5 | Graphical models: Petri nets | The Heiner et al. survey | |
| 6 | Kinetic modeling of cellular processes with an application to gene regulation | ODEs in Matlab (courtesy of P. Howard), The Kuznetsov et al. paper | |
| 7 | Dynamics of regulatory networks: Basic building blocks | Tyson et al., (2003) | |
| 8 | Graph-theoretic properties of networks | Newman's survey; Community detection in graphs | |
| 9 | Graph-theoretic properties of biological networks | ||
| 10 | Network motifs | ||
| 11 | Comparative network analysis | ||
| 12 | Elucidating network properties from stoichiometric matrices | Schilling et al. paper | |
| 13 | Flux balance analysis |