MAE 298, Winter 2008
Network Theory and Applications
Class schedule and lectures (SUBJECT TO CHANGE)

Date Topic Assignments/Further readingHWs/Notes
Jan 7 Intro to course and to networks. (Lecture 1) Newman 1-19
Jan 9Random graphs and phase transitions. (Lecture 2) Newman 20-25, Durrett Ch 1 & 2
Jan 14Power laws and preferential attachment. (Lecture 3) -BA (1999) Science, Newman 30-35, Durrett Ch 4
Jan 16Exploring 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 21MLK Holiday (no class)
Jan 23Optimization and network growth. (Lecture 5) -D'Souza, et al (2007) PNAS
-Gastner and Newman, (2006) Phys Rev E
(for starting on class project)
Jan 28Percolation 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 30Epidemiology (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 4Web search (Lecture 8)
Feb 6Decentralized search on small-worlds (Lecture 9)

"Network Theory for Biologists"
(From CS177 Introduction to Bioinformatics, GWU)

-Watts and Strogatz (1998) Nature
-Kleinberg (2000) Nature
-Milo, et al (2002) Science (Network motifs)
Feb 11Community structure in networks (Lecture 10)Dr. Soumen Roy
UCD Comp Sci & Eng
Feb 13In-class discussion of project (hand-in) HW2 due (date change)
HW3 assigned
Feb 18President's Holiday (no class)
Feb 20Flows on spatial networks (Lecture 11)
worldmapper.orgHW1 soln
Feb 25Flows on networks II (Lecture 12)
-M. Kurant and P. Thiran (2006) Phys Rev Lett
-David Aldous page
Feb 272 views of Biological Networks (and sign-up for presentation)
(Almaas ppt), (Nuzhdin doc)
HW3 due
Mar 3Spectral methods and applications to self-organizing networks (Lecture 14)

Online reference materials (Including Rcode).

-Dan Spielman's Spectral Graph Theory Course
Mar 5Prof. Julin Maloof
Microarrays and Genetic Regulatory Networks (Lecture 15)
Mar 10Model selection (Lecture 16)
Student presentations
-Middendorf, et al (2005) PNAS
-SCHEDULE of presentations
Mar 12Student presentations
Mar 17Student presentations Class Project Due! Basic template for final project