Summary: PHYS 597A: Graphs and networks in systems biology
Project assignment 1, due Tuesday March 16
It is now time to decide your term project topics. As a reminder, you
will give an in-class presentation on your projects during the last two weeks
of the semester, and write a paper due on the Monday after classes end.
Two types of papers are envisioned
(i) A comprehensive and critical review of the literature on a network-
related topic. For example, a review of search problems in networks, a re-
view of constructing protein-protein interaction networks and analyzing their
properties, a review of dynamic modeling of biological networks etc.
(ii) The development of a new network model or method that either
combines previous ideas in a novel way or proposes new ideas for network
modeling. The model should be analyzed with the methods learned in class,
and compared to other models or real systems.
(iii) An original project that is related to networks and to your thesis
research. For example, it could be the construction of an interaction network
for a biological process or social organization, analysis of its properties and/or
modeling of its dynamics.
The goal of this assignment is to help you select your research topic. A
list of topics is given below. For each topic several leads (papers, websites)