Roded Sharan, Tel Aviv University, Israel

Elucidating the topology and logic of cellular pathways
A fundemantal problem in network biology is to infer the signaling-regulatory pathways that underlie a process of interest. This inference task starts with elucidating the topology of the pathway, continues with assigning directions and influence signs to its interactions and ends with a full logical model that describes its workings. In this set of talks we will review methods for network reconstruction, orientation, sign assignment and Boolean modeling. We will demonstrate the applications of these methods to decipher disease mechanisms and drug response pathways.

Reading list: (provided as links to the papers)
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002690
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0045969
http://link.springer.com/chapter/10.1007/978-3-642-33122-0_27
http://www.ncbi.nlm.nih.gov/pubmed/22300318
http://dl.acm.org/citation.cfm?id=2247426.2247454
http://www.ncbi.nlm.nih.gov/pubmed/19953085
http://stke.sciencemag.org/cgi/content/abstract/4/196/pl1
http://projecteuclid.org/DPubS?service=UI&version=1.0&verb=Display&handle=euclid.im/1323367278
http://online.liebertpub.com/doi/full/10.1089/cmb.2011.0163
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000641
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000635
http://www.ncbi.nlm.nih.gov/pubmed/15285891
http://www.nature.com/msb/journal/v5/n1/full/msb20093.html
http://www.nature.com/ng/journal/v41/n3/abs/ng.337.html
http://genome.cshlp.org/content/18/4/644.long
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3159979/