Great primer on network theory MT @russskinner PRISM… analysis: Paul Revere identified by his connections to others http://bit.ly/11DK8R9
http://www.slate.com/articles/health_and_science/science/2013/06/prism_metadata_analysis_paul_revere_identified_by_his_connections_to_other.single.html
a detailed comparison of
MetaCyc versus KEGG:
MetaCyc contains more than 10 times as many metabolic pathways as KEGG “modules” (the comparable type of pathway in KEGG).
http://www.biomedcentral.com/1471-2105/14/112/abstract
http://www.ncbi.nlm.nih.gov/pubmed/17369648
Comput Syst Bioinformatics Conf. 2006:299-310.
Evolution versus “intelligent design”: comparing the topology of protein-protein interaction networks to the Internet.
Yang Q, Siganos G, Faloutsos M, Lonardi S.
http://dx.doi.org/10.1016/j.bpj.2013.01.033
Cross Talk and Interference Enhance Information Capacity of a Signaling Pathway Sahand Hormoz
QT:”
A recurring motif in gene regulatory networks is transcription factors (TFs) that regulate each other and then bind to overlapping sites on DNA, where they interact and synergistically control transcription of a target gene. Here, we suggest that this motif maximizes information flow in a noisy network. Gene expression is an inherently noisy process due to thermal fluctuations and the small number of molecules involved. A consequence of multiple TFs interacting at overlapping binding sites is that their binding noise becomes correlated. Using concepts from information theory, we show that in general a signaling pathway transmits more information if 1), noise of one input is correlated with that of the other; and 2), input signals are not chosen independently.
“
QT:” looked at the entire human metabolic network and found that concentrations of about 10 percent of the body’s 2,763 metabolites could be used to determine the levels of all the rest.”
http://www.scientificamerican.com/article.cfm?id=influential-few-predict-behavior
used the singlish/multi concept. Then used machine learning to predict whether a protein is singlish or multi
PLOS ONE
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056833
Taner Z. Sen