Editing Bacteriophage (section)

== Systems biology ==
The field of [[systems biology]] investigates the complex [[Biological network|networks of interactions]] within an organism, usually using computational tools and modeling.<ref name="Klipp_2009">{{cite book|title=Systems biology: a textbook|date=2009|publisher=Wiley-VCH| vauthors = Klipp E |isbn=978-3-527-31874-2|location=Weinheim|oclc=288986435}}</ref> For example, a phage genome that enters into a bacterial host cell may express hundreds of phage proteins which will affect the expression of numerous host genes or the host's [[metabolism]]. All of these complex interactions can be described and simulated in computer models.<ref name="Klipp_2009" />

For instance, infection of ''[[Pseudomonas aeruginosa]]'' by the temperate phage PaP3 changed the expression of 38% (2160/5633) of its host's genes. Many of these effects are probably indirect, hence the challenge becomes to identify the direct interactions among bacteria and phage.<ref name="pmid26750429">{{cite journal | vauthors = Zhao X, Chen C, Shen W, Huang G, Le S, Lu S, Li M, Zhao Y, Wang J, Rao X, Li G, Shen M, Guo K, Yang Y, Tan Y, Hu F | title = Global Transcriptomic Analysis of Interactions between Pseudomonas aeruginosa and Bacteriophage PaP3 | journal = Scientific Reports | volume = 6 | page = 19237 | date = January 2016 | pmid = 26750429 | pmc = 4707531 | doi = 10.1038/srep19237 | bibcode = 2016NatSR...619237Z }}</ref>

Several attempts have been made to map [[protein–protein interaction]]s among phage and their host. For instance, bacteriophage lambda was found to interact with its host, [[Escherichia coli|''E. coli'']], by dozens of interactions. Again, the significance of many of these interactions remains unclear, but these studies suggest that there most likely are several key interactions and many indirect interactions whose role remains uncharacterized.<ref name="pmid24049175">{{cite journal | vauthors = Blasche S, Wuchty S, Rajagopala SV, Uetz P | title = The protein interaction network of bacteriophage lambda with its host, Escherichia coli | journal = Journal of Virology | volume = 87 | issue = 23 | pages = 12745–12755 | date = December 2013 | pmid = 24049175 | pmc = 3838138 | doi = 10.1128/JVI.02495-13 }}</ref>