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=== Human and pathogen transcriptomes ===
RNA-Seq of human [[pathogen]]s has become an established method for quantifying gene expression changes, identifying novel [[virulence factors]], predicting [[Antimicrobial resistance|antibiotic resistance]], and unveiling [[Host–pathogen interaction|host-pathogen immune interactions]].<ref name="#18284925">{{cite journal | vauthors = Wu HJ, Wang AH, Jennings MP | title = Discovery of virulence factors of pathogenic bacteria | journal = Current Opinion in Chemical Biology | volume = 12 | issue = 1 | pages = 93–101 | date = February 2008 | pmid = 18284925 | doi = 10.1016/j.cbpa.2008.01.023 | url = http://ntur.lib.ntu.edu.tw/bitstream/246246/219228/-1/26.pdf }}</ref><ref name="#25517437">{{cite journal | vauthors = Suzuki S, Horinouchi T, Furusawa C | title = Prediction of antibiotic resistance by gene expression profiles | journal = Nature Communications | volume = 5 | pages = 5792 | date = December 2014 | pmid = 25517437 | pmc = 4351646 | doi = 10.1038/ncomms6792 | bibcode = 2014NatCo...5.5792S }}</ref> A primary aim of this technology is to develop optimised [[infection control]] measures and targeted [[Personalized medicine|individualised treatment]].<ref name="#26996076" />
Transcriptomic analysis has predominantly focused on either the host or the pathogen. Dual RNA-Seq has been applied to simultaneously profile RNA expression in both the pathogen and host throughout the infection process. This technique enables the study of the dynamic response and interspecies [[gene regulatory network]]s in both interaction partners from initial contact through to invasion and the final persistence of the pathogen or clearance by the host immune system.<ref name="#22890146">{{cite journal | vauthors = Westermann AJ, Gorski SA, Vogel J | title = Dual RNA-seq of pathogen and host | journal = Nature Reviews. Microbiology | volume = 10 | issue = 9 | pages = 618–30 | date = September 2012 | pmid = 22890146 | doi = 10.1038/nrmicro2852 | s2cid = 205498287 | url = https://opus.bibliothek.uni-wuerzburg.de/files/11246/Dissertation_Westermann_Alexander.pdf }}</ref><ref name="#25914674">{{cite journal | vauthors = Durmuş S, Çakır T, Özgür A, Guthke R | title = A review on computational systems biology of pathogen-host interactions | journal = Frontiers in Microbiology | volume = 6 | pages = 235 | date = 2015 | pmid = 25914674 | pmc = 4391036 | doi = 10.3389/fmicb.2015.00235 | doi-access = free }}</ref>
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