id	author	title	date	pages	extension	mime	words	sentences	flesch	summary	cache	txt
cord-341879-vubszdp2	Li, Lucy M	Genomic analysis of emerging pathogens: methods, application and future trends	2014-11-22		.txt	text/plain	5029	253	36	In this review, we evaluate methods that exploit pathogen sequences and the contribution of genomic analysis to understand the epidemiology of recently emerged infectious diseases. In this review, we provide an overview of recent developments in genomic methods in the context of infectious diseases, evaluate integrative methods that incorporate genetic data in epidemiological analysis, and discuss the application of these methods to EIDs. Over the last two decades, sequence data have increased in quality, length and volume due to improvements in the underlying technology and decreasing costs. In recent cases of EIDs, genomic data have helped to classify and characterize the pathogen, uncover the population history of the disease, and produce estimates of epidemiological parameters. Just as compartmental models can be fitted to surveillance data to infer the epidemiological dynamics of an infectious disease (Box 1), the coalescent framework allows inference of population history from pathogen sequences.	./cache/cord-341879-vubszdp2.txt	./txt/cord-341879-vubszdp2.txt