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As @Corvus said before me, the core of your post talks about mathematical modelling of host-pathogen interactions. The title talks about analyzing omics data. What are you really interested in? I will assume you are interested in modelling of host-pathogen interactions (as @Corvus did). I agree with @Corvus (+1) that Modeling infectious diseases and humans ...


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I'm a bit confused because your title and your question description don't seem to align perfectly (-omics data versus host-pathogen interactions). If you are interested in host-pathogen dynamics, in my opinion, the best general introductory text in this area is Keeling and Rohani Modeling infectious diseases and humans and animals.


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You are a bit confused with your terms here. Remember, when you are talking about natural regulation of a transcriptome, you can control it at the level of the genome, transcriptome and the epigenome. The Repressor protein is a DNA- or RNA-binding protein that inhibits the expression of one or more genes by binding to the operator or associated silencers. ...


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In general, a read simulator does the following: Selects regions from a reference sequence with some sort of predefined or user-specified size distribution. Converts the sequence from those regions into single or paired end reads with quality scores. The quality scores and read lengths are typically user defined. Introduces errors into the aforementioned ...



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