Bioinformatics is of course a very huge field, and I'm trying to wrap my head around the different areas on which it touches, to get an overview of what is what. To being with, there are a whole number of -omics fields within this realm. As far as I've understood, there are the following fields:

• Epigenomics: the study of regulation of gene expression by DNA methylation, histone modification, etc. These processes largely determine which parts of the DNA will be transcribed.
• Genomics: the study of the genome itself, i.e. the DNA code of an organism. Some of this DNA, namely the exome regions, is transcribed into mRNA.
• Transcriptomics: the study of gene expression by looking at the RNA products of transcription from the genome. The mRNA fraction of this RNA is later translated into protein.
• Proteomics: the study of the proteins that are made. Some of these proteins function as enzymes that are involved in converting one metabolite into another.
• Metabolomics: the study of the metabolites involved in physiological processes.

First of all, how correct is this understanding? Secondly, my main question: what are the different bioinformatics methods that exist at each of these -omics levels? These are the ones that I have heard of:

• Epigenomics: ChIP-sequencing
• Genomics: whole genome sequencing. Exome sequencing (i.e. sequencing the portion of DNA that is to be transcribed).
• Transcriptomics: RNA-sequencing (sequencing the mRNA that has already been transcribed)

If this is too large a question to be asking (as I suspect that it probably is), do you know of any books or websites that target these questions directly?