We describe current research that applies epigenetics to a novel understanding 
of the immuno-neuropathogenesis of HIV-1 viral infection and NeuroAIDS. We 
propose the hypothesis that HIV-1 alters the structure-function relationship of 
chromatin, coding DNA and non-coding DNA, including RNA transcribed from these 
regions resulting in pathogenesis in AIDS, drug abuse, and NeuroAIDS. We discuss 
the general implications of molecular epigenetics with special emphasis on drug 
abuse, bar-codes, pyknons, and miRNAs for translational and clinical research. 
We discuss the application of the recent recursive algorithm of biology to this 
field and propose to synthesize the Genomic and Epigenomic views into a holistic 
approach of HoloGenomics.