Over the past several decades, research in animal models has advanced our understanding of the neurobiological underpinnings of substance use disorders. Influences on drug abuse liability are broad and multifaceted, and include environmental, genetic and epigenetic factors. A history of chronic drug use may also induce persistent changes in the brain that contribute to high rates of relapse. The collection of studies described herein serves to further our understanding of substance dependence across genetic, neural and behavioral scales. First, we apply systems approaches to characterize changes in the functional architecture of the brain following chronic opiate exposure. We relate these changes to patterns of interregional gene expression and identify regions of the brain that may drive opiate-induced alterations in the state of the brain. We then examine the influence of a common genetic variant on cellular physiology and behavior relevant to opiate abuse liability. Finally, we identify a potential novel therapeutic target for treating symptoms of withdrawal in a mouse model of nicotine dependence. This body of work contributes to our understanding of how genetics, behavior, and neural circuitry contribute to the initiation and maintenance of drug dependence and demonstrates the utility of a mouse model of nicotine dependence for assessing novel treatment approaches for substance use disorders.