The field of psychiatry is approaching a major inflection point. The basic science behind cognition, emotion, behavior and social processes has been advancing rapidly in the past 20 years. However, clinical research supporting the classification system in psychiatry has not kept up with these scientific advances. In order to begin organizing the basic science of psychiatry in a comprehensive manner, we begin by selecting fragile X syndrome (FraX), a neurogenetic disease with cognitive-behavioral manifestations, to illustrate key concepts in an integrative, multi-dimensional model. Specifically, we will describe key genetic and molecular mechanisms (e.g. GABAergic dysfunction and mGluR5-associated long-term depression) relevant to the pathophysiology of FraX, as well as neural correlates of cognitive-behavioral symptoms. We will then describe what we have learned from FraX, which may be applicable to other psychiatric disorders. We conclude the article by discussing on-going and future opportunities in both diagnosing and treating psychiatric diseases in the future.