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A variety of life functions and cognitive processes (CPs) have been identified in cognitive informatics, psychology, cognitive science, and neurophilosophy. This paper attempts to develop a layered reference model of the brain (LRMB) that formally and rigorously explains the functional mechanisms and CPs of natural intelligence. A comprehensive and coherent set of mental processes and their relationships is identified in LRMB that encompasses 37 CPs at six layers known as the sensation, memory, perception, action, metacognitive, and higher cognitive layers from the bottom-up. The LRMB reference model provides an integrated framework for modeling the brain and the mind. LRMB also enables future extension and refinement of the CPs within the same hierarchical framework. LRMB can be applied to explain a wide range of physiological, psychological, and cognitive phenomena in cognitive informatics, particularly the relationships and interactions between the inherited and the acquired life functions, as well as those of the subconscious and conscious CPs.