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Advances in human and mouse genomes are revolutionizing research in lung biology and pulmonary medicine. Genomic strategies are available that link functional variation to molecular structure, and these approaches are currently being applied to the study of ventilatory control mechanisms. In this review, the author discusses the functional data obtained from inbred murine models in which genetic mutations and polymorphisms play a role in altered breathing. At the conclusion of this review, the author emphasizes the relatively small number of studies that have incorporated the use of genomics to link differential ventilatory function to molecular structure.