Mechanical loading is a potent anabolic stimulus that substantially strengthens bones, and the time course of bone formation after initiating mechanical loading is well characterized. However, the time sequence for gene expression, the time sequence for regulatory activities, and the extent of alternative splicing in a bone subjected to mechanical loading have not been studied genome-wide over an extended period of time. The overall objective of this work was to incorporate high-throughput measurements of gene and exon expression and various bioinformatics approaches to study loading-induced gene expression patterns, regulatory mechanisms, and alternative splicing across time. A standard model for bone loading was employed to evaluate genome-wide, loading-induced gene expression over a time course of 4 hours to 32 days. Time-dependent patterns of gene expression were identified over the time course and categorized into clusters. Next, the gene expression data were analyzed to determine which regulatory factors most likely regulated gene expression over the time course. Finally, exon level data were analyzed to evaluate the extent of alternative splicing. The work in this dissertation aids our understanding of the time-dependent sequence of events that occurs in response to loading and ultimately results in bone formation, and is necessary to comprehend bone biology and mechanotransduction at a systems level.