Magnetic Tunnel Junctions (MTJs) consisting of two ferromagnetic layers separated by an insulator layer have attracted great interest due to their applications in magnetic read heads and potential applications in magnetic random access memory. Materials science plays an important role in the performance of the MTJs. The goal of this research was to focus on how the materials properties affect the tunneling magnetoresistance (TMR) of AlOx-based MTJs with (Co, Fe) electrodes. A method was developed to fabricate epitaxial (Co, Fe) (001) thin films on Si substrates using TiN buffer and a novel processing technique in order to achieve smooth interfaces between the electrode and the AlOx tunnel barrier. The (Co, Fe) thin films with other orientations, i.e. (110) and (211), were also grown on TiN buffered substrates of Si (111) and (011). Numerous MTJs with epitaxial bottom electrode were fabricated to investigate the effect of the materials properties of the (Co, Fe) electrode on the TMR of these junctions. A strain induced TMR enhancement was discovered, where the trend of increasing TMR of the MTJs is the same as that of the strain of the bottom electrode. The strain was originated from the lattice mismatch between (Co, Fe) electrode and the buffer layers in the MTJs, which will vary with annealing temperatures. Since the interface roughness and the barrier properties were the same within the uncertainties of the measurement, this TMR enhancement was attributed to the presence of strain. The TMR values were also compared for MTJs with the bottom electrode in the (001), (110) and (211) orientations. The anisotropic property of (Co, Fe) was confirmed and the (001) orientation has larger spin polarization than the (110) and (211) orientations. By careful manipulation of the bottom electrode, including strain, roughness and orientation, 77% TMR was obtained for AlOx-based MTJs. The phase transformation of Pt0.5-xMn0.5+x from fcc to Ll0 was investigated. The experimental results showed the onset temperature for phase transformation increase as the composition deviates from stoichiometry but slows down the kinetics of transformation.