Parasitic contact resistance increasingly limits modern CMOS performance. Atomistic scale features and quantum effects play an important role in determining silicide-silicon contact properties. We develop ab initio quantum transport simulation capabilities for silicide-silicon contacts, which provide first principle descriptions of interfacial structural, electronic, and transport properties. It is found that transmission through the CoSi2-Si contact of the primed valleys can be distinctively different from that of the unprimed valleys, due to the size of the CoSi2 Fermi surface. Interfacial atomistic doping can modulate the barrier height, but, at the same time, lower the transmission and induce localized bandgap states. The primary effect of strain is to modulate the barrier height instead of quantum transmission. The physical insights obtained here would not have been possible by tight binding simulations, where reliable interface binding parameters lack.