Résumé : Boundary-layer transition from a laminar to a turbulent regime is a critical driver in the design of high-speed vehicles. The aerothermodynamic loads associated with transitional or fully turbulent hypersonic boundary layers are several times higher than those associated with laminar flow. The presence of isolated roughness elements on the surface of a body can accelerate the growth of incoming disturbances and introduce additional instability mechanisms in the flow field, eventually leading to a premature occurrence of transition. This dissertation studies the instabilities induced by three-dimensional discrete roughness elements located inside a high-speed boundary layer developing on a flat plate. Two-dimensional local linear stability theory (2D-LST) is employed to identify the instabilities evolving in the three-dimensional flow field that characterizes the wake induced by the roughness elements and to investigate their evolution downstream. A formulation of the disturbance energy evolution equation available for base flows depending on a single spatial direction is generalized for the first time to base flows featuring two inhomogeneous directions and perturbations depending on three spatial directions. This generalization allows to obtain a decomposition of the temporal growth rate of 2D-LST instabilities into the different contributions that lead to the production and dissipation of the total disturbance energy. This novel extension of the formulation provides an additional layer of information for understanding the energy exchange mechanisms between a three-dimensional base flow and the perturbations resulting from 2D-LST. Stability computations for a calorically perfect gas illustrate that the wake induced by the roughness elements supports the growth of different sinuous and varicose instabilities which coexist together with the Mack-mode perturbations that evolve in the flat-plate boundary layer, and which become modulated by the roughness-element wake. A single pair of sinuous and varicose disturbances is found to dominate the wake instability in the vicinity of the obstacles. The application of the newly developed decomposition of the temporal growth rate reveals that the roughness-induced wake modes extract most of their potential energy from the transport of entropy fluctuations across the base-flow temperature gradients and most of their kinetic energy from the work of the disturbance Reynolds stresses against the base-flow velocity gradients. Further downstream, the growth rate of the wake instabilities is found to be influenced by the presence of Mack-mode disturbances developing on the flat plate. Strong evidence is observed of a continuous synchronization mechanism between the wake instabilities and the Mack-mode perturbations. This phenomenon leads to an enhancement of the amplification rate of the wake modes far downstream of the roughness element, ultimately increasing the associated integrated amplification factors for some of the investigated conditions. The effects of vibrational molecular excitation and chemical non-equilibrium on the instabilities induced by a roughness element are studied for the case of a high-temperature boundary layer developing on a sharp wedge configuration. For this purpose, a 2D-LST solver for chemical non-equilibrium flows is developed for the first time, featuring a fully consistent implementation of the thermal and transport models employed for the base flow and the perturbation fields. This is achieved thanks to the automatic derivation and implementation tool (ADIT) available within the von Karman Institute extensible stability and transition analysis (VESTA) tool-kit, which enables an automatic derivation and implementation of the 2D-LST governing equations for different thermodynamic flow assumptions and models. The stability computations for this configuration show that sinuous and varicose disturbances also dominate the wake instability in the presence of vibrational molecular energy mode excitation and chemical reactions. The resulting base-flow cooling associated with the modeling of such high-temperature phenomena is found to have opposite stabilizing and destabilizing effects on the streamwise evolution of the sinuous and varicose instabilities. The modeling of vibrational excitation and chemical non-equilibrium acting exclusively on the perturbations is found to have a stabilizing influence in all cases.