Theories of planet formation predict the birth of giant planets in the inner, dense, and gas-rich regions of the circumstellar disks around young stars. These are the regions from which strong CO emission is expected. Observations have so far been unable to confirm the presence of planets caught in formation. We have developed a novel method to detect a giant planet still embedded in a circumstellar disk by the distortions of the CO molecular line profiles emerging from the protoplanetary disk's surface. The method is based on the fact that a giant planet significantly perturbs the gas velocity flow in addition to distorting the disk surface density. We have calculated the emerging molecular line profiles by combining hydrodynamical models with semianalytic radiative transfer calculations. Our results have shown that a giant Jupiter-like planet can be detected using contemporary or future high-resolution near-IR spectrographs such as VLT/CRIRES or ELT/METIS. We have also studied the effects of binarity on disk perturbations. The most interesting results have been found for eccentric circumprimary disks in mid-separation binaries, for which the disk eccentricity - detectable from the asymmetric line profiles - arises from the gravitational effects of the companion star. Our detailed simulations shed new light on how to constrain the disk kinematical state as well as its eccentricity profile. Recent findings by independent groups have shown that core-accretion is severely affected by disk eccentricity, hence detection of an eccentric protoplanetary disk in a young binary system would further constrain planet formation theories.