His research interests are focused on understanding high-energy astrophysical sources gathering data from radio to VHE, as well as modeling emission processes in different scenarios, which can lead to major progress in our knowledge about particle acceleration processes and radiation mechanisms in the Universe. At the beginning of his scientific career, he was involved in the ESA Hipparcos Mission as an optical observer in the Input Catalogue Consortium and worked in identifying and monitoring radio stars for the Task Linking the Hipparcos frame to an extragalactic frame. High-resolution radio interferometric observations (VLBI) of some of these radio stars carried out in close collaboration with his colleagues and students, lead in 1993 to the discovery of jets in LSI+61303, being one of the first cases that relativistic jets were associated with stars. Another of these selected stars was Cygnus X-3, of which his student and he modeled satisfactorily the first historical strong radio outburst covering two decades in frequency and later observed with the VLA the development of a two-sided relativistic jet. These results allowed us to better understand the physical processes that occur in these sources and allowed us to make predictions about the possibility that emit gamma-rays.

Since 2000 he has been studying the sources of High Energy (HE) and Very High Energy (VHE) gamma-rays in the Milky Way with a multi-wavelength approach. His group comprises scientists with contrasted expertise in multi-wavelength observations from radio to VHEs, theoretical astrophysical developments, and data processing techniques. The observational part of his research has involved many first-class ground-based and space-borne instruments, including both planned and target-of-opportunity observations of transient and unpredictable phenomena.

His most relevant work was the discovery of an X-ray binary system (LS 5039) with persistent HE gamma-ray emission, implying the existence of a new type of gamma-ray emitting galactic sources (Paredes et al. 2000, Science 288, 2340). This work was cited among the Scientific Highlights of the report presented at the IAU General Assembly in Sydney (2003) and he received the City of Barcelona 2000 Award for scientific research.

In 2006 he was prominently involved in the discovery of variable VHE gamma-ray emission from the X-ray binary LS I +61 303 using the MAGIC telescope (Albert et al.2006, Science 312, 1771). He contributed to the discovery of the first Be X-ray binary system containing a black hole (Casares et al. 2014, Nature, 505, 378). This is a key system with broad implications in many areas of Astrophysics, such as the study of Be X-ray binaries, massive binary evolution, and the production of VHE radiation. More recently he was involved in observations that showed for the first time a galactic microquasar mimicking winged radio galaxies (Martí et al. 2017, Nature Comm. 8, 1757).