Heavy ion collisions (HICs) are the appropriate tools to study the so-called quark-gluon plasma
(QGP). This thesis is focused on the analysis of two types of effects arising in HICs: initial state
effects and final state effects. Among the former, there are the nuclear parton distribution functions
(nPDFs), whose precise determination is crucial for the correct interpretation of any observable
used in HICs. In this thesis a global analysis of nPDFs at next-to-next-to-leading-order in
perturbative QCD (pQCD) is performed. Another very interesting issue regarding the initial stage of
HICs are the collective phenomena that give rise to the QGP. These are addressed within the string
percolation model (SPM). The results obtained in this framework for different observables are
compared to available experimental data. Amongst the final state it is worth stressing hard probes,
which are observables characterized by a high energy or mass. An analysis of single-inclusive
suppression of hard particles at different center of mass energies and centralities in presented. The
main result of this work is the extraction of the so-called jet quenching coefficient