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Heavy flavor and electromagnetic probes play an important role in characterizing matter produced in relativistic heavy-ion collisions. Thermal photons and dileptons were originally proposed to measure the temperature of the system. Suppression of heavy quarkonia was proposed by Matsui and Satz as a probe of deconfinement and as a thermometer of the medium. Open heavy flavor production provides important insight into the problem of thermalization and the mechanism of energy loss.

In recent years RHIC has provided interesting results both on hidden and open heavy flavor production, including Υ suppression and J/ψ elliptic flow, as well as for dilepton production. The start of LHC heavy-ion program opened a new era in the physics of heavy flavor probes. For the first time measurements of excited heavy bottomonium states appeared and evidence for strong in-medium modification of open heavy flavor probes was also found. In the following we discuss separately the open problems and opportunities in heavy quarkonium and open heavy flavor production and electromagnetic probes in more detail emphasizing the common themes in these subtopics. The proposed one month program aims to bring together the different relevant theory communities to achieve a quantitative understanding of these probes in heavy-ion collisions, based on first principles. We anticipate the active participation of experimentalists in all aspects of this program.