  The past several years have witnessed important developments in the QCD
theory of jet production and jet substructure in hadronic collisions. In the
framework of soft-collinear effective theory, semi-inclusive jet functions and
semi-inclusive fragmenting jet functions have allowed us to combine higher
order calculations with resummation of potentially large logarithms of the jet
radius, $\ln R$. Very recently, the semi-inclusive jet functions for partons
fragmenting into heavy flavor jets were computed by Dai, Kim and Leibovich. In
this paper we show how the formalism can be extended to c-jet and b-jet
production in heavy ion collisions. The semi-inclusive jet functions for heavy
flavor jets in a QCD medium are evaluated up to the next-to-leading order in
$\alpha_s$ and first order in opacity. For phenomenological applications, we
also consider the inclusion of the cold nuclear matter effects and the jet
energy dissipation due to collisional interactions in matter. We present the
numerical predictions for the cross sections and the corresponding nuclear
modification factors in proton-nucleus and nucleus-nucleus collisions and
compare our results to data from the Large Hadron Collider.
