In publications arising from the use of Wannier90 please cite

Wannier90: A Tool for Obtaining Maximally-Localised Wannier Functions
A. A. Mostofi, J. R. Yates, Y.-S. Lee, I. Souza, D. Vanderbilt and N. Marzari
Comput. Phys. Commun. 178, 685 (2008) [ONLINE JOURNAL]

Other papers on the MLWF method

Papers that use MLWF/Wannier90