In publications arising from the use of Wannier90 please cite

Wannier90 as a community code: new features and applications
G. Pizzi, V. Vitale, R. Arita, S. Blügel, F. Freimuth, G. Géranton, M. Gibertini, D. Gresch, C. Johnson, T.Koretsune, J. Ibañez-Azpiroz, H. Lee, J. M. Lihm, D. Marchand, A. Marrazzo, Y. Mokrousov, J. I. Mustafa, Y. Nohara, Y. Nomura, L. Paulatto, S. Poncé, T. Ponweiser, J. Qiao, F. Thöle, S. S. Tsirkin, M. Wierzbowska, N. Marzari, D. Vanderbilt, I. Souza, A. A. Mostofi, and J. R. Yates, J. Phys. Cond. Matt. 32, 165902 (2020) [ONLINE JOURNAL, OPEN ACCESS]

If you are using v.2.x or earlier, please cite instead:

An updated version of wannier90: A tool for obtaining maximally-localised Wannier functions
AA Mostofi, JR Yates, G Pizzi, YS Lee, I Souza, D Vanderbilt, N Marzari
Comput. Phys. Commun. 185, 2309 (2014) [ONLINE JOURNAL]

Papers introducing MLWFs and their applications

  • Maximally localized Wannier functions: Theory and applications
    Nicola Marzari, Arash A. Mostofi, Jonathan R. Yates, Ivo Souza, David Vanderbilt, Rev. Mod. Phys. 84, 1419 (2012) [ONLINE JOURNAL]  [OPEN ACCESS]
  • 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]  [OPEN ACCESS]
  • Maximally localized generalized Wannier functions for composite energy bands
    N. Marzari and D. Vanderbilt, Phys. Rev. B 56, 12847 (1997) [ONLINE JOURNAL] [OPEN ACCESS]
  • Maximally localized Wannier functions for entangled energy bands
    I. Souza, N. Marzari and D. Vanderbilt, Phys. Rev. B 65, 035109 (2002) [ONLINE JOURNAL] [OPEN ACCESS]
  • Ab initio transport properties of nanostructures from maximally localized Wannier functions
    A. Calzolari, N. Marzari, I. Souza and M. B. Nardelli, Phys. Rev. B 69, 035108 (2004) [ONLINE JOURNAL] [OPEN ACCESS]
  • Band structure and quantum conductance of nanostructures from maximally localized Wannier functions: The case of functionalized carbon nanotubes
    Y. S. Lee, M. B. Nardelli and N. Marzari, Phys. Rev. Lett. 95, 076804 (2005) [ONLINE JOURNAL] [OPEN ACCESS]
  • Spectral and Fermi surface properties from Wannier interpolation
    J. R. Yates, X. Wang, D. Vanderbilt and I. Souza, Phys. Rev. B 75, 195121 (2007) [ONLINE JOURNAL] [OPEN ACCESS]
  • BoltzWann: A code for the evaluation of thermoelectric and electronic transport properties with a maximally-localized Wannier functions basis
    G. Pizzi, D. Volja, B. Kozinsky, M. Fornari, N. Marzari, Comput. Phys. Commun. 185, 422 (2014) [ONLINE JOURNAL] [OPEN ACCESS]

Other Wannier-related papers

We used to maintain a list of all the papers published using Wannier90. But there are now over 1000 papers and new ones appear at the rate of 2-3 each week! So here is link to the citations of the Comput. Phys. Commun. article from Google Scholar.