A brief note to students who are publishing research results: it's considered proper form to give, as your academic affiliation, the institution to which you were affiliated when you conducted the research. You can then also note your "current address" for communication purposes.
For example, if you're publishing an article based on research you conducted while a Master's student at University of X, your affiliation on the article should be DepartmentX/University of X, even if you're now in the PhD program at Department Y/University of Y. Give credit where it's due. Then, when you're publishing your dissertation results, list your affiliation as University of Y, even if you've moved on to a postdoc at University of Z.
You'll commonly see these different affiliations on the first page of publications, where a footnote or other indicator gives the "current address" or "correspondence to." It can sometimes be difficult to make it clear with online submissions, but you can always clarify in your cover note to the editor. Remember: You don't want to inadvertently offend your supervisor or others involved in your research, which could happen even though you thank them in the acknowledgments. Many institutions/research centres want to be listed with the authors, especially if unique or expensive research infrastructure was involved.