Research papers that feature Greek text should employ a Greek font for that text. Although no method is standard, there are several ways to type Greek with full diacritical marks.
These are two good programs which are available for purchase:
There are also methods of inputting Greek with the software native to both Macintosh and Windows platforms:
Note: If you copy and paste Greek from a website, such as from the Thesaurus Linguae Graecae, you often have to use the font Palatino Lintotype in order to ensure that the diacritics look right.