As @Eric Shain mentioned in a comment, you would need to become the applicant by getting assignments of the applications from the company back to you. The specific application US 20160091609 you mentioned was prosecuted very seriously by the assignee (Track I, RCE, etc.) so it might not be easy to get a patent even if it was revived.
To revive a patent application, it must have been unintentionally abandoned. At the bureaucratic USPTO level they will likely take the your word for that as long as there was not an explicit abandonment (explicit abandonments are very rare) by the assignee. However, if you got a patent and ever tried to assert it the defendant would get discovery and very likely find emails where people at the university discussed letting the applications go. If you try to get the university to assign it to you, will they mention in an email to you "we decided to let it go because . . . "? If revived under a false statement of unintentionally it will likely be invalidated.