Recently I have a paper acceptance from a tier-1 conference in our field of telecommunication. I have also submitted the extended version in IEEE Transactions as well.
Is it ok (and acceptable) for me to write the patent out these papers? (I understand that paper acceptance does not guarantee patent acceptance)
What will be the academic/career benefits for me to write the patent at this stage when I am writing my thesis?
Any information which you disclosed in your publication will count as prior art, and cannot be patented by you or by anyone else. If you wish to write publications about an invention which you also wish to patent, you must file for patents first. Hence, a paper cannot be "transformed" into a patent. If you have an invention which builds upon the information disclosed in the paper, this may be patentable.
Patents cost money to file, and expensive to maintain. There is also considerable skill in writing patents. There is no point in filing for a patent unless you intend to exploit it. As such, the academic/career benefits do not justify filing for a patent per se, and without a good plan to commercialise the invention, it will simply be a waste of money.
Patent law varies from place to place, of course, but generally relies on priority in time. I don't see any academic objection to filing a patent, but it can be expensive. Perhaps you need to consult a patent attorney (also expensive).
On the other hand, your work may be solid enough to establish 'prior art' if anyone should try to beat you to a patent. But in actual practice, there are anomalies.
The comment of user MJeffryes implies that the struck comment is probably incorrect. Wikipedia has a discussion of prior art.
Note that I prefer conservative (i.e. safe) solutions. If I'm wrong in this answer, I apologize, but will leave it in place as a bit of a warning (aka Humble Pie). I stand by the statement that there is no Academic objection, but the OP needs to behave in an optimal way, and not depend on possibly wishful thinking answers (mine). See the answer of MJeffryes for better advice.
In my view of academic ethics, the filing of patents is immoral. It calls on states' coercive power to prevent the use and further development of technology. The justification of helping individual inventors to support themselves financially should be rejected, for multiple reasons (see bottom link) - the damages far outweight the benefits; the main owners of patents are large corporations; and the very mechanism of enforcement is highly problematic.
Consider gowing through this overview of some of the criticism of and objections to patents on Wikipedia.
In this particular case, you seem to want to try to take knowledge and know-how that has already been made publicly available and usable, and tie it up with a patent protection. Frankly, that sounds like an insidious idea, and many people may come to resent you if you succeed, or even if they realize you've tried doing so. The very knowledge that the taint of IP registration, patenting in particular, may be in touch with some piece of research is enough to drive many potential adopters away from it.
So just say no to tem-patent-ation...
