I have recently filed an Indian patent and got my application number.. Is it ok for me to publish a research on the same now, by mentioning application number in my publication?
Anything published after the filing of an application can not be used against that application.
I don't see a reason to include the patent number in the paper, you certainly don't have to, but if you want, you could.
In some countries you might have to wait for an authorisation from the army/ministry of defence to divulge it.