what are the recent hot topics in bioinformatics , on which a M.Tech computer science student can do research?
It would depend on where you get admitted for graduate program and the expertise of the mentors in that department. You would need to decide what area is of interest to you and go from there.
With a M.Tech in computer science, I think that you stand a great chance to transition into bioinformatics. I did a B.Sc. in Computer Science before branching into biology. I would encourage you to push toward doing a Ph.D., as you will then progress a lot quicker in your career. A Masters is usually good enough for most roles, but higher positions will require a Ph.D. minimum.
Hot topics come and go, and are usually things that have long been used already in our (or other) fields, but that others outside our field are just getting word of. Latest include lasso regression and machine learning. Bioinformatics was itself a hot topic a few years ago. Bayesian statistics always raises an eyebrow, too... Others that have come and gone include Systems Biology, unbiased clustering, etc.