Theano in deep learning research
Theano used to be very popular in the last few years. However, from seeing what the top research labs in the world currently use instead of theano (Facebook AI and Google Deepmind), I would either go for caffe or Torch7, with a stronger preference on the latter.
The reason is that you can implement from Recurrent Neural Nets to Convolutional Neural Networks very easily and there is a wide range of examples on github.
Graduate students in NYU, Stanford, Oxford definitely implement advanced models in their studies; your background will help you a lot, a great place to start and familiarise with such models, and implement them in Torch7, is the lessons of Prof. Nando de Freitas.