I had recommended to me from several prominent faculty the paper:
The Yang-Mills Equations over Riemann Surfaces Author(s): M. F. Atiyah and R. Bott Source: Philosophical Transactions of the Royal Society of London. Series A, Mathematical and Physical Sciences, Vol. 308, No. 1505 (Mar. 17, 1983), pp. 523-615 Published by: The Royal Society Stable URL: http://www.jstor.org/stable/37156
One professor called it "the basis for truly 21st century mathematics." It is also reportedly accessible by beginning graduate students with some exposure to differential geometry and suitable for independent study or as a reading course. It is a 93 page paper and develops a lot of fundamental constructions and ideas from scratch. Here is Martin Guest's review on MathSciNet.