One might start with Luscombe et al. (2002) for an introduction to bioinformatics.

Specific fields are highlighted in other short papers:

Data integration for function prediction

Gerstein et al. (2002), Bertone and Gerstein (2001), Greenbaum et al. (2001)

Simulation on molecular structure

Gerstein and Levitt (1998); Gerstein and Chothia (1999)

Pseudogenes and genome annotation

Gerstein and Snyder (2003); Harrison and Gerstein (2002)

Structural genomics

Gerstein (2000); Teichmann et al. (1999)

E-publishing

Gerstein (1999)

Expression analysis

Gerstein and Jansen (2000)

Unfortunately, none of these papers give one much detail on the mathematical or computational aspects of the work. For this, it's best to look at some samples of recent research, which are listed below, to get a sense of the type of mining that we are doing -- e.g. Yu & Gerstein (2006), Du et al. (2006), Lu et al., (2005), Yip et al., (2007), and Echols et al. (2003).