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These constitute a good selection of papers to introduce one to the lab and the general field of bioinformatics.

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

Cheng, et al. PLoS Comput. Biol. (2011); Cheng, et al., Genome Biol. (2011); Khurana, et al., PLoS Comput. Biol. (2013)

Structural Variation

Abyzov, et al., Genome Res. (2011)

Pseudogenes and loss of function

Pei, et al., Genome Biol. (2012); Khurana, et al., Nucleic Acids Res. (2010); Habegger, et al., Bioinfo. (2012)

Structure

Voss and Gerstein, Nucleic Acids Res. (2010); Bhardwaj, et al., Protein Sci. (2011)

Networks

Yan, et al., Proc Natl Acad Sci. (2010); Bhardwaj, et al., Sci Signal. (2010); Yu and Gerstein, Proc Natl Acad Sci. (2006)

Expression Analysis

Cheng, et al., Genome Res. (2012); Sboner, et al., Genome Res. (2011); Habegger, et al., Bioinfo. (2011)

Data Science Issues

Gerstein, Nature (2012); Greenbaum, et al., PLoS Comput Biol. (2011); Greenbaum and Gerstein, SF Op Ed (2012)

In each list, it is probably best to read the papers listed first.

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 intro-cs

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