Examples of references for mathematical approaches in bioinformatics that are applicable to linguistics?
There are a number of more recent papers dealing with phylogenetic methods in reconstructing language history as well, including work by Colin Renfrew and Quentin Atkinson.

Here are two recent high-profile papers. Unfortunately, both are still behind paywalls, but even reading the list of papers they cite / that cite them would be a great way to answer your question.


 Bouchard-Côté A, Hall D, Griffiths TL, Klein D. 2013. Automated reconstruction of ancient languages using probabilistic models of sound change. Proceedings of the National Academy of Sciences 110: 4224–4229.
 Gray RD, Drummond AJ, Greenhill SJ. 2009. Language phylogenies reveal expansion pulses and pauses in Pacific settlement. Science 323: 479–483.


Maybe not quite as high-profile, but available online, one of my classmates did his (superb) undergraduate thesis as a Biology/Linguistics double major in exactly this topic. I think it could be a very useful place to start, although there have certainly been developments in the field in the last six years:


 Saunders, A. 2006. Linguistic Phylogenetics of the Austronesian Family: a performance review of methods adapted from biology.


See also the wikipedia page Quantitative Comparative Linguistics, this Stanford how-to, and this interesting article Linguistic Phylogenies Are Not the Same as Biological Phylogenies.