Physical Bioinformatics is the application of theoretical tools from chemistry and physics to Bioinformatics, allowing more information to be extracted from some next-generation sequencing techniques than previously possible. In this talk, I will discuss the application of physical bioinformatics to the next-generation sequencing technique known as ribosome profiling, which measures the location of every actively translating ribosome on every mRNA in a cell. I will illustrate how by applying chemistry and physics models we can extract absolute rates of translation from such data, and how we can extract molecular level information of the factors influencing the rate of protein synthesis by the ribosome. Finally, I will offer some personal anecdotes and reflections on issues of reproducibility in this field, and the intersection of this field with statistics, including how a professor of statistics from Penn State saved us from Reviewer 3 torpedoing a manuscript.