These are the Jupyter notebooks that I used for the paper:
Reeves DB, Peterson CW, Kiem H-P, Schiffer JT. 2017. Autologous stem cell transplantation disrupts adaptive immune responses during rebound simian/human immunodeficiency virus viremia. J Virol 91:e00095-17. https://doi.org/10.1128/JVI.00095-17.
Which is a mathematical modeling study of non-human primate data. The model uses ODEs and is fit to the data to show how transplant affects the kinetics of HIV infection. The study was inspired by the Berlin patient, the only known patient cured of HIV.