To cite miRBaseConverter in publications use:

  Taosheng Xu, Ning Su, Lin Liu, Junpeng Zhang, Hongqiang Wang, Weijia
  Zhang, Jie Gui, Kui Yu, Jiuyong Li and Thuc Duy Le. miRBaseConverter:
  An R/Bioconductor Package for Converting and Retrieving miRNA Name,
  Accession, Sequence and Family Information in Different Versions of
  miRBase. BMC Bioinformatics 19 (s19) :514 (2018).
  doi:/10.1186/s12859-018-2531-5

A BibTeX entry for LaTeX users is

  @Article{,
    title = {miRBaseConverter: A comprehensive and high-efficiency tool for converting and retrieving the information of miRNAs in different miRBase versions},
    author = {Taosheng Xu and Ning Su and Lin Liu and Junpeng Zhang and Hongqiang Wang and Weijia Zhang and Jie Gui and Kui Yu and {et.al.}},
    journal = {BMC Bioinformatics},
    year = {2018},
    volume = {19},
    number = {s19},
    pages = {514},
    url = {https://doi.org/10.1186/s12859-018-2531-5},
  }