To cite TMB in publications use:

  Kasper Kristensen, Anders Nielsen, Casper W. Berg, Hans Skaug,
  Bradley M. Bell (2016). TMB: Automatic Differentiation and Laplace
  Approximation. Journal of Statistical Software, 70(5), 1-21.
  doi:10.18637/jss.v070.i05

A BibTeX entry for LaTeX users is

  @Article{,
    title = {{TMB}: Automatic Differentiation and {L}aplace Approximation},
    author = {Kasper Kristensen and Anders Nielsen and Casper W. Berg and Hans Skaug and Bradley M. Bell},
    journal = {Journal of Statistical Software},
    year = {2016},
    volume = {70},
    number = {5},
    pages = {1--21},
    doi = {10.18637/jss.v070.i05},
  }

Residuals computed with the oneStepPredict() function should cite:

  Uffe H. Thygesen, Christoffer M. Albertsen, Casper W. Berg, Kasper
  Kristensen, Anders Nielsen (2017). Validation of ecological state
  space models using the Laplace approximation. Environmental and
  Ecological Statistics. doi:10.1007/s10651-017-0372-4

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Validation of ecological state space models using the {L}aplace approximation},
    author = {Uffe H. Thygesen and Christoffer M. Albertsen and Casper W. Berg and Kasper Kristensen and Anders Nielsen},
    journal = {Environmental and Ecological Statistics},
    year = {2017},
    pages = {1--23},
    doi = {10.1007/s10651-017-0372-4},
  }