To cite bipartite in publications please use:

Dormann, C.F., Fründ, J., Blüthgen, N. & Gruber B. 2009. Indices, graphs and null models: analyzing bipartite ecological networks. The Open Ecology Journal, 2, 7-24.
Dormann, C.F., Gruber B. & Fründ, J. (2008). Introducing the bipartite Package: Analysing Ecological Networks. R news Vol 8/2, 8 - 11.

Corresponding BibTeX entries:

  @Article{,
    title = {Indices, graphs and null models: analyzing bipartite
      ecological networks.},
    author = {C. F. Dormann and J. Fründ and N. Blüthgen and B.
      Gruber},
    journal = {The Open Ecology Journal},
    volume = {2},
    pages = {7-24},
    year = {2009},
  }
  @Article{,
    title = {Introducing the bipartite Package: Analysing Ecological
      Networks.},
    author = {C. F. Dormann and B. Gruber and J. Fründ},
    journal = {R news},
    volume = {8},
    number = {2},
    pages = {8-11},
    year = {2008},
  }