To cite bipartite in publications please use Dormann et al. (2008 R News); for network-level analyses Dormann et al. (2009 Open Ecol J) and for species-level analyses Dormann (2011 Network Biology):

Dormann, C.F., Fruend, J., Bluethgen, 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. & Fruend, J. (2008). Introducing the bipartite Package: Analysing Ecological Networks. R news Vol 8/2, 8 - 11.
Dormann, C.F. (2011). How to be a specialist? Quantifying specialisation in pollination networks. Network Biology 1, 1 - 20.

Corresponding BibTeX entries:

  @Article{,
    title = {Indices, graphs and null models: analyzing bipartite
      ecological networks.},
    author = {C. F. Dormann and J. Frueund and N. Bluethgen 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. Fruend},
    journal = {R News},
    volume = {8},
    number = {2},
    pages = {8-11},
    year = {2008},
  }
  @Article{,
    title = {How to be a specialist? Quantifying specialisation in
      pollination networks.},
    author = {C. F. Dormann},
    journal = {Network Biology},
    volume = {1},
    number = {1},
    pages = {1-20},
    year = {2011},
  }