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, 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, Gruber B, Fruend J (2008). “Introducing the bipartite Package: Analysing Ecological Networks.” R News, 8(2), 8-11.

Dormann C (2011). “How to be a specialist? Quantifying specialisation in pollination networks.” Network Biology, 1(1), 1-20.

Corresponding BibTeX entries:

  @Article{,
    title = {Indices, graphs and null models: analyzing bipartite
      ecological networks.},
    author = {Carsten F. Dormann and Jochen Fruend and Nico Bluethgen
      and Bernd Gruber},
    journal = {The Open Ecology Journal},
    volume = {2},
    pages = {7-24},
    year = {2009},
  }

  @Article{,
    title = {Introducing the bipartite Package: Analysing Ecological
      Networks.},
    author = {Carsten F. Dormann and Bernd Gruber and Jochen 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 = {Carsten F. Dormann},
    journal = {Network Biology},
    volume = {1},
    number = {1},
    pages = {1-20},
    year = {2011},
  }