To cite package ‘monocle’ in publications use:

  Cole Trapnell and Davide Cacchiarelli et al (2014): The dynamics and
  regulators of cell fate decisions are revealed by pseudo-temporal
  ordering of single cells. Nature Biotechnology

A BibTeX entry for LaTeX users is

  @Article{,
    title = {The dynamics and regulators of cell fate decisions are revealed by pseudo-temporal ordering of single cells},
    author = {Cole Trapnell and Davide Cacchiarelli and Jonna Grimsby and Prapti Pokharel and Shuqiang Li and Michael Morse and Niall J. Lennon and Kenneth J. Livak and Tarjei S. Mikkelsen and John L. Rinn},
    year = {2014},
    journal = {Nature Biotechnology},
  }

  Xiaojie Qiu, Andrew Hill, Cole Trapnell et al (2017): Single-cell
  mRNA quantification and differential analysis with Census. Nature
  Methods

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Single-cell mRNA quantification and differential analysis with Census},
    author = {Xiaojie Qiu and Andrew Hill and Jonathan Packer and Dejun Lin and Yi-An Ma and Cole Trapnell},
    year = {2017},
    journal = {Nature Methods},
  }

  Xiaojie Qiu, Cole Trapnell et al (2017): Reverse graph embedding
  resolves complex single-cell developmental trajectories. BioRxiv

A BibTeX entry for LaTeX users is

  @Article{,
    title = {Reverse graph embedding resolves complex single-cell developmental trajectories.},
    author = {Xiaojie Qiu and Qi Mao and Ying Tang and Li Wang and Raghav Chawla and Hannah Pliner and Cole Trapnell},
    year = {2017},
    journal = {BioRxiv},
  }