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

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

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

Corresponding BibTeX entries:

  @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},
  }

  @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},
  }

  @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},
  }