articles.bib

@Article{ellwanger2018,
  title   = {Transcriptional dynamics of hair-bundle morphogenesis revealed with CellTrails},
  author  = {DC Ellwanger and M Scheibinger and RA Dumont and PG Barr-Gillespie and S Heller},
  journal = {Cell Reports},
  year    = {2018},
  month   = {6},
  volume  = {23},
  number  = {10},
  pages   = {2901-2914},
  note    = {doi: 10.1016/j.celrep.2018.05.002e}
}

@Article{vdmaaten2008,
  title   = {Visualizing high-dimensional data using t-SNE},
  author  = {LJP van der Maaten and GE Hinton},
  journal = {Journal of Machine Learning Research},
  year    = {2008},
  volume  = {9},
  pages   = {2579-2605},
}

@Article{belkin2003,
  title   = {Laplacian eigenmaps for dimensionality reduction and data representation},
  author  = {M Belkin and P Niyogi},
  journal = {Neural computation},
  year    = {2003},
  volume  = {15},
  pages   = {1373-1396},
}

@Article{sussman2012,
  title   = {A consistent adjacency spectral embedding for stochastic blockmodel graphs},
  author  = {DL Sussman and M Tang and DE Fishkind and CE Priebe},
  journal = {J Am Stat Assoc},
  year    = {2012},
  volume  = {107},
  number  = {},
  pages   = {1119-1128},
}
    
@Article{daub2004,
  title   = {Estimating mutual information using B-spline functions--an improved similarity measure for analysing gene expression data},
  author  = {CO Daub and R Steuer and J Selbig and S Kloska},
  journal = {BMC Bioinformatics},
  year    = {2012},
  volume  = {5},
  pages   = {118},
}

@Article{ward1963,
  title   = {Hierarchical grouping to optimize an objective function},
  author  = {JH Ward and },
  journal = {Journal of the American Statistical Association},
  year    = {1963},
  volume  = {58},
  pages   = {236-244},
}

@Article{peto1972,
  title   = {Asymptotically efficient bank invariant test procedures (with discussion)},
  author  = {R Peto and J Peto},
  journal = {Journal of the Royal Statistical Society},
  year    = {1972},
  volume  = {Series A 135},
  pages   = {185-206},
}
    
@Article{benjamini1995,
  title   = {Controlling the false discovery rate: a practical and powerful approach to multiple testing},
  author  = {Y Benjamini and Y. Hochberg},
  journal = {Journal of the Royal Statistical Society},
  year    = {1995},
  volume  = {Series B 57},
  pages   = {289-300},
}

  
@Article{kruskal1956,
  title   = {On the shortest spanning subtree of a graph and the traveling salesman problem},
  author  = {JB Kruskal},
  journal = {Proc Amer Math Soc},
  year    = {1956},
  volume  = {7},
  pages   = {48-50},
}    

@Article{bedall1979,
  title   = {Algorithm AS143. The mediancentre.},
  author  = {FK Bedall and H Zimmermann},
  journal = {Appl Statist},
  year    = {1979},
  volume  = {28},
  pages   = {325-328},
}

@Article{sakoe1978,
  title   = {Dynamic programming algorithm optimization for spoken word recognition},
  author  = {H Sakoe and S Chiba},
  journal = {IEEE Transactions on Acoustics, Speech, and Signaling Processing},
  year    = {1978},
  volume  = {26},
  pages   = {43-49},
}

@Article{biobase,
    author = {W Huber and JV Carey and R Gentleman and S Anders and M Carlson and BS Carvalho and HC Bravo and S Davis and  L Gatto and  T Girke and R Gottardo and F Hahne and KD Hansen and RA Irizarry and  M Lawrence and MI Love and J MacDonald and V Obenchain and AK {{Ole's}} and H {{Pag`es}} and A Reyes and P Shannon and GK Smyth and D Tenenbaum and L Waldron and M Morgan},
    title = {{O}rchestrating high-throughput genomic analysis with {B}ioconductor},
    journal = {Nature Methods},
    year = {2015},
    volume = {12},
    number = {2},
    pages = {115--121}
  }

@Article{mahata2014,
  title   = {Single-cell RNA sequencing reveals T helper cells synthesizing steroids de novo to contribute to immune homeostasis},
  author  = {B Mahata and X Zhang and AA Kolodziejczyk and V Proserpio and L Haim-Vilmovsky and AE Taylor and D Hebenstreit and FA Dingler and V Moignard and B Goettgens and W Arlt and AN McKenzie and SA Teichmann},
  journal = {Cell Reports},
  year    = {2014},
  volume  = {7},
  number  = {4},
  pages   = {1130-42},
}

@Article{buettner2015,
  title   = {Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells},
  author  = {F Buettner and KN Natarajan and FP Casale and V Proserpio and A Scialdone and FJ Theis and SA Teichmann and JC Marioni and O Stegle},
  journal = {Nature Biotechnology},
  year    = {2015},
  month   = {},
  volume  = {33},
  number  = {2},
  pages   = {155-160},
}

@Article{scran,
  author  = {ATL Lun and DJ McCarthy and JC Marioni},
  title   = {A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor},
  journal = {F1000Res.},
  year    = {2016},
  volume  = {5},
  pages   = {2122},
}

@Article{destiny,
  title   = {destiny: diffusion maps for large-scale single-cell data in R},
  author  = {P Angerer and L Haghverdi and M Buettner and FJ Theis and C Marr and F Buettner},
  journal = {Bioinformatics},
  year    = {2015},
  volume  = {32},
  pages   = {1241-1243},
}  

@Article{scater,
  title   = {Scater: pre-processing, quality control, normalisation and visualisation of single-cell RNA-seq data in R},
  author  = {DJ McCarthy and KR Campbell and ATL Lun and QF Wills},
  journal = {Bioinformatics},
  year    = {2017},
  volume  = {14},
  pages   = {1179-1186},
}

@Article{fr,
  title   = {Graph Drawing by Force-directed Placement},
  author  = {TMJ Fruchterman and EM Reingold},
  journal = {Software - Practice and Experience},
  year    = {1991},
  volume  = {21},
  number  = {11},
  pages   = {1129-1164},
}

@Article{burns2015,
  title   = {Single-cell RNA-Seq resolves cellular complexity in sensory organs from the neonatal inner ear},
  author  = {JC Burns and MC Kelly and M Hoa and RJ Morell and MW Kelley},
  journal = {Nature Communications},
  year    = {2015},
  month   = {Oct},
  volume  = {15},
  number  = {6},
  pages   = {8557},
  note    = {doi: 10.1038/ncomms9557},
}

@Manual{R-Orgmmegdb,
  title   = {org.Mm.eg.db: genome wide annotation for mouse.},
  author  = {M Carlson},
  year    = {2017},
  note    = {R package version 3.5.0},
}

@Manual{R-SingleCellExperiment,
  title = {SingleCellExperiment: S4 Classes for Single Cell Data},
  author = {ATL Lun and D Risso},
  year = {2017},
  note = {R package version 1.0.0},
}

@Manual{R-AnnotationDbi,
  title = {AnnotationDbi: Annotation Database Interface},
  author = {H Pag{è}s and M Carlson and S Falcon and N Li},
  year = {2017},
  note = {R package version 1.40.0},
}