@article{Aevermann2018,
author = {Aevermann, Brian D. and Novotny, Mark and Bakken, Trygve and Miller, Jeremy A. and Diehl, Alexander D. and Osumi-Sutherland, David and Lasken, Roger S. and Lein, Ed S. and Scheuermann, Richard H.},
doi = {10.1093/hmg/ddy100},
file = {:Users/stvjc/PDFS/scheuermannOntolHCA.pdf:pdf},
issn = {14602083},
journal = {Human Molecular Genetics},
number = {R1},
pages = {R40--R47},
pmid = {29590361},
title = {{Cell type discovery using single-cell transcriptomics: Implications for ontological representation}},
volume = {27},
year = {2018}
}

@article{Bakken2017,
author = {Bakken, Trygve and Cowell, Lindsay and Aevermann, Brian D. and Novotny, Mark and Hodge, Rebecca and Miller, Jeremy A. and Lee, Alexandra and Chang, Ivan and McCorrison, Jamison and Pulendran, Bali and Qian, Yu and Schork, Nicholas J. and Lasken, Roger S. and Lein, Ed S. and Scheuermann, Richard H.},
doi = {10.1186/s12859-017-1977-1},
file = {:Users/stvjc/PDFS/bakkenOntol.pdf:pdf},
isbn = {1471-2105 (Electronic) 1471-2105 (Linking)},
issn = {14712105},
journal = {BMC Bioinformatics},
keywords = {Cell ontology,Cell phenotype,Cytometry,Marker genes,Neuron,Next generation sequencing,Open biomedical ontologies,Peripheral blood mononuclear cells,Single cell transcriptomics},
number = {Suppl 17},
pmid = {29322913},
title = {{Cell type discovery and representation in the era of high-content single cell phenotyping}},
volume = {18},
year = {2017}
}

@Article{Westbury2015,
author="Westbury, Sarah K.
and Turro, Ernest
and Greene, Daniel
and Lentaigne, Claire
and Kelly, Anne M.
and Bariana, Tadbir K.
and Simeoni, Ilenia
and Pillois, Xavier
and Attwood, Antony
and Austin, Steve
and Jansen, Sjoert Bg
and Bakchoul, Tamam
and Crisp-Hihn, Abi
and Erber, Wendy N.
and Favier, R{\'e}mi
and Foad, Nicola
and Gattens, Michael
and Jolley, Jennifer D.
and Liesner, Ri
and Meacham, Stuart
and Millar, Carolyn M.
and Nurden, Alan T.
and Peerlinck, Kathelijne
and Perry, David J.
and Poudel, Pawan
and Schulman, Sol
and Schulze, Harald
and Stephens, Jonathan C.
and Furie, Bruce
and Robinson, Peter N.
and van Geet, Chris
and Rendon, Augusto
and Gomez, Keith
and Laffan, Michael A.
and Lambert, Michele P.
and Nurden, Paquita
and Ouwehand, Willem H.
and Richardson, Sylvia
and Mumford, Andrew D.
and Freson, Kathleen
and {BRIDGE-BPD Consortium}",
title="Human phenotype ontology annotation and cluster analysis to unravel genetic defects in 707 cases with unexplained bleeding and platelet disorders.",
journal="Genome medicine",
year=2015,
month=04,
day=09,
volume=7,
number=1,
pages=36,
abstract="Heritable bleeding and platelet disorders (BPD) are heterogeneous and frequently have an unknown genetic basis. The BRIDGE-BPD study aims to discover new causal genes for BPD by high throughput sequencing using cluster analyses based on improved and standardised deep, multi-system phenotyping of cases.",
issn="1756-994X",
doi="10.1186/s13073-015-0151-5",
url="http://www.ncbi.nlm.nih.gov/pubmed/25949529",
language="eng"
}


@article{Leek:2010aa,
	Author = {Leek, Jeffrey T and Scharpf, Robert B and Bravo, H{\'e}ctor Corrada and Simcha, David and Langmead, Benjamin and Johnson, W Evan and Geman, Donald and Baggerly, Keith and Irizarry, Rafael A},
	Date-Added = {2019-01-10 22:02:05 +0000},
	Date-Modified = {2019-01-10 22:02:05 +0000},
	Doi = {10.1038/nrg2825},
	Journal = {Nat Rev Genet},
	Journal-Full = {Nature reviews. Genetics},
    Month = {10},
	Number = {10},
	Pages = {733-9},
	Pmc = {PMC3880143},
	Pmid = {20838408},
	Pst = {ppublish},
	Title = {Tackling the widespread and critical impact of batch effects in high-throughput data},
	Volume = {11},
	Year = {2010}}

@Article{butler,
    author = {Andrew Butler and Paul Hoffman and Peter Smibert and
      Efthymia Papalexi and Rahul Satija},
    title = {Integrating single-cell transcriptomic data across
      different conditions, technologies, and species},
    journal = {Nature Biotechnology},
    year = {2018},
    doi = {10.1038/nbt.4096},
    issn = {1087-0156},
    url = {https://www.nature.com/articles/nbt.4096},
  }
