bibliography.bib

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@UNPUBLISHED{Dale2017-rc,
  title    = "Bioconda: A sustainable and comprehensive software distribution
              for the life sciences",
  author   = "Dale, Ryan and Gr{\"u}ning, Bj{\"o}rn and Sj{\"o}din, Andreas and
              Rowe, Jillian and Chapman, Brad A and Tomkins-Tinch, Christopher
              H and Valieris, Renan and {The Bioconda Team} and K{\"o}ster,
              Johannes",
  journal  = "bioRxiv",
  pages    = "207092",
  month    =  oct,
  year     =  2017,
  url      = "https://www.biorxiv.org/content/early/2017/10/21/207092",
  language = "en",
  doi      = "10.1101/207092"
}

@ARTICLE{Ward1963-xf,
  title     = "Hierarchical grouping to optimize an objective function",
  author    = "Ward, Jr, Joe H",
  journal   = "Journal of the American Statistical Association",
  publisher = "Taylor \& Francis",
  volume    =  58,
  number    =  301,
  pages     = "236--244",
  year      =  1963,
  url       = "http://www.tandfonline.com/doi/abs/10.1080/01621459.1963.10500845",
  doi       = "10.1080/01621459.1963.10500845"
}

@ARTICLE{Kiselev2017-wj,
  title       = "{SC3}: consensus clustering of single-cell {RNA-seq} data",
  author      = "Kiselev, Vladimir Yu and Kirschner, Kristina and Schaub,
                 Michael T and Andrews, Tallulah and Yiu, Andrew and Chandra,
                 Tamir and Natarajan, Kedar N and Reik, Wolf and Barahona,
                 Mauricio and Green, Anthony R and Hemberg, Martin",
  affiliation = "Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
                 Cambridge Institute for Medical Research, Wellcome Trust/MRC
                 Stem Cell Institute and Department of Haematology, University
                 of Cambridge, Hills Road, Cambridge, UK. Department of
                 Mathematics and naXys, University of Namur, Namur, Belgium.
                 ICTEAM, Universit{\'e} Catholique de Louvain,
                 Louvain-la-Neuve, Belgium. Epigenetics Programme, The Babraham
                 Institute, Babraham, Cambridge, UK. EMBL-European
                 Bioinformatics Institute, Hinxton, Cambridge, UK. Centre for
                 Trophoblast Research, University of Cambridge, Cambridge, UK.
                 Department of Mathematics, Imperial College London, London,
                 UK.",
  journal     = "Nat. Methods",
  volume      =  14,
  number      =  5,
  pages       = "483--486",
  month       =  may,
  year        =  2017,
  url         = "http://dx.doi.org/10.1038/nmeth.4236",
  language    = "en",
  issn        = "1548-7091, 1548-7105",
  pmid        = "28346451",
  doi         = "10.1038/nmeth.4236",
  pmc         = "PMC5410170"
}

@ARTICLE{Wang2017-jj,
  title       = "Visualization and analysis of single-cell {RNA-seq} data by
                 kernel-based similarity learning",
  author      = "Wang, Bo and Zhu, Junjie and Pierson, Emma and Ramazzotti,
                 Daniele and Batzoglou, Serafim",
  affiliation = "Department of Computer Science, Stanford University, Stanford,
                 California, USA. Department of Electrical Engineering,
                 Stanford University, Stanford, California, USA. Department of
                 Pathology, Stanford University, Stanford, California, USA.",
  journal     = "Nat. Methods",
  volume      =  14,
  number      =  4,
  pages       = "414--416",
  month       =  apr,
  year        =  2017,
  url         = "http://dx.doi.org/10.1038/nmeth.4207",
  language    = "en",
  issn        = "1548-7091, 1548-7105",
  pmid        = "28263960",
  doi         = "10.1038/nmeth.4207"
}

@ARTICLE{Ilicic2016-yc,
  title       = "Classification of low quality cells from single-cell {RNA-seq}
                 data",
  author      = "Ilicic, Tomislav and Kim, Jong Kyoung and Kolodziejczyk,
                 Aleksandra A and Bagger, Frederik Otzen and McCarthy, Davis
                 James and Marioni, John C and Teichmann, Sarah A",
  affiliation = "European Molecular Biology Laboratory, European Bioinformatics
                 Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton,
                 Cambridge, CB10 1SD, UK. ti243@cam.ac.uk. Wellcome Trust
                 Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge,
                 CB10 1SA, UK. ti243@cam.ac.uk. European Molecular Biology
                 Laboratory, European Bioinformatics Institute (EMBL-EBI),
                 Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD,
                 UK. Wellcome Trust Sanger Institute, Wellcome Genome Campus,
                 Hinxton, Cambridge, CB10 1SA, UK. Department of Haematology,
                 University of Cambridge, Cambridge Biomedical Campus,
                 Cambridge, CB2 0PT, UK. National Health Service (NHS) Blood
                 and Transplant, Cambridge Biomedical Campus, Cambridge, CB2
                 0PT, UK. St Vincent's Institute of Medical Research, Fitzroy,
                 Victoria, 3065, Australia. University of Cambridge, Cancer
                 Research UK Cambridge Institute, Robinson Way, Cambridge, CB2
                 0RE, UK. European Molecular Biology Laboratory, European
                 Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome
                 Campus, Hinxton, Cambridge, CB10 1SD, UK. st9@sanger.ac.uk.
                 Wellcome Trust Sanger Institute, Wellcome Genome Campus,
                 Hinxton, Cambridge, CB10 1SA, UK. st9@sanger.ac.uk. Cavendish
                 Laboratory, Dept Physics, University of Cambridge, JJ Thomson
                 Avenue, Cambridge, CB3 0HE, UK. st9@sanger.ac.uk.",
  journal     = "Genome Biol.",
  volume      =  17,
  pages       = "29",
  month       =  feb,
  year        =  2016,
  url         = "http://dx.doi.org/10.1186/s13059-016-0888-1",
  language    = "en",
  issn        = "1465-6906",
  pmid        = "26887813",
  doi         = "10.1186/s13059-016-0888-1",
  pmc         = "PMC4758103"
}

@UNPUBLISHED{Soneson2017-st,
  title    = "Bias, Robustness And Scalability In Differential Expression
              Analysis Of {Single-Cell} {RNA-Seq} Data",
  author   = "Soneson, Charlotte and Robinson, Mark D",
  journal  = "bioRxiv",
  pages    = "143289",
  month    =  may,
  year     =  2017,
  url      = "http://www.biorxiv.org/content/early/2017/05/28/143289",
  language = "en",
  doi      = "10.1101/143289"
}

@ARTICLE{Van_den_Berge_undated-kp,
  title  = "zingeR: unlocking {RNA-seq} tools for zero-in ation and single cell
            applications",
  author = "Van den Berge, Koen and Soneson, Charlotte and Love, Michael I and
            Robinson, Mark D and Clement, Lieven",
  url    = "http://dx.doi.org/10.1101/157982",
  doi    = "10.1101/157982"
}

@ARTICLE{Qiu2017-my,
  title     = "Reversed graph embedding resolves complex single-cell
               trajectories",
  author    = "Qiu, Xiaojie and Mao, Qi and Tang, Ying and Wang, Li and Chawla,
               Raghav and Pliner, Hannah A and Trapnell, Cole",
  journal   = "Nat. Methods",
  publisher = "Nature Research",
  month     =  aug,
  year      =  2017,
  url       = "http://dx.doi.org/10.1038/nmeth.4402",
  language  = "en",
  issn      = "1548-7091, 1548-7105",
  doi       = "10.1038/nmeth.4402"
}

@UNPUBLISHED{Griffiths2017-ob,
  title    = "Detection and removal of barcode swapping in single-cell
              {RNA-seq} data",
  author   = "Griffiths, Jonathan A and Lun, Aaron T L and Richard, Arianne C
              and Bach, Karsten and Marioni, John C",
  journal  = "bioRxiv",
  pages    = "177048",
  month    =  aug,
  year     =  2017,
  url      = "http://www.biorxiv.org/content/early/2017/08/16/177048",
  language = "en",
  doi      = "10.1101/177048"
}

@UNPUBLISHED{Butler2017-qe,
  title    = "Integrated analysis of single cell transcriptomic data across
              conditions, technologies, and species",
  author   = "Butler, Andrew and Satija, Rahul",
  journal  = "bioRxiv",
  pages    = "164889",
  month    =  jul,
  year     =  2017,
  url      = "http://www.biorxiv.org/content/early/2017/07/18/164889",
  language = "en",
  doi      = "10.1101/164889"
}

@ARTICLE{Lun2016-bp,
  title       = "Pooling across cells to normalize single-cell {RNA} sequencing
                 data with many zero counts",
  author      = "Lun, Aaron T L and Bach, Karsten and Marioni, John C",
  affiliation = "Cancer Research UK Cambridge Institute, University of
                 Cambridge, Li Ka Shing Centre, Robinson Way, CB2 0RE,
                 Cambridge, UK. aaron.lun@cruk.cam.ac.uk. EMBL European
                 Bioinformatics Institute, Wellcome Genome Campus, Hinxton,
                 CB10 1SD, Cambridge, UK. Cancer Research UK Cambridge
                 Institute, University of Cambridge, Li Ka Shing Centre,
                 Robinson Way, CB2 0RE, Cambridge, UK. marioni@ebi.ac.uk. EMBL
                 European Bioinformatics Institute, Wellcome Genome Campus,
                 Hinxton, CB10 1SD, Cambridge, UK. marioni@ebi.ac.uk. Wellcome
                 Trust Sanger Institute, Wellcome Genome Campus, Hinxton, CB10
                 1SA, Cambridge, UK. marioni@ebi.ac.uk.",
  journal     = "Genome Biol.",
  volume      =  17,
  pages       = "75",
  month       =  apr,
  year        =  2016,
  url         = "http://dx.doi.org/10.1186/s13059-016-0947-7",
  language    = "en",
  issn        = "1465-6906",
  pmid        = "27122128",
  doi         = "10.1186/s13059-016-0947-7",
  pmc         = "PMC4848819"
}

@UNPUBLISHED{Weinreb2017-ch,
  title    = "{SPRING}: a kinetic interface for visualizing high dimensional
              single-cell expression data",
  author   = "Weinreb, Caleb and Wolock, Samuel and Klein, Allon",
  journal  = "bioRxiv",
  pages    = "090332",
  month    =  mar,
  year     =  2017,
  url      = "http://www.biorxiv.org/content/early/2017/03/18/090332",
  language = "en",
  doi      = "10.1101/090332"
}

@ARTICLE{Zilionis2017-tn,
  title       = "Single-cell barcoding and sequencing using droplet
                 microfluidics",
  author      = "Zilionis, Rapolas and Nainys, Juozas and Veres, Adrian and
                 Savova, Virginia and Zemmour, David and Klein, Allon M and
                 Mazutis, Linas",
  affiliation = "Institute of Biotechnology, Vilnius University, Vilnius,
                 Lithuania. Department of Systems Biology, Harvard Medical
                 School, Boston, Massachusetts, USA. Department of Stem Cell
                 and Regenerative Biology, Harvard University, Cambridge,
                 Massachusetts, USA. Harvard Stem Cell Institute, Harvard
                 University, Cambridge, Massachusetts, USA. Division of
                 Immunology, Department of Microbiology and Immunobiology,
                 Harvard Medical School, Boston, Massachusetts, USA.",
  journal     = "Nat. Protoc.",
  volume      =  12,
  number      =  1,
  pages       = "44--73",
  month       =  jan,
  year        =  2017,
  url         = "http://dx.doi.org/10.1038/nprot.2016.154",
  language    = "en",
  issn        = "1754-2189, 1750-2799",
  pmid        = "27929523",
  doi         = "10.1038/nprot.2016.154"
}

@ARTICLE{Setty2016-au,
  title       = "Wishbone identifies bifurcating developmental trajectories
                 from single-cell data",
  author      = "Setty, Manu and Tadmor, Michelle D and Reich-Zeliger, Shlomit
                 and Angel, Omer and Salame, Tomer Meir and Kathail, Pooja and
                 Choi, Kristy and Bendall, Sean and Friedman, Nir and Pe'er,
                 Dana",
  affiliation = "Department of Biological Sciences, Department of Systems
                 Biology, Columbia University, New York, New York, USA.
                 Department of Immunology, Weizmann Institute of Science,
                 Rehovot, Israel. Department of Mathematics, University of
                 British Columbia, Vancouver, British Columbia, Canada.
                 Biological Services Unit, Weizmann Institute of Science,
                 Rehovot, Israel. Department of Pathology, Stanford University,
                 Stanford, California, USA.",
  journal     = "Nat. Biotechnol.",
  volume      =  34,
  number      =  6,
  pages       = "637--645",
  month       =  jun,
  year        =  2016,
  url         = "http://dx.doi.org/10.1038/nbt.3569",
  language    = "en",
  issn        = "1087-0156, 1546-1696",
  pmid        = "27136076",
  doi         = "10.1038/nbt.3569",
  pmc         = "PMC4900897"
}

@ARTICLE{Villani2017-cs,
  title       = "Single-cell {RNA-seq} reveals new types of human blood
                 dendritic cells, monocytes, and progenitors",
  author      = "Villani, Alexandra-Chlo{\'e} and Satija, Rahul and Reynolds,
                 Gary and Sarkizova, Siranush and Shekhar, Karthik and
                 Fletcher, James and Griesbeck, Morgane and Butler, Andrew and
                 Zheng, Shiwei and Lazo, Suzan and Jardine, Laura and Dixon,
                 David and Stephenson, Emily and Nilsson, Emil and Grundberg,
                 Ida and McDonald, David and Filby, Andrew and Li, Weibo and De
                 Jager, Philip L and Rozenblatt-Rosen, Orit and Lane, Andrew A
                 and Haniffa, Muzlifah and Regev, Aviv and Hacohen, Nir",
  affiliation = "Broad Institute of MIT and Harvard, Cambridge, MA, USA.
                 cvillani@broadinstitute.org m.a.haniffa@newcastle.ac.uk
                 aregev@broadinstitute.org nhacohen@mgh.harvard.edu. Center for
                 Cancer Research, Massachusetts General Hospital, Department of
                 Medicine, Boston, MA, USA. Broad Institute of MIT and Harvard,
                 Cambridge, MA, USA. New York Genome Center, New York
                 University Center for Genomics and Systems Biology, New York,
                 NY, USA. New York University Center for Genomics and Systems
                 Biology, New York, NY, USA. Institute of Cellular Medicine,
                 Newcastle University, Newcastle upon Tyne, UK. Ragon Institute
                 of Massachusetts General Hospital, Massachusetts Institute of
                 Technology, and Harvard University, Cambridge, MA, USA.
                 Department of Medical Oncology, Dana-Farber Cancer Institute,
                 Harvard Medical School, Boston, MA, USA. Olink Proteomics,
                 Watertown, MA, USA. Program in Translational NeuroPsychiatric
                 Genomics, Department of Neurology, Brigham and Women's
                 Hospital and Harvard Medical School. Institute of Cellular
                 Medicine, Newcastle University, Newcastle upon Tyne, UK.
                 cvillani@broadinstitute.org m.a.haniffa@newcastle.ac.uk
                 aregev@broadinstitute.org nhacohen@mgh.harvard.edu. Department
                 of Dermatology, Royal Victoria Infirmary, Newcastle Hospitals
                 NHS Foundation Trust, UK. Department of Biology and Koch
                 Institute, Massachusetts Institute of Technology, Cambridge,
                 MA, USA. Howard Hughes Medical Institute, Chevy Chase, MD,
                 USA.",
  journal     = "Science",
  volume      =  356,
  number      =  6335,
  month       =  apr,
  year        =  2017,
  url         = "http://dx.doi.org/10.1126/science.aah4573",
  language    = "en",
  issn        = "0036-8075, 1095-9203",
  pmid        = "28428369",
  doi         = "10.1126/science.aah4573"
}

@ARTICLE{Stegle2015-yu,
  title       = "Computational and analytical challenges in single-cell
                 transcriptomics",
  author      = "Stegle, Oliver and Teichmann, Sarah A and Marioni, John C",
  affiliation = "European Molecular Biology Laboratory European Bioinformatics
                 Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
                 CB10 1SD, UK. 1] European Molecular Biology Laboratory
                 European Bioinformatics Institute, Wellcome Trust Genome
                 Campus, Hinxton, Cambridge, CB10 1SD, UK. [2] Wellcome Trust
                 Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
                 Cambridge, CB10 1SA, UK.",
  journal     = "Nat. Rev. Genet.",
  volume      =  16,
  number      =  3,
  pages       = "133--145",
  month       =  mar,
  year        =  2015,
  url         = "http://dx.doi.org/10.1038/nrg3833",
  language    = "en",
  issn        = "1471-0056, 1471-0064",
  pmid        = "25628217",
  doi         = "10.1038/nrg3833"
}

@ARTICLE{Satija2015-rr,
  title       = "Spatial reconstruction of single-cell gene expression data",
  author      = "Satija, Rahul and Farrell, Jeffrey A and Gennert, David and
                 Schier, Alexander F and Regev, Aviv",
  affiliation = "Broad Institute of MIT and Harvard, Cambridge, Massachusetts,
                 USA. Department of Molecular and Cellular Biology, Harvard
                 University, Cambridge, Massachusetts, USA. 1] Broad Institute
                 of MIT and Harvard, Cambridge, Massachusetts, USA. [2]
                 Department of Molecular and Cellular Biology, Harvard
                 University, Cambridge, Massachusetts, USA. [3] Center for
                 Brain Science, Harvard University, Cambridge, Massachusetts,
                 USA. [4] Harvard Stem Cell Institute, Harvard University,
                 Cambridge, Massachusetts, USA. [5] Center for Systems Biology,
                 Harvard University, Cambridge, Massachusetts, USA. 1] Broad
                 Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
                 [2] Howard Hughes Medical Institute, Department of Biology,
                 Massachusetts Institute of Technology, Cambridge,
                 Massachusetts, USA.",
  journal     = "Nat. Biotechnol.",
  volume      =  33,
  number      =  5,
  pages       = "495--502",
  month       =  may,
  year        =  2015,
  url         = "http://dx.doi.org/10.1038/nbt.3192",
  language    = "en",
  issn        = "1087-0156, 1546-1696",
  pmid        = "25867923",
  doi         = "10.1038/nbt.3192",
  pmc         = "PMC4430369"
}

@ARTICLE{Kharchenko2014-it,
  title       = "Bayesian approach to single-cell differential expression
                 analysis",
  author      = "Kharchenko, Peter V and Silberstein, Lev and Scadden, David T",
  affiliation = "1] Center for Biomedical Informatics, Harvard Medical School,
                 Boston, Massachusetts, USA. [2] Hematology/Oncology Program,
                 Children's Hospital, Boston, Massachusetts, USA. [3] Harvard
                 Stem Cell Institute, Cambridge, Massachusetts, USA. 1] Harvard
                 Stem Cell Institute, Cambridge, Massachusetts, USA. [2] Center
                 for Regenerative Medicine, Massachusetts General Hospital,
                 Boston, Massachusetts, USA. [3] Department of Stem Cell and
                 Regenerative Biology, Harvard University, Cambridge,
                 Massachusetts, USA.",
  journal     = "Nat. Methods",
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  month       =  jul,
  year        =  2014,
  url         = "http://dx.doi.org/10.1038/nmeth.2967",
  language    = "en",
  issn        = "1548-7091, 1548-7105",
  pmid        = "24836921",
  doi         = "10.1038/nmeth.2967",
  pmc         = "PMC4112276"
}

@ARTICLE{McCarthy2017-fb,
  title       = "Scater: pre-processing, quality control, normalization and
                 visualization of single-cell {RNA-seq} data in {R}",
  author      = "McCarthy, Davis J and Campbell, Kieran R and Lun, Aaron T L
                 and Wills, Quin F",
  affiliation = "European Molecular Biology Laboratory, European Bioinformatics
                 Institute, Wellcome Genome Campus, CB10 1SD Hinxton,
                 Cambridge, UK. Wellcome Trust Centre for Human Genetics,
                 University of Oxford, Oxford OX3 7BN, UK. St Vincent's
                 Institute of Medical Research, Fitzroy, Victoria 3065,
                 Australia. Department of Physiology, Anatomy and Genetics,
                 University of Oxford, Oxford OX1 3QX, UK. CRUK Cambridge
                 Institute, University of Cambridge, Cambridge CB2 0RE, UK.
                 Weatherall Institute for Molecular Medicine, University of
                 Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK.",
  journal     = "Bioinformatics",
  volume      =  33,
  number      =  8,
  pages       = "1179--1186",
  month       =  apr,
  year        =  2017,
  url         = "http://dx.doi.org/10.1093/bioinformatics/btw777",
  language    = "en",
  issn        = "1367-4803, 1367-4811",
  pmid        = "28088763",
  doi         = "10.1093/bioinformatics/btw777",
  pmc         = "PMC5408845"
}

@ARTICLE{Qiu2017-vh,
  title       = "Single-cell {mRNA} quantification and differential analysis
                 with Census",
  author      = "Qiu, Xiaojie and Hill, Andrew and Packer, Jonathan and Lin,
                 Dejun and Ma, Yi-An and Trapnell, Cole",
  affiliation = "Department of Genome Sciences, University of Washington,
                 Seattle, Washington, USA. Molecular and Cellular Biology
                 Program, University of Washington, Seattle, Washington, USA.
                 Department of Applied Mathematics, University of Washington,
                 Seattle, Washington, USA.",
  journal     = "Nat. Methods",
  volume      =  14,
  number      =  3,
  pages       = "309--315",
  month       =  mar,
  year        =  2017,
  url         = "http://dx.doi.org/10.1038/nmeth.4150",
  language    = "en",
  issn        = "1548-7091, 1548-7105",
  pmid        = "28114287",
  doi         = "10.1038/nmeth.4150",
  pmc         = "PMC5330805"
}

@ARTICLE{Fan2016-lt,
  title       = "Characterizing transcriptional heterogeneity through pathway
                 and gene set overdispersion analysis",
  author      = "Fan, Jean and Salathia, Neeraj and Liu, Rui and Kaeser,
                 Gwendolyn E and Yung, Yun C and Herman, Joseph L and Kaper,
                 Fiona and Fan, Jian-Bing and Zhang, Kun and Chun, Jerold and
                 Kharchenko, Peter V",
  affiliation = "Department of Biomedical Informatics, Harvard Medical School,
                 Boston, Massachusetts, USA. Illumina Inc., San Diego,
                 California, USA. Department of Bioengineering, University of
                 California, San Diego, California, USA. Department of
                 Molecular and Cellular Neuroscience, Dorris Neuroscience
                 Center, The Scripps Research Institute, La Jolla, California,
                 USA. Present address: AnchorDx Corporation, International
                 Biotech Island, Guangzhou, Guangdong, China.",
  journal     = "Nat. Methods",
  volume      =  13,
  number      =  3,
  pages       = "241--244",
  month       =  mar,
  year        =  2016,
  url         = "http://dx.doi.org/10.1038/nmeth.3734",
  language    = "en",
  issn        = "1548-7091, 1548-7105",
  pmid        = "26780092",
  doi         = "10.1038/nmeth.3734",
  pmc         = "PMC4772672"
}

@ARTICLE{Ntranos2016-ff,
  title       = "Fast and accurate single-cell {RNA-seq} analysis by clustering
                 of transcript-compatibility counts",
  author      = "Ntranos, Vasilis and Kamath, Govinda M and Zhang, Jesse M and
                 Pachter, Lior and Tse, David N",
  affiliation = "Department of Electrical Engineering and Computer Sciences,
                 University of California, Berkeley, CA, USA. Department of
                 Electrical Engineering, Stanford University, Stanford, CA,
                 USA. Departments of Mathematics and Molecular and Cell
                 Biology, University of California, Berkeley, CA, USA.
                 lpachter@math.berkeley.edu. Department of Electrical
                 Engineering and Computer Sciences, University of California,
                 Berkeley, CA, USA. dntse@stanford.edu. Department of
                 Electrical Engineering, Stanford University, Stanford, CA,
                 USA. dntse@stanford.edu.",
  journal     = "Genome Biol.",
  volume      =  17,
  number      =  1,
  pages       = "112",
  month       =  may,
  year        =  2016,
  url         = "http://dx.doi.org/10.1186/s13059-016-0970-8",
  language    = "en",
  issn        = "1465-6906",
  pmid        = "27230763",
  doi         = "10.1186/s13059-016-0970-8",
  pmc         = "PMC4881296"
}

@ARTICLE{Navin2011-hk,
  title       = "Tumour evolution inferred by single-cell sequencing",
  author      = "Navin, Nicholas and Kendall, Jude and Troge, Jennifer and
                 Andrews, Peter and Rodgers, Linda and McIndoo, Jeanne and
                 Cook, Kerry and Stepansky, Asya and Levy, Dan and Esposito,
                 Diane and Muthuswamy, Lakshmi and Krasnitz, Alex and McCombie,
                 W Richard and Hicks, James and Wigler, Michael",
  affiliation = "Cold Spring Harbor Laboratory, Cold Spring Harbor, New York
                 11724, USA.",
  journal     = "Nature",
  volume      =  472,
  number      =  7341,
  pages       = "90--94",
  month       =  apr,
  year        =  2011,
  url         = "http://dx.doi.org/10.1038/nature09807",
  language    = "en",
  issn        = "0028-0836, 1476-4687",
  pmid        = "21399628",
  doi         = "10.1038/nature09807",
  pmc         = "PMC4504184"
}

@UNPUBLISHED{Qiu2017-pu,
  title    = "Reversed graph embedding resolves complex single-cell
              developmental trajectories",
  author   = "Qiu, Xiaojie and Mao, Qi and Tang, Ying and Wang, Li and Chawla,
              Raghav and Pliner, Hannah and Trapnell, Cole",
  journal  = "bioRxiv",
  pages    = "110668",
  month    =  feb,
  year     =  2017,
  url      = "http://www.biorxiv.org/content/early/2017/02/21/110668",
  language = "en",
  doi      = "10.1101/110668"
}

@ARTICLE{Finak2015-ah,
  title       = "{MAST}: a flexible statistical framework for assessing
                 transcriptional changes and characterizing heterogeneity in
                 single-cell {RNA} sequencing data",
  author      = "Finak, Greg and McDavid, Andrew and Yajima, Masanao and Deng,
                 Jingyuan and Gersuk, Vivian and Shalek, Alex K and Slichter,
                 Chloe K and Miller, Hannah W and McElrath, M Juliana and
                 Prlic, Martin and Linsley, Peter S and Gottardo, Raphael",
  affiliation = "Vaccine and Infectious Disease Division, Fred Hutchinson
                 Cancer Research Center, Seattle, WA, 98109, USA.
                 gfinak@fredhutch.org. Vaccine and Infectious Disease Division,
                 Fred Hutchinson Cancer Research Center, Seattle, WA, 98109,
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                 Division, Fred Hutchinson Cancer Research Center, Seattle, WA,
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                 Seattle, WA, 98109, USA. jdeng@fredhutch.org. Benaroya
                 Research Institute at Virginia Mason, Seattle, WA, 98101, USA.
                 vgersuk@benaroyaresearch.org. Institute for Medical
                 Engineering \& Science, MIT, Boston, MA, 01239-4307, USA.
                 shalek@mit.edu. Department of Chemistry, MIT, Boston, MA,
                 01239-4307, USA. shalek@mit.edu. Ragon Institute of MGH, MIT,
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                 Institute of MIT \& Harvard, Boston, MA, 01242, USA.
                 shalek@mit.edu. Vaccine and Infectious Disease Division, Fred
                 Hutchinson Cancer Research Center, Seattle, WA, 98109, USA.
                 cslichte@fredhutch.org. Vaccine and Infectious Disease
                 Division, Fred Hutchinson Cancer Research Center, Seattle, WA,
                 98109, USA. hwmiller@fredhutch.org. Vaccine and Infectious
                 Disease Division, Fred Hutchinson Cancer Research Center,
                 Seattle, WA, 98109, USA. jmcelrat@fredhutch.org. Vaccine and
                 Infectious Disease Division, Fred Hutchinson Cancer Research
                 Center, Seattle, WA, 98109, USA. mprlic@fredhutch.org.
                 Benaroya Research Institute at Virginia Mason, Seattle, WA,
                 98101, USA. plinsley@benaroyaresearch.org. Vaccine and
                 Infectious Disease Division, Fred Hutchinson Cancer Research
                 Center, Seattle, WA, 98109, USA. rgottard@fredhutch.org.
                 Public Health Sciences Division, Fred Hutchinson Cancer
                 Research Center, Seattle, WA, 98109, USA.
                 rgottard@fredhutch.org.",
  journal     = "Genome Biol.",
  volume      =  16,
  pages       = "278",
  month       =  dec,
  year        =  2015,
  url         = "http://dx.doi.org/10.1186/s13059-015-0844-5",
  language    = "en",
  issn        = "1465-6906",
  pmid        = "26653891",
  doi         = "10.1186/s13059-015-0844-5",
  pmc         = "PMC4676162"
}

@ARTICLE{Korthauer2016-ba,
  title       = "A statistical approach for identifying differential
                 distributions in single-cell {RNA-seq} experiments",
  author      = "Korthauer, Keegan D and Chu, Li-Fang and Newton, Michael A and
                 Li, Yuan and Thomson, James and Stewart, Ron and Kendziorski,
                 Christina",
  affiliation = "Department of Biostatistics and Computational Biology,
                 Dana-Farber Cancer Institute, Boston, 02215, MA, USA.
                 Department of Biostatistics, Harvard T. H. Chan School of
                 Public Health, Boston, 02115, MA, USA. Morgridge Institute for
                 Research, University of Wisconsin, Madison, 53706, WI, USA.
                 Department of Biostatistics, University of Wisconsin, Madison,
                 53706, WI, USA. Department of Statistics, University of
                 Wisconsin, Madison, 53706, WI, USA. Department of Cell and
                 Regenerative Biology, University of Wisconsin, Madison, 53706,
                 WI, USA. Department of Molecular, Cellular, and Developmental
                 Biology, University of California, Santa Barbara, 93106, CA,
                 USA. Department of Biostatistics, University of Wisconsin,
                 Madison, 53706, WI, USA. kendzior@biostat.wisc.edu. Department
                 of Statistics, University of Wisconsin, Madison, 53706, WI,
                 USA. kendzior@biostat.wisc.edu.",
  journal     = "Genome Biol.",
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  year        =  2016,
  url         = "http://dx.doi.org/10.1186/s13059-016-1077-y",
  language    = "en",
  issn        = "1465-6906",
  pmid        = "27782827",
  doi         = "10.1186/s13059-016-1077-y",
  pmc         = "PMC5080738"
}

@ARTICLE{Kolodziejczyk2015-em,
  title       = "The technology and biology of single-cell {RNA} sequencing",
  author      = "Kolodziejczyk, Aleksandra A and Kim, Jong Kyoung and Svensson,
                 Valentine and Marioni, John C and Teichmann, Sarah A",
  affiliation = "European Molecular Biology Laboratory, European Bioinformatics
                 Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton,
                 Cambridge CB10 1SD, UK; Wellcome Trust Sanger Institute,
                 Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK.
                 European Molecular Biology Laboratory, European Bioinformatics
                 Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton,
                 Cambridge CB10 1SD, UK. European Molecular Biology Laboratory,
                 European Bioinformatics Institute (EMBL-EBI), Wellcome Trust
                 Genome Campus, Hinxton, Cambridge CB10 1SD, UK; Wellcome Trust
                 Sanger Institute, Wellcome Trust Genome Campus, Hinxton,
                 Cambridge CB10 1SA, UK. Electronic address: saraht@ebi.ac.uk.",
  journal     = "Mol. Cell",
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  year        =  2015,
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@ARTICLE{Junker2015-xn,
  title       = "Single-cell transcriptomics enters the age of mass production",
  author      = "Junker, Jan Philipp and van Oudenaarden, Alexander",
  affiliation = "Hubrecht Institute-KNAW and University Medical Center Utrecht,
                 3584 CT Utrecht, the Netherlands; Berlin Institute for Medical
                 Systems Biology, Max Delbr{\"u}ck Center for Molecular
                 Medicine, 13092 Berlin-Buch, Germany. Electronic address:
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                 Medical Center Utrecht, 3584 CT Utrecht, the Netherlands.
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  journal     = "Mol. Cell",
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  year        =  2015,
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  pmid        = "26000840",
  doi         = "10.1016/j.molcel.2015.05.019"
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@ARTICLE{Klein2015-oz,
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                 embryonic stem cells",
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                 Tallapragada, Naren and Veres, Adrian and Li, Victor and
                 Peshkin, Leonid and Weitz, David A and Kirschner, Marc W",
  affiliation = "Department of Systems Biology, Harvard Medical School, Boston,
                 MA 02115, USA. School of Engineering and Applied Sciences
                 (SEAS), Harvard University, Cambridge, MA 02138, USA; Vilnius
                 University Institute of Biotechnology, Vilnius LT-02241,
                 Lithuania. School of Engineering and Applied Sciences (SEAS),
                 Harvard University, Cambridge, MA 02138, USA. Department of
                 Systems Biology, Harvard Medical School, Boston, MA 02115,
                 USA; Department of Stem Cell and Regenerative Biology, Harvard
                 University, Cambridge, MA 02138, USA; Harvard Stem Cell
                 Institute, Harvard University, Cambridge, MA 02138, USA.
                 School of Engineering and Applied Sciences (SEAS), Harvard
                 University, Cambridge, MA 02138, USA. Electronic address:
                 weitz@seas.harvard.edu. Department of Systems Biology, Harvard
                 Medical School, Boston, MA 02115, USA. Electronic address:
                 marc@hms.harvard.edu.",
  journal     = "Cell",
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  year        =  2015,
  url         = "http://dx.doi.org/10.1016/j.cell.2015.04.044",
  language    = "en",
  issn        = "0092-8674, 1097-4172",
  pmid        = "26000487",
  doi         = "10.1016/j.cell.2015.04.044",
  pmc         = "PMC4441768"
}

@UNPUBLISHED{Hicks2017-ok,
  title    = "Missing Data and Technical Variability in {Single-Cell} {RNA-}
              Sequencing Experiments",
  author   = "Hicks, Stephanie C and William Townes, F and Teng, Mingxiang and
              Irizarry, Rafael A",
  journal  = "bioRxiv",
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  month    =  may,
  year     =  2017,
  url      = "http://www.biorxiv.org/content/early/2017/05/08/025528",
  language = "en",
  doi      = "10.1101/025528"
}

@ARTICLE{Macosko2015-zz,
  title       = "Highly Parallel Genome-wide Expression Profiling of Individual
                 Cells Using Nanoliter Droplets",
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                 Nemesh, James and Shekhar, Karthik and Goldman, Melissa and
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                 Martersteck, Emily M and Trombetta, John J and Weitz, David A
                 and Sanes, Joshua R and Shalek, Alex K and Regev, Aviv and
                 McCarroll, Steven A",
  affiliation = "Department of Genetics, Harvard Medical School, Boston, MA
                 02115, USA; Stanley Center for Psychiatric Research, Broad
                 Institute of Harvard and MIT, Cambridge, MA 02142, USA;
                 Program in Medical and Population Genetics, Broad Institute of
                 Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:
                 emacosko@genetics.med.harvard.edu. Klarman Cell Observatory,
                 Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA;
                 School of Engineering and Applied Sciences, Harvard
                 University, Cambridge, MA 02138, USA. Klarman Cell
                 Observatory, Broad Institute of Harvard and MIT, Cambridge, MA
                 02142, USA; New York Genome Center, New York, NY 10013, USA;
                 Department of Biology, New York University, New York, NY
                 10003, USA. Department of Genetics, Harvard Medical School,
                 Boston, MA 02115, USA; Stanley Center for Psychiatric
                 Research, Broad Institute of Harvard and MIT, Cambridge, MA
                 02142, USA; Program in Medical and Population Genetics, Broad
                 Institute of Harvard and MIT, Cambridge, MA 02142, USA.
                 Klarman Cell Observatory, Broad Institute of Harvard and MIT,
                 Cambridge, MA 02142, USA. Department of Genetics, Harvard
                 Medical School, Boston, MA 02115, USA; Stanley Center for
                 Psychiatric Research, Broad Institute of Harvard and MIT,
                 Cambridge, MA 02142, USA. The Program in Cellular and
                 Molecular Medicine, Children's Hospital Boston, Boston, MA
                 02115, USA. Department of Molecular and Cellular Biology and
                 Center for Brain Science, Harvard University, Cambridge, MA
                 02138, USA. School of Engineering and Applied Sciences,
                 Harvard University, Cambridge, MA 02138, USA; Department of
                 Physics, Harvard University, Cambridge, MA 02138, USA. Klarman
                 Cell Observatory, Broad Institute of Harvard and MIT,
                 Cambridge, MA 02142, USA; Ragon Institute of MGH, MIT, and
                 Harvard, Cambridge, MA 02139, USA; Institute for Medical
                 Engineering and Science and Department of Chemistry, MIT,
                 Cambridge, MA 02139, USA. Klarman Cell Observatory, Broad
                 Institute of Harvard and MIT, Cambridge, MA 02142, USA;
                 Department of Biology, MIT, Cambridge, MA 02139, USA; Howard
                 Hughes Medical Institute, Chevy Chase, MD 20815, USA.
                 Department of Genetics, Harvard Medical School, Boston, MA
                 02115, USA; Stanley Center for Psychiatric Research, Broad
                 Institute of Harvard and MIT, Cambridge, MA 02142, USA;
                 Program in Medical and Population Genetics, Broad Institute of
                 Harvard and MIT, Cambridge, MA 02142, USA. Electronic address:
                 mccarroll@genetics.med.harvard.edu.",
  journal     = "Cell",
  volume      =  161,
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  month       =  may,
  year        =  2015,
  url         = "http://dx.doi.org/10.1016/j.cell.2015.05.002",
  language    = "en",
  issn        = "0092-8674, 1097-4172",
  pmid        = "26000488",
  doi         = "10.1016/j.cell.2015.05.002",
  pmc         = "PMC4481139"
}

@ARTICLE{Aflalo2015-fw,
  title     = "Decoding motor imagery from the posterior parietal cortex of a
               tetraplegic human",
  author    = "Aflalo, Tyson and Kellis, Spencer and Klaes, Christian and Lee,
               Brian and Shi, Ying and Pejsa, Kelsie and Shanfield, Kathleen
               and Hayes-Jackson, Stephanie and Aisen, Mindy and Heck, Christi
               and Liu, Charles and Andersen, Richard A",
  journal   = "Science",
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  volume    =  348,
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  pages     = "906--910",
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  year      =  2015,
  url       = "http://science.sciencemag.org/content/348/6237/906",
  language  = "en",
  issn      = "0036-8075, 1095-9203",
  pmid      = "25999506",
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}

@ARTICLE{Hashimshony2016-vu,
  title       = "{CEL-Seq2}: sensitive highly-multiplexed single-cell {RNA-Seq}",
  author      = "Hashimshony, Tamar and Senderovich, Naftalie and Avital, Gal
                 and Klochendler, Agnes and de Leeuw, Yaron and Anavy, Leon and
                 Gennert, Dave and Li, Shuqiang and Livak, Kenneth J and
                 Rozenblatt-Rosen, Orit and Dor, Yuval and Regev, Aviv and
                 Yanai, Itai",
  affiliation = "Department of Biology, Technion - Israel Institute of
                 Technology, Haifa, Israel. Department of Developmental Biology
                 and Cancer Research, The Institute for Medical Research
                 Israel-Canada, The Hebrew University-Hadassah Medical School,
                 Jerusalem, Israel. Klarman Cell Observatory, Broad Institute
                 of Harvard and MIT, Cambridge, MA, 02142, USA. Department of
                 Biology, MIT, Cambridge, MA, 02139, USA. Howard Hughes Medical
                 Institute, Department of Biology, Massachusetts Institute of
                 Technology, Cambridge, MA, 02140, USA. Fluidigm Corporation,
                 7000 Shoreline Court, Suite 100, South San Francisco, CA,
                 94080, USA. Department of Biology, Technion - Israel Institute
                 of Technology, Haifa, Israel. yanai@technion.ac.il.",
  journal     = "Genome Biol.",
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  month       =  apr,
  year        =  2016,
  url         = "http://dx.doi.org/10.1186/s13059-016-0938-8",
  language    = "en",
  issn        = "1465-6906",
  pmid        = "27121950",
  doi         = "10.1186/s13059-016-0938-8",
  pmc         = "PMC4848782"
}

@UNPUBLISHED{Cao2017-hv,
  title    = "Comprehensive single cell transcriptional profiling of a
              multicellular organism by combinatorial indexing",
  author   = "Cao, Junyue and Packer, Jonathan S and Ramani, Vijay and
              Cusanovich, Darren A and Huynh, Chau and Daza, Riza and Qiu,
              Xiaojie and Lee, Choli and Furlan, Scott N and Steemers, Frank J
              and Adey, Andrew and Waterston, Robert H and Trapnell, Cole and
              Shendure, Jay",
  journal  = "bioRxiv",
  pages    = "104844",
  month    =  feb,
  year     =  2017,
  url      = "http://www.biorxiv.org/content/early/2017/02/02/104844",
  language = "en",
  doi      = "10.1101/104844"
}

@ARTICLE{Buettner2015-ur,
  title       = "Computational analysis of cell-to-cell heterogeneity in
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                 Fabian J and Teichmann, Sarah A and Marioni, John C and
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                 Laboratory, European Bioinformatics Institute, Wellcome Trust
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                 Wellcome Trust Sanger Institute, Hinxton, UK. European
                 Molecular Biology Laboratory, European Bioinformatics
                 Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge,
                 UK. 1] Helmholtz Zentrum M{\"u}nchen-German Research Center
                 for Environmental Health, Institute of Computational Biology,
                 Neuherberg, Germany. [2] Department of Mathematics, Technische
                 Universit{\"a}t M{\"u}nchen, Munich, Germany.",
  journal     = "Nat. Biotechnol.",
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  url         = "http://dx.doi.org/10.1038/nbt.3102",
  language    = "en",
  issn        = "1087-0156, 1546-1696",
  pmid        = "25599176",
  doi         = "10.1038/nbt.3102"
}

@ARTICLE{Brennecke2013-iz,
  title       = "Accounting for technical noise in single-cell {RNA-seq}
                 experiments",
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                 Ko{\l}odziejczyk, Aleksandra A and Zhang, Xiuwei and
                 Proserpio, Valentina and Baying, Bianka and Benes, Vladimir
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  affiliation = "1] European Molecular Biology Laboratory (EMBL), Heidelberg,
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  issn        = "1548-7091, 1548-7105",
  pmid        = "24056876",
  doi         = "10.1038/nmeth.2645"
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@ARTICLE{Blainey2014-ym,
  title   = "Points of Significance: Replication",
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