% Updated 2019-09-10.



% General                                                                   {{{1
% ==============================================================================

@ARTICLE{Casper2018-ua,
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@BOOK{Wickham2009-si,
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}



% RNA-seq                                                                   {{{1
% ==============================================================================

@ARTICLE{Anders2010-sh,
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% Single-cell RNA-seq                                                       {{{1
% ==============================================================================

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                 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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  language    = "en",
  issn        = "1465-6906",
  pmid        = "27121950",
  doi         = "10.1186/s13059-016-0938-8",
  pmc         = "PMC4848782"
}

@ARTICLE{Hicks2017-ec,
  title       = "Missing data and technical variability in single-cell
                 {RNA-sequencing} experiments",
  author      = "Hicks, Stephanie C and Townes, F William and Teng, Mingxiang
                 and Irizarry, Rafael A",
  affiliation = "Department of Biostatistics, Harvard T. H. Chan School of
                 Public Health, Boston, MA, USA and Department of Biostatistics
                 and Computational Biology, Dana-Farber Cancer Institute,
                 Boston, MA, USA. Department of Biostatistics, Harvard T.H.
                 Chan School of Public Health, Boston, MA, USA. Department of
                 Biostatistics, Harvard T.H. Chan School of Public Health,
                 Boston, MA, USA and Department of Biostatistics and
                 Computational Biology, Dana-Farber Cancer Institute, Boston,
                 MA, USA.",
  journal     = "Biostatistics",
  month       =  nov,
  year        =  2017,
  url         = "http://dx.doi.org/10.1093/biostatistics/kxx053",
  language    = "en",
  issn        = "1465-4644, 1468-4357",
  pmid        = "29121214",
  doi         = "10.1093/biostatistics/kxx053"
}

@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.",
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  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"
}

@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:
                 j.junker@hubrecht.eu. Hubrecht Institute-KNAW and University
                 Medical Center Utrecht, 3584 CT Utrecht, the Netherlands.
                 Electronic address: a.vanoudenaarden@hubrecht.eu.",
  journal     = "Mol. Cell",
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  pmid        = "26000840",
  doi         = "10.1016/j.molcel.2015.05.019"
}

@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.",
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  language    = "en",
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@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",
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  language    = "en",
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  doi         = "10.1038/nmeth.4236",
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}

@ARTICLE{Klein2015-oz,
  title       = "Droplet barcoding for single-cell transcriptomics applied to
                 embryonic stem cells",
  author      = "Klein, Allon M and Mazutis, Linas and Akartuna, Ilke and
                 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.",
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  language    = "en",
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  pmid        = "26000487",
  doi         = "10.1016/j.cell.2015.04.044",
  pmc         = "PMC4441768"
}

@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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  pmid        = "26000846",
  doi         = "10.1016/j.molcel.2015.04.005"
}

@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.",
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  language    = "en",
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  pmc         = "PMC5080738"
}

@ARTICLE{Levine2015-hr,
  title       = "{Data-Driven} Phenotypic Dissection of {AML} Reveals
                 Progenitor-like Cells that Correlate with Prognosis",
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                 Davis, Kara L and Amir, El-Ad D and Tadmor, Michelle D and
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  affiliation = "Departments of Biological Sciences and Systems Biology,
                 Columbia University, New York, NY 10027, USA. Baxter
                 Laboratory in Stem Cell Biology, Department of Microbiology
                 and Immunology, Stanford University, Stanford, CA 94305, USA.
                 Department of Pathology, Stanford University, Stanford, CA
                 94305, USA. Department of Pathology, St. Jude Children's
                 Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105,
                 USA. Departments of Biological Sciences and Systems Biology,
                 Columbia University, New York, NY 10027, USA. Electronic
                 address: dpeer@biology.columbia.edu. Baxter Laboratory in Stem
                 Cell Biology, Department of Microbiology and Immunology,
                 Stanford University, Stanford, CA 94305, USA. Electronic
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  pmc         = "PMC4508757"
}

@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.",
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  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"
}

@ARTICLE{Macosko2015-zz,
  title       = "Highly Parallel Genome-wide Expression Profiling of Individual
                 Cells Using Nanoliter Droplets",
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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
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                 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
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                 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.",
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  doi         = "10.1016/j.cell.2015.05.002",
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}

@ARTICLE{McCarthy2017-fb,
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  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.",
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}

@ARTICLE{Navin2011-hk,
  title       = "Tumour evolution inferred by single-cell sequencing",
  author      = "Navin, Nicholas and Kendall, Jude and Troge, Jennifer and
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@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.
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                 Electrical Engineering, Stanford University, Stanford, CA,
                 USA. dntse@stanford.edu.",
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@ARTICLE{Qiu2017-my,
  title     = "Reversed graph embedding resolves complex single-cell
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@ARTICLE{Qiu2017-vh,
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                 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.",
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@ARTICLE{Satija2015-rr,
  title       = "Spatial reconstruction of single-cell gene expression data",
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  affiliation = "Broad Institute of MIT and Harvard, Cambridge, Massachusetts,
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                 Cambridge, Massachusetts, USA. [5] Center for Systems Biology,
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                 Institute of MIT and Harvard, Cambridge, Massachusetts, USA.
                 [2] Howard Hughes Medical Institute, Department of Biology,
                 Massachusetts Institute of Technology, Cambridge,
                 Massachusetts, USA.",
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  pmid        = "25867923",
  doi         = "10.1038/nbt.3192",
  pmc         = "PMC4430369"
}

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                 Rehovot, Israel. Department of Pathology, Stanford University,
                 Stanford, California, USA.",
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@ARTICLE{Villani2017-cs,
  title       = "Single-cell {RNA-seq} reveals new types of human blood
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                 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.",
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@ARTICLE{Wang2017-jj,
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                 kernel-based similarity learning",
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  journal     = "Nat. Methods",
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@ARTICLE{Wattenberg2016-wv,
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@ARTICLE{Xu2015-je,
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@ARTICLE{Zilionis2017-tn,
  title       = "Single-cell barcoding and sequencing using droplet
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  author      = "Zilionis, Rapolas and Nainys, Juozas and Veres, Adrian and
                 Savova, Virginia and Zemmour, David and Klein, Allon M and
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  affiliation = "Institute of Biotechnology, Vilnius University, Vilnius,
                 Lithuania. Department of Systems Biology, Harvard Medical
                 School, Boston, Massachusetts, USA. Department of Stem Cell
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@UNPUBLISHED{Butler2017-qe,
  title    = "Integrated analysis of single cell transcriptomic data across
              conditions, technologies, and species",
  author   = "Butler, Andrew and Satija, Rahul",
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  url      = "http://www.biorxiv.org/content/early/2017/07/18/164889",
  language = "en",
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@UNPUBLISHED{Cao2017-hv,
  title    = "Comprehensive single cell transcriptional profiling of a
              multicellular organism by combinatorial indexing",
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              Shendure, Jay",
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@UNPUBLISHED{Griffiths2017-ob,
  title    = "Detection and removal of barcode swapping in single-cell
              {RNA-seq} data",
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@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
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@UNPUBLISHED{Qiu2017-pu,
  title    = "Reversed graph embedding resolves complex single-cell
              developmental trajectories",
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@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",
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@UNPUBLISHED{Van_den_Berge2017-hv,
  title    = "zingeR: unlocking {RNA-seq} tools for zero-inflation and single
              cell applications",
  author   = "Van den Berge, Koen and Soneson, Charlotte and Love, Michael I
              and Robinson, Mark D and Clement, Lieven",
  journal  = "bioRxiv",
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  url      = "https://www.biorxiv.org/content/early/2017/06/30/157982",
  language = "en",
  doi      = "10.1101/157982"
}

@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"
}
