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@BOOK{Lawson1995-NNLS2,
  title     = "Solving Least Squares Problems",
  author    = "Lawson, Charles L and Hanson, Richard J",
  publisher = "SIAM",
  year      =  1995,
  address   = "Philadelphia, PA"
}

@BOOK{Lawson1974-NNLS1,
  title     = "Solving least squares problems prentice-hall",
  author    = "Lawson, Charles L and Hanson, R J",
  publisher = "Prentice Hall",
  year      =  1974,
  address   = "Englewood Cliffs, NJ"
}

@ARTICLE{Coursey2015,
  title   = "Atomic weights and isotopic compositions with relative atomic
             masses",
  author  = "Coursey, J S and Schwab, D J and Tsai, J J and Dragoset, R A",
  journal = "NIST Physical Measurement Laboratory",
  year    =  2015
}

@ARTICLE{Finney1971,
  title     = "Probit Analysis",
  author    = "Finney, D J",
  journal   = "Journal of Pharmaceutical Sciences",
  publisher = "Elsevier",
  volume    =  60,
  number    =  9,
  pages     = "1432",
  year      =  1971
}

@ARTICLE{Bodenmiller2012,
  title    = "Multiplexed mass cytometry profiling of cellular states perturbed
              by small-molecule regulators",
  author   = "Bodenmiller, Bernd and Zunder, Eli R and Finck, Rachel and Chen,
              Tiffany J and Savig, Erica S and Bruggner, Robert V and Simonds,
              Erin F and Bendall, Sean C and Sachs, Karen and Krutzik, Peter O
              and Nolan, Garry P",
  journal  = "Nature Biotechnology",
  volume   =  30,
  number   =  9,
  pages    = "858--867",
  year     =  2012,
  language = "en"
}

@ARTICLE{Ritz2015,
  title   = "{Dose-Response} Analysis Using {R}",
  author  = "Ritz, Christian and Baty, Florent and Streibig, Jens C and
             Gerhard, Daniel",
  journal = "PLoS One",
  volume  =  10,
  number  =  12,
  pages   = "e0146021",
  year    =  2015
}

@ARTICLE{Monti2003-ConsensusClusterPlus,
  title   = "Consensus Clustering: A {Resampling-Based} Method for Class
             Discovery and Visualization of Gene Expression Microarray Data",
  author  = "Monti, Stefano and Tamayo, Pablo and Mesirov, Jill and Golub, Todd",
  journal = "Machine Learning",
  volume  =  52,
  number  =  1,
  pages   = "91--118",
  year    =  2003
}

@ARTICLE{Zunder2015-debarcoding,
  title   = "Palladium-based mass tag cell barcoding with a doublet-filtering
             scheme and single-cell deconvolution algorithm",
  author  = "Zunder, Eli R and Finck, Rachel and Behbehani, Gregory K and Amir,
             El-Ad D and Krishnaswamy, Smita and Gonzalez, Veronica D and
             Lorang, Cynthia G and Bjornson, Zach and Spitzer, Matthew H and
             Bodenmiller, Bernd and Fantl, Wendy J and Pe'er, Dana and Nolan,
             Garry P",
  journal = "Nature Protocols",
  volume  =  10,
  number  =  2,
  pages   = "316--333",
  year    =  2015
}

@ARTICLE{Finck2013-normalization,
  title    = "Normalization of mass cytometry data with bead standards",
  author   = "Finck, Rachel and Simonds, Erin F and Jager, Astraea and
              Krishnaswamy, Smita and Sachs, Karen and Fantl, Wendy and Pe'er,
              Dana and Nolan, Garry P and Bendall, Sean C",
  journal  = "Cytometry A",
  volume   =  83,
  number   =  5,
  pages    = "483--494",
  year     =  2013,
  language = "en"
}

@ARTICLE{Weber2016-clustering,
  title   = "Comparison of clustering methods for high-dimensional single-cell
             flow and mass cytometry data",
  author  = "Weber, Lukas M and Robinson, Mark D",
  journal = "Cytometry A",
  volume  =  89,
  number  =  12,
  pages   = "1084--1096",
  year    =  2016
}

@ARTICLE{Nowicka2019-F1000,
  title   = "{CyTOF} workflow: differential discovery in high-throughput
             high-dimensional cytometry datasets",
  author  = "Nowicka, Malgorzata and Krieg, Carsten and Crowell, Helena L and
             Weber, Lukas M and Hartmann, Felix J and Guglietta, Silvia and
             Becher, Burkhard and Levesque, Mitchell P and Robinson, Mark D",
  journal = "F1000Research",
  volume  =  6,
  pages   = "748",
  year    =  2019
}

@ARTICLE{Kang2018-demuxlet,
  title   = "Multiplexed droplet single-cell {RNA-sequencing} using natural
             genetic variation",
  author  = "Kang, Hyun Min and Subramaniam, Meena and Targ, Sasha and Nguyen,
             Michelle and Maliskova, Lenka and McCarthy, Elizabeth and Wan,
             Eunice and Wong, Simon and Byrnes, Lauren and Lanata, Cristina M
             and Gate, Rachel E and Mostafavi, Sara and Marson, Alexander and
             Zaitlen, Noah and Criswell, Lindsey A and Ye, Chun Jimmie",
  journal = "Nature Biotechnology",
  volume  =  36,
  number  =  1,
  pages   = "89--94",
  year    =  2018
}

@ARTICLE{Freytag2018-clustering,
  title    = "Comparison of clustering tools in {R} for medium-sized 10x
              Genomics single-cell {RNA-sequencing} data",
  author   = "Freytag, Saskia and Tian, Luyi and L{\"o}nnstedt, Ingrid and Ng,
              Milica and Bahlo, Melanie",
  journal  = "F1000Research",
  volume   =  7,
  pages    = "1297",
  year     =  2018
}

@ARTICLE{Chevrier2018-CATALYST,
  title   = "Compensation of Signal Spillover in Suspension and Imaging Mass
             Cytometry",
  author  = "Chevrier, St{\'e}phane and Crowell, Helena L and Zanotelli, Vito R
             T and Engler, Stefanie and Robinson, Mark D and Bodenmiller, Bernd",
  journal = "Cell Systems",
  volume  =  6,
  number  =  5,
  pages   = "612--620.e5",
  year    =  2018
}

@ARTICLE{Bruggner2014-CITRUS,
  title   = "Automated identification of stratifying signatures in cellular
             subpopulations",
  author  = "Bruggner, Robert V and Bodenmiller, Bernd and Dill, David L and
             Tibshirani, Robert J and Nolan, Garry P",
  journal = "PNAS",
  volume  =  111,
  number  =  26,
  pages   = "E2770--7",
  year    =  2014
}

@ARTICLE{Weber2019-diffcyt,
  title   = "diffcyt: Differential discovery in high-dimensional cytometry via
             high-resolution clustering",
  author  = "Weber, Lukas M and Nowicka, Malgorzata and Soneson, Charlotte and
             Robinson, Mark D",
  journal = "Communications Biology",
  volume  =  2,
  pages   = "183",
  year    =  2019
}
