countland.bib

@article{wang2009rna,
  title={{R}{N}{A}-Seq: a revolutionary tool for transcriptomics},
  author={Wang, Zhong and Gerstein, Mark and Snyder, Michael},
  journal={Nature Reviews Genetics},
  volume={10},
  number={1},
  pages={57--63},
  year={2009},
  publisher={Nature Publishing Group}
}
@article{van2013rna,
  title={{R}{N}{A}-Seq: revelation of the messengers},
  author={Van Verk, Marcel C and Hickman, Richard and Pieterse, Corn{\'e} MJ and Van Wees, Saskia CM},
  journal={Trends in Plant Science},
  volume={18},
  number={4},
  pages={175--179},
  year={2013},
  publisher={Elsevier}
}
@article{booeshaghi2022depth,
  title={Depth normalization for single-cell genomics count data},
  author={Booeshaghi, A Sina and Hallgrímsdóttir, Ingileif B and Gálvez-Merchán, Ángel and Pachter, Lior},
  journal={BioRxiv},
  year={2022},
  publisher={Cold Spring Harbor Laboratory}
}
@article{wagner2012measurement,
  title={Measurement of m{R}{N}{A} abundance using {R}{N}{A}-seq data: RPKM measure is inconsistent among samples},
  author={Wagner, G{\"u}nter P and Kin, Koryu and Lynch, Vincent J},
  journal={Theory in Biosciences},
  volume={131},
  number={4},
  pages={281--285},
  year={2012},
  publisher={Springer}
}
@article{qiu2020embracing,
  title={Embracing the dropouts in single-cell {R}{N}{A}-seq analysis},
  author={Qiu, Peng},
  journal={Nature Communications},
  volume={11},
  number={1},
  pages={1--9},
  year={2020},
  publisher={Nature Publishing Group}
}
@article{warton2018you,
  title={Why you cannot transform your way out of trouble for small counts},
  author={Warton, David I},
  journal={Biometrics},
  volume={74},
  number={1},
  pages={362--368},
  year={2018},
  publisher={Wiley Online Library}
}
@article{houle2011measurement,
  title={Measurement and meaning in biology},
  author={Houle, David and P{\'e}labon, Christophe and Wagner, G{\"u}nter P and Hansen, Thomas F},
  journal={The Quarterly Review of Biology},
  volume={86},
  number={1},
  pages={3--34},
  year={2011},
  publisher={The University of Chicago Press}
}
@article{luecken2019current,
  title={Current best practices in single-cell {R}{N}{A}-seq analysis: a tutorial},
  author={Luecken, Malte D and Theis, Fabian J},
  journal={Molecular Systems Biology},
  volume={15},
  number={6},
  pages={e8746},
  year={2019}
}
@article{john2020spectrum,
  title={Spectrum: fast density-aware spectral clustering for single and multi-omic data},
  author={John, Christopher R and Watson, David and Barnes, Michael R and Pitzalis, Costantino and Lewis, Myles J},
  journal={Bioinformatics},
  volume={36},
  number={4},
  pages={1159--1166},
  year={2020},
  publisher={Oxford University Press}
}
@inproceedings{perros2018sustain,
  title={{S}{U}{S}{T}ain: Scalable unsupervised scoring for tensors and its application to phenotyping},
  author={Perros, Ioakeim and Papalexakis, Evangelos E and Park, Haesun and Vuduc, Richard and Yan, Xiaowei and Defilippi, Christopher and Stewart, Walter F and Sun, Jimeng},
  booktitle={Proceedings of the 24th ACM SIGKDD International Conference on Knowledge Discovery \& Data Mining},
  pages={2080--2089},
  year={2018}
}
@article{lin2005integer,
  title={Integer matrix factorization and its application},
  author={Lin, Matthew M and Dong, Bo and Chu, Moody T},
  journal={Technical Reports},
  year={2005}
}
@article{chari2021specious,
  title={The specious art of single-cell genomics},
  author={Chari, Tara and Banerjee, Joeyta and Pachter, Lior},
  journal={BioRxiv},
  year={2021},
  publisher={Cold Spring Harbor Laboratory}
}
@article{ng2001spectral,
  title={On spectral clustering: Analysis and an algorithm},
  author={Ng, Andrew and Jordan, Michael and Weiss, Yair},
  journal={Advances in Neural Information Processing Systems},
  pages={1--8},
  volume={14},
  year={2001}
}
@article{lun2018overcoming,
  title={Overcoming systematic errors caused by log-transformation of normalized single-cell {R}{N}{A} sequencing data},
  author={Lun, Aaron},
  journal={BioRxiv},
  pages={404962},
  year={2018},
  publisher={Cold Spring Harbor Laboratory}
}
@article{stuart2019comprehensive,
  title={Comprehensive integration of single-cell data},
  author={Stuart, Tim and Butler, Andrew and Hoffman, Paul and Hafemeister, Christoph and Papalexi, Efthymia and Mauck III, William M and Hao, Yuhan and Stoeckius, Marlon and Smibert, Peter and Satija, Rahul},
  journal={Cell},
  volume={177},
  number={7},
  pages={1888--1902},
  year={2019},
  publisher={Elsevier}
}
@article{pedregosa2011scikit,
  title={Scikit-learn: Machine learning in Python},
  author={Pedregosa, Fabian and Varoquaux, Ga{\"e}l and Gramfort, Alexandre and Michel, Vincent and Thirion, Bertrand and Grisel, Olivier and Blondel, Mathieu and Prettenhofer, Peter and Weiss, Ron and Dubourg, Vincent and others},
  journal={The Journal of Machine Learning Research},
  volume={12},
  pages={2825--2830},
  year={2011},
  publisher={JMLR. org}
}
@article{freytag2018comparison,
  title={Comparison of clustering tools in R for medium-sized 10x Genomics single-cell {R}{N}{A}-sequencing data},
  author={Freytag, Saskia and Tian, Luyi and L{\"o}nnstedt, Ingrid and Ng, Milica and Bahlo, Melanie},
  journal={F1000Research},
  volume={7},
  year={2018},
  publisher={Faculty of 1000 Ltd}
}
@article{townes2019feature,
  title={Feature selection and dimension reduction for single-cell {R}{N}{A}-Seq based on a multinomial model},
  author={Townes, F William and Hicks, Stephanie C and Aryee, Martin J and Irizarry, Rafael A},
  journal={Genome Biology},
  volume={20},
  number={1},
  pages={1--16},
  year={2019},
  publisher={BioMed Central}
}
@article{van2020cell,
  title={Cell atlas of aqueous humor outflow pathways in eyes of humans and four model species provides insight into glaucoma pathogenesis},
  author={van Zyl, Tav{\'e} and Yan, Wenjun and McAdams, Alexi and Peng, Yi-Rong and Shekhar, Karthik and Regev, Aviv and Juric, Dejan and Sanes, Joshua R},
  journal={Proceedings of the National Academy of Sciences},
  volume={117},
  number={19},
  pages={10339--10349},
  year={2020},
  publisher={National Acad Sciences}
}
@article{sebe2018early,
  title={Early metazoan cell type diversity and the evolution of multicellular gene regulation},
  author={Seb{\'e}-Pedr{\'o}s, Arnau and Chomsky, Elad and Pang, Kevin and Lara-Astiaso, David and Gaiti, Federico and Mukamel, Zohar and Amit, Ido and Hejnol, Andreas and Degnan, Bernard M and Tanay, Amos},
  journal={Nature Ecology \& Evolution},
  volume={2},
  number={7},
  pages={1176--1188},
  year={2018},
  publisher={Nature Publishing Group}
}
@article{zheng2017massively,
  title={Massively parallel digital transcriptional profiling of single cells},
  author={Zheng, Grace XY and Terry, Jessica M and Belgrader, Phillip and Ryvkin, Paul and Bent, Zachary W and Wilson, Ryan and Ziraldo, Solongo B and Wheeler, Tobias D and McDermott, Geoff P and Zhu, Junjie and others},
  journal={Nature Communications},
  volume={8},
  number={1},
  pages={1--12},
  year={2017},
  publisher={Nature Publishing Group}
}
@article{satija2015spatial,
  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},
  journal={Nature Biotechnology},
  volume={33},
  number={5},
  pages={495--502},
  year={2015},
  publisher={Nature Publishing Group}
}
@article{wolf2018scanpy,
  title={SCANPY: large-scale single-cell gene expression data analysis},
  author={Wolf, F Alexander and Angerer, Philipp and Theis, Fabian J},
  journal={Genome Biology},
  volume={19},
  number={1},
  pages={1--5},
  year={2018},
  publisher={Springer}
}
@article{sarkar2021separating,
  title={Separating measurement and expression models clarifies confusion in single-cell {R}{N}{A} sequencing analysis},
  author={Sarkar, Abhishek and Stephens, Matthew},
  journal={Nature Genetics},
  volume={53},
  number={6},
  pages={770--777},
  year={2021},
  publisher={Nature Publishing Group}
}
@article{svensson2020droplet,
  title={Droplet sc{R}{N}{A}-seq is not zero-inflated},
  author={Svensson, Valentine},
  journal={Nature Biotechnology},
  volume={38},
  number={2},
  pages={147--150},
  year={2020},
  publisher={Nature Publishing Group}
}
@article{hicks2018missing,
  title={Missing data and technical variability in single-cell {R}{N}{A}-sequencing experiments},
  author={Hicks, Stephanie C and Townes, F William and Teng, Mingxiang and Irizarry, Rafael A},
  journal={Biostatistics},
  volume={19},
  number={4},
  pages={562--578},
  year={2018},
  publisher={Oxford University Press}
}
@article{saliba2014single,
  title={Single-cell {R}{N}{A}-seq: advances and future challenges},
  author={Saliba, Antoine-Emmanuel and Westermann, Alexander J and Gorski, Stanislaw A and Vogel, J{\"o}rg},
  journal={Nucleic Acids Research},
  volume={42},
  number={14},
  pages={8845--8860},
  year={2014},
  publisher={Oxford University Press}
}
@article{cao2021umi,
  title={UMI or not UMI, that is the question for sc{R}{N}{A}-seq zero-inflation},
  author={Cao, Yingying and Kitanovski, Simo and K{\"u}ppers, Ralf and Hoffmann, Daniel},
  journal={Nature Biotechnology},
  volume={39},
  number={2},
  pages={158--159},
  year={2021},
  publisher={Nature Publishing Group}
}
@article{silverman2020naught,
  title={Naught all zeros in sequence count data are the same},
  author={Silverman, Justin D and Roche, Kimberly and Mukherjee, Sayan and David, Lawrence A},
  journal={Computational and Structural Biotechnology Journal},
  volume={18},
  pages={2789--2798},
  year={2020},
  publisher={Elsevier}
}
@article{jiang2022statistics,
  title={Statistics or biology: the zero-inflation controversy about sc{R}{N}{A}-seq data},
  author={Jiang, Ruochen and Sun, Tianyi and Song, Dongyuan and Li, Jingyi Jessica},
  journal={Genome Biology},
  volume={23},
  number={1},
  pages={1--24},
  year={2022},
  publisher={Springer}
}
@article{liu2016single,
  title={Single-cell transcriptome sequencing: recent advances and remaining challenges},
  author={Liu, Serena and Trapnell, Cole},
  journal={F1000Research},
  volume={5},
  year={2016},
  publisher={Faculty of 1000 Ltd}
}