ref.bib

@article{svensson2020droplet,
  title={Droplet {scRNA}-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{choi2020bayesian,
  title={Bayesian model selection reveals biological origins of zero inflation in single-cell transcriptomics},
  author={Choi, Kwangbom and Chen, Yang and Skelly, Daniel A and Churchill, Gary A},
  journal={Genome Biology},
  volume={21},
  pages={183},
  year={2020},
  publisher={Springer}
}

@article{kim2020demystifying,
  title={Demystifying ``drop-outs'' in single-cell {UMI} data},
  author={Kim, Tae Hyun and Zhou, Xiang and Chen, Mengjie},
  journal={Genome Biology},
  volume={21},
  number={1},
  pages={196},
  year={2020},
  publisher={Springer}
}

@article{pan2023poisson,
  title={The {P}oisson distribution model fits {UMI}-based single-cell {RNA}-sequencing data},
  author={Pan, Yue and Landis, Justin T and Moorad, Razia and Wu, Di and Marron, J S and Dittmer, Dirk P},
  journal={BMC Bioinformatics},
  volume={24},
  pages={256},
  year={2023},
  publisher={Springer}
}

@article{pierson2015zifa,
  title={{ZIFA}: Dimensionality reduction for zero-inflated single-cell gene expression analysis},
  author={Pierson, Emma and Yau, Christopher},
  journal={Genome Biology},
  volume={16},
  number={1},
  pages={241},
  year={2015},
  publisher={Springer}
}

@article{townes2019feature,
  title={Feature selection and dimension reduction for single-cell {RNA-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},
  pages={295},
  year={2019},
  publisher={Springer}
}

@article{lopez2018deep,
  title={Deep generative modeling for single-cell transcriptomics},
  author={Lopez, Romain and Regier, Jeffrey and Cole, Michael B and Jordan, Michael I and Yosef, Nir},
  journal={Nature Methods},
  volume={15},
  number={12},
  pages={1053--1058},
  year={2018},
  publisher={Nature Publishing Group}
}

@article{jiang2022statistics,
  title={Statistics or biology: the zero-inflation controversy about {scRNA}-seq data},
  author={Jiang, Ruochen and Sun, Tianyi and Song, Dongyuan and Li, Jingyi Jessica},
  journal={Genome Biology},
  volume={23},
  number={1},
  pages={31},
  year={2022},
  publisher={Springer}
}

@article{risso2018general,
  title={A general and flexible method for signal extraction from single-cell {RNA}-seq data},
  author={Risso, Davide and Perraudeau, Fanny and Gribkova, Svetlana and Dudoit, Sandrine and Vert, Jean-Philippe},
  journal={Nature Communications},
  volume={9},
  number={1},
  pages={284},
  year={2018},
  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={15},
  year={2018},
  publisher={Springer}
}

@article{kass1995bayes,
  title={Bayes factors},
  author={Kass, Robert E and Raftery, Adrian E},
  journal={Journal of the American Statistical Association},
  volume={90},
  number={430},
  pages={773--795},
  year={1995},
  publisher={Taylor \& Francis}
}