references.bib

@misc{Amid2019,
  author    = {Amid, Ehsan and Warmuth, Manfred K.},
  doi       = {10.48550/ARXIV.1910.00204},
  url       = {https://arxiv.org/abs/1910.00204},
  keywords  = {Machine Learning (cs.LG), Machine Learning (stat.ML), FOS: Computer and information sciences, FOS: Computer and information sciences},
  title     = {TriMap: Large-scale Dimensionality Reduction Using Triplets},
  publisher = {arXiv},
  year      = {2019},
  copyright = {arXiv.org perpetual, non-exclusive license},
}

@article{Amir2013,
  author    = {Amir, El-ad David and Davis, Kara L and Tadmor, Michelle D and Simonds, Erin F and Levine, Jacob H and Bendall, Sean C and Shenfeld, Daniel K and Krishnaswamy, Smita and Nolan, Garry P and Pe’er, Dana},
  title     = {viSNE enables visualization of high dimensional single-cell data and reveals phenotypic heterogeneity of leukemia},
  volume    = {31},
  issn      = {1546-1696},
  url       = {https://doi.org/10.1038/nbt.2594},
  doi       = {10.1038/nbt.2594},
  number    = {6},
  journal   = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  year      = {2013},
  month     = {may},
  pages     = {545--552},
}

@article{Angerer2015,
  author    = {Angerer, Philipp and Haghverdi, Laleh and Büttner, Maren and Theis, Fabian J. and Marr, Carsten and Buettner, Florian},
  title     = {destiny: diffusion maps for large-scale single-cell data in R},
  volume    = {32},
  issn      = {1367-4803},
  url       = {https://doi.org/10.1093/bioinformatics/btv715},
  doi       = {10.1093/bioinformatics/btv715},
  number    = {8},
  journal   = {Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  year      = {2015},
  month     = {dec},
  pages     = {1241--1243},
}

@article{Baron2016,
  author    = {Baron, Maayan and Veres, Adrian and Wolock, Samuel L. and Faust, Aubrey L. and Gaujoux, Renaud and Vetere, Amedeo and Ryu, Jennifer Hyoje and Wagner, Bridget K. and Shen-Orr, Shai S. and Klein, Allon M. and Melton, Douglas A. and Yanai, Itai},
  title     = {A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure},
  volume    = {3},
  issn      = {2405-4712},
  url       = {https://doi.org/10.1016/j.cels.2016.08.011},
  doi       = {10.1016/j.cels.2016.08.011},
  number    = {4},
  journal   = {Cell Systems},
  publisher = {Elsevier BV},
  year      = {2016},
  month     = {oct},
  pages     = {346--360.e4},
}

@article{Becht2018,
  author    = {Becht, Etienne and McInnes, Leland and Healy, John and Dutertre, Charles-Antoine and Kwok, Immanuel W H and Ng, Lai Guan and Ginhoux, Florent and Newell, Evan W},
  title     = {Dimensionality reduction for visualizing single-cell data using UMAP},
  volume    = {37},
  issn      = {1546-1696},
  url       = {https://doi.org/10.1038/nbt.4314},
  doi       = {10.1038/nbt.4314},
  number    = {1},
  journal   = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  year      = {2018},
  month     = {dec},
  pages     = {38--44},
}

@article{Bernstein2020,
  author    = {Bernstein, Nicholas J. and Fong, Nicole L. and Lam, Irene and Roy, Margaret A. and Hendrickson, David G. and Kelley, David R.},
  title     = {Solo: Doublet Identification in Single-Cell RNA-Seq via Semi-Supervised Deep Learning},
  volume    = {11},
  issn      = {2405-4712},
  url       = {https://doi.org/10.1016/j.cels.2020.05.010},
  doi       = {10.1016/j.cels.2020.05.010},
  number    = {1},
  journal   = {Cell Systems},
  publisher = {Elsevier BV},
  year      = {2020},
  month     = {jul},
  pages     = {95--101.e5},
}

@article{Blondel2008,
  author    = {Blondel, Vincent D and Guillaume, Jean-Loup and Lambiotte, Renaud and Lefebvre, Etienne},
  title     = {Fast unfolding of communities in large networks},
  volume    = {2008},
  issn      = {1742-5468},
  url       = {https://doi.org/10.1088/1742-5468/2008/10/P10008},
  doi       = {10.1088/1742-5468/2008/10/p10008},
  number    = {10},
  journal   = {Journal of Statistical Mechanics: Theory and Experiment},
  publisher = {IOP Publishing},
  year      = {2008},
  month     = {oct},
  pages     = {P10008},
}

@article{Butler2018,
  author    = {Butler, Andrew and Hoffman, Paul and Smibert, Peter and Papalexi, Efthymia and Satija, Rahul},
  title     = {Integrating single-cell transcriptomic data across different conditions, technologies, and species},
  volume    = {36},
  issn      = {1546-1696},
  url       = {https://doi.org/10.1038/nbt.4096},
  doi       = {10.1038/nbt.4096},
  number    = {5},
  journal   = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  year      = {2018},
  month     = {apr},
  pages     = {411--420},
}

@misc{Chippada2018,
  author       = {Chippada, Bhargav},
  title        = {ForceAtlas2 for Python},
  year         = {2018},
  publisher    = {GitHub},
  journal      = {GitHub repository},
  url          = {https://github.com/bhargavchippada/forceatlas2},
  howpublished = {\url{https://github.com/bhargavchippada/forceatlas2}},
}

@article{Coifman2005,
  author    = {Coifman, R. R. and Lafon, S. and Lee, A. B. and Maggioni, M. and Nadler, B. and Warner, F. and Zucker, S. W.},
  title     = {Geometric diffusions as a tool for harmonic analysis and structure definition of data: Diffusion maps},
  volume    = {102},
  issn      = {1091-6490},
  url       = {https://doi.org/10.1073/pnas.0500334102},
  doi       = {10.1073/pnas.0500334102},
  number    = {21},
  journal   = {Proceedings of the National Academy of Sciences},
  publisher = {Proceedings of the National Academy of Sciences},
  year      = {2005},
  month     = {may},
  pages     = {7426--7431},
}

@article{Csardi2006,
  author   = {Csárdi, G. and Nepusz, T.},
  added-at = {2011-03-14T01:02:14.000+0100},
  url      = {https://www.bibsonomy.org/bibtex/252e3e774bac8424cc9a3845a9c597344/lantiq},
  groups   = {public},
  journal  = {InterJournal Complex Systems},
  keywords = {networks graphs},
  pages    = {1695},
  title    = {The igraph software package for complex network research},
  year     = {2006},
}

@article{Eraslan2019,
  author    = {Eraslan, G\"{o}kcen and Simon, Lukas M. and Mircea, Maria and Mueller, Nikola S. and Theis, Fabian J.},
  title     = {Single-cell RNA-seq denoising using a deep count autoencoder},
  volume    = {10},
  issn      = {2041-1723},
  url       = {https://doi.org/10.1038/s41467-018-07931-2},
  doi       = {10.1038/s41467-018-07931-2},
  number    = {1},
  journal   = {Nature Communications},
  publisher = {Springer Science and Business Media LLC},
  year      = {2019},
  month     = {jan},
}

@misc{Fechtner2018,
  author       = {Fechtner, Ron},
  title        = {PyPairs - A python scRNA-Seq classifier},
  year         = {2018},
  publisher    = {GitHub},
  journal      = {GitHub repository},
  url          = {https://github.com/rfechtner/pypairs},
  howpublished = {\url{https://github.com/rfechtner/pypairs}},
}

@article{Fruchterman1991,
  author    = {Fruchterman, Thomas M. J. and Reingold, Edward M.},
  title     = {Graph drawing by force‐directed placement},
  volume    = {21},
  issn      = {1097-024X},
  url       = {https://doi.org/10.1002/spe.4380211102},
  doi       = {10.1002/spe.4380211102},
  number    = {11},
  journal   = {Software: Practice and Experience},
  publisher = {Wiley},
  year      = {1991},
  month     = {nov},
  pages     = {1129--1164},
}

@article{Gardner2000,
  author    = {Gardner, Timothy S. and Cantor, Charles R. and Collins, James J.},
  title     = {Construction of a genetic toggle switch in Escherichia coli},
  volume    = {403},
  issn      = {1476-4687},
  url       = {https://doi.org/10.1038/35002131},
  doi       = {10.1038/35002131},
  number    = {6767},
  journal   = {Nature},
  publisher = {Springer Science and Business Media LLC},
  year      = {2000},
  month     = {jan},
  pages     = {339--342},
}

@article{Haghverdi2015,
  author    = {Haghverdi, Laleh and Buettner, Florian and Theis, Fabian J.},
  title     = {Diffusion maps for high-dimensional single-cell analysis of differentiation data},
  volume    = {31},
  issn      = {1367-4803},
  url       = {https://doi.org/10.1093/bioinformatics/btv325},
  doi       = {10.1093/bioinformatics/btv325},
  number    = {18},
  journal   = {Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  year      = {2015},
  month     = {may},
  pages     = {2989--2998},
}

@article{Haghverdi2016,
  author    = {Haghverdi, Laleh and Büttner, Maren and Wolf, F Alexander and Buettner, Florian and Theis, Fabian J},
  title     = {Diffusion pseudotime robustly reconstructs lineage branching},
  volume    = {13},
  issn      = {1548-7105},
  url       = {https://doi.org/10.1038/nmeth.3971},
  doi       = {10.1038/nmeth.3971},
  number    = {10},
  journal   = {Nature Methods},
  publisher = {Springer Science and Business Media LLC},
  year      = {2016},
  month     = {aug},
  pages     = {845--848},
}

@article{Haghverdi2018,
  author    = {Haghverdi, Laleh and Lun, Aaron T L and Morgan, Michael D and Marioni, John C},
  title     = {Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors},
  volume    = {36},
  issn      = {1546-1696},
  url       = {https://doi.org/10.1038/nbt.4091},
  doi       = {10.1038/nbt.4091},
  number    = {5},
  journal   = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  year      = {2018},
  month     = {apr},
  pages     = {421--427},
}

@article{Hie2019,
  author    = {Hie, Brian and Bryson, Bryan and Berger, Bonnie},
  title     = {Efficient integration of heterogeneous single-cell transcriptomes using Scanorama},
  volume    = {37},
  issn      = {1546-1696},
  url       = {https://doi.org/10.1038/s41587-019-0113-3},
  doi       = {10.1038/s41587-019-0113-3},
  number    = {6},
  journal   = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  year      = {2019},
  month     = {may},
  pages     = {685--691},
}

@article{Islam2011,
  author    = {Islam, Saiful and Kjällquist, Una and Moliner, Annalena and Zajac, Pawel and Fan, Jian-Bing and Lönnerberg, Peter and Linnarsson, Sten},
  title     = {Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq},
  volume    = {21},
  issn      = {1088-9051},
  url       = {https://doi.org/10.1101/gr.110882.110},
  doi       = {10.1101/gr.110882.110},
  number    = {7},
  journal   = {Genome Research},
  publisher = {Cold Spring Harbor Laboratory},
  year      = {2011},
  month     = {may},
  pages     = {1160--1167},
}

@article{Jacomy2014,
  author    = {Jacomy, Mathieu and Venturini, Tommaso and Heymann, Sebastien and Bastian, Mathieu},
  editor    = {Muldoon, Mark R.},
  title     = {ForceAtlas2, a Continuous Graph Layout Algorithm for Handy Network Visualization Designed for the Gephi Software},
  volume    = {9},
  issn      = {1932-6203},
  url       = {https://doi.org/10.1371/journal.pone.0098679},
  doi       = {10.1371/journal.pone.0098679},
  number    = {6},
  journal   = {PLoS ONE},
  publisher = {Public Library of Science (PLoS)},
  year      = {2014},
  month     = {jun},
  pages     = {e98679},
}

@article{Johnson2006,
  author    = {Johnson, W. Evan and Li, Cheng and Rabinovic, Ariel},
  title     = {Adjusting batch effects in microarray expression data using empirical Bayes methods},
  volume    = {8},
  issn      = {1465-4644},
  url       = {https://doi.org/10.1093/biostatistics/kxj037},
  doi       = {10.1093/biostatistics/kxj037},
  number    = {1},
  journal   = {Biostatistics},
  publisher = {Oxford University Press (OUP)},
  year      = {2006},
  month     = {apr},
  pages     = {118--127},
}

@misc{Kang2018,
  author       = {Kang, Chris},
  title        = {mnnpy - MNN-correct in python},
  year         = {2018},
  publisher    = {GitHub},
  journal      = {GitHub repository},
  url          = {https://github.com/chriscainx/mnnpy},
  howpublished = {\url{https://github.com/chriscainx/mnnpy}},
}

@article{Korsunsky2019,
  author    = {Korsunsky, Ilya and Millard, Nghia and Fan, Jean and Slowikowski, Kamil and Zhang, Fan and Wei, Kevin and Baglaenko, Yuriy and Brenner, Michael and Loh, Po-ru and Raychaudhuri, Soumya},
  title     = {Fast, sensitive and accurate integration of single-cell data with Harmony},
  volume    = {16},
  issn      = {1548-7105},
  url       = {https://doi.org/10.1038/s41592-019-0619-0},
  doi       = {10.1038/s41592-019-0619-0},
  number    = {12},
  journal   = {Nature Methods},
  publisher = {Springer Science and Business Media LLC},
  year      = {2019},
  month     = {nov},
  pages     = {1289--1296},
}

@article{Krumsiek2011,
  author    = {Krumsiek, Jan and Marr, Carsten and Schroeder, Timm and Theis, Fabian J.},
  editor    = {Pesce, Maurizio},
  title     = {Hierarchical Differentiation of Myeloid Progenitors Is Encoded in the Transcription Factor Network},
  volume    = {6},
  issn      = {1932-6203},
  url       = {https://doi.org/10.1371/journal.pone.0022649},
  doi       = {10.1371/journal.pone.0022649},
  number    = {8},
  journal   = {PLoS ONE},
  publisher = {Public Library of Science (PLoS)},
  year      = {2011},
  month     = {aug},
  pages     = {e22649},
}

@article{LaManno2018,
  author    = {La Manno, Gioele and Soldatov, Ruslan and Zeisel, Amit and Braun, Emelie and Hochgerner, Hannah and Petukhov, Viktor and Lidschreiber, Katja and Kastriti, Maria E. and Lönnerberg, Peter and Furlan, Alessandro and Fan, Jean and Borm, Lars E. and Liu, Zehua and van Bruggen, David and Guo, Jimin and He, Xiaoling and Barker, Roger and Sundström, Erik and Castelo-Branco, Gonçalo and Cramer, Patrick and Adameyko, Igor and Linnarsson, Sten and Kharchenko, Peter V.},
  title     = {RNA velocity of single cells},
  volume    = {560},
  issn      = {1476-4687},
  url       = {https://doi.org/10.1038/s41586-018-0414-6},
  doi       = {10.1038/s41586-018-0414-6},
  number    = {7719},
  journal   = {Nature},
  publisher = {Springer Science and Business Media LLC},
  year      = {2018},
  month     = {aug},
  pages     = {494--498},
}

@article{Lambiotte2014,
  author    = {Lambiotte, Renaud and Delvenne, Jean-Charles and Barahona, Mauricio},
  title     = {Random Walks, Markov Processes and the Multiscale Modular Organization of Complex Networks},
  volume    = {1},
  issn      = {2327-4697},
  url       = {https://doi.org/10.1109/TNSE.2015.2391998},
  doi       = {10.1109/tnse.2015.2391998},
  number    = {2},
  journal   = {IEEE Transactions on Network Science and Engineering},
  publisher = {Institute of Electrical and Electronics Engineers (IEEE)},
  year      = {2014},
  month     = {jul},
  pages     = {76--90},
}

@article{Lause2021,
  author    = {Lause, Jan and Berens, Philipp and Kobak, Dmitry},
  title     = {Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data},
  volume    = {22},
  issn      = {1474-760X},
  url       = {https://doi.org/10.1186/s13059-021-02451-7},
  doi       = {10.1186/s13059-021-02451-7},
  number    = {1},
  journal   = {Genome Biology},
  publisher = {Springer Science and Business Media LLC},
  year      = {2021},
  month     = {sep},
}

@misc{Leek2012,
  author    = {Leek, Jeffrey T. and Johnson, W. Evan and Parker, Hilary S. and J.Fertig, Elana and Jaffe, Andrew E. and Storey, John D. and Zhang, Yuqing and Torres, Leonardo Collado},
  doi       = {10.18129/B9.BIOC.SVA},
  url       = {https://bioconductor.org/packages/sva},
  title     = {sva},
  publisher = {Bioconductor},
  year      = {2017},
}

@article{Levine2015,
  author    = {Levine, Jacob H. and Simonds, Erin F. and Bendall, Sean C. and Davis, Kara L. and Amir, El-ad D. and Tadmor, Michelle D. and Litvin, Oren and Fienberg, Harris G. and Jager, Astraea and Zunder, Eli R. and Finck, Rachel and Gedman, Amanda L. and Radtke, Ina and Downing, James R. and Pe’er, Dana and Nolan, Garry P.},
  title     = {Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis},
  volume    = {162},
  issn      = {0092-8674},
  url       = {https://doi.org/10.1016/j.cell.2015.05.047},
  doi       = {10.1016/j.cell.2015.05.047},
  number    = {1},
  journal   = {Cell},
  publisher = {Elsevier BV},
  year      = {2015},
  month     = {jul},
  pages     = {184--197},
}

@article{Lotfollahi2019,
  author    = {Lotfollahi, Mohammad and Wolf, F. Alexander and Theis, Fabian J.},
  title     = {scGen predicts single-cell perturbation responses},
  volume    = {16},
  issn      = {1548-7105},
  url       = {https://doi.org/10.1038/s41592-019-0494-8},
  doi       = {10.1038/s41592-019-0494-8},
  number    = {8},
  journal   = {Nature Methods},
  publisher = {Springer Science and Business Media LLC},
  year      = {2019},
  month     = {jul},
  pages     = {715--721},
}

@inproceedings{Luecken2021,
  author    = {Luecken, Malte and Burkhardt, Daniel and Cannoodt, Robrecht and Lance, Christopher and Agrawal, Aditi and Aliee, Hananeh and Chen, Ann and Deconinck, Louise and Detweiler, Angela and Granados, Alejandro and Huynh, Shelly and Isacco, Laura and Kim, Yang and Klein, Dominik and De Kumar, Bony and Kuppasani, Sunil and Lickert, Heiko and McGeever, Aaron and Melgarejo, Joaquin and Mekonen, Honey and Morri, Maurizio and Müller, Michaela and Neff, Norma and Paul, Sheryl and Rieck, Bastian and Schneider, Kaylie and Steelman, Scott and Sterr, Michael and Treacy, Daniel and Tong, Alexander and Villani, Alexandra-Chloe and Wang, Guilin and Yan, Jia and Zhang, Ce and Pisco, Angela and Krishnaswamy, Smita and Theis, Fabian and Bloom, Jonathan M},
  editor    = {Vanschoren, J. and Yeung, S.},
  booktitle = {Proceedings of the Neural Information Processing Systems Track on Datasets and Benchmarks},
  pages     = {},
  publisher = {Curran},
  title     = {A sandbox for prediction and integration of DNA, RNA, and proteins in single cells},
  url       = {https://datasets-benchmarks-proceedings.neurips.cc/paper_files/paper/2021/file/158f3069a435b314a80bdcb024f8e422-Paper-round2.pdf},
  volume    = {1},
  year      = {2021},
}

@article{McCarthy2017,
  author    = {McCarthy, Davis J and Campbell, Kieran R and Lun, Aaron T L and Wills, Quin F},
  editor    = {Hofacker, Ivo},
  doi       = {10.1093/bioinformatics/btw777},
  url       = {https://doi.org/10.1093/bioinformatics/btw777},
  year      = {2017},
  month     = {jan},
  publisher = {Oxford University Press ({OUP})},
  volume    = {33},
  number    = {8},
  pages     = {1179--1186},
  title     = {Scater: pre-processing, quality control, normalization and visualization of single-cell {RNA}-seq data in R},
  journal   = {Bioinformatics},
}

@misc{McInnes2018,
  author    = {McInnes, Leland and Healy, John and Melville, James},
  doi       = {10.48550/ARXIV.1802.03426},
  url       = {https://arxiv.org/abs/1802.03426},
  keywords  = {Machine Learning (stat.ML), Computational Geometry (cs.CG), Machine Learning (cs.LG), FOS: Computer and information sciences, FOS: Computer and information sciences},
  title     = {UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction},
  publisher = {arXiv},
  year      = {2018},
  copyright = {arXiv.org perpetual, non-exclusive license},
}

@article{Moignard2015,
  author    = {Moignard, Victoria and Woodhouse, Steven and Haghverdi, Laleh and Lilly, Andrew J and Tanaka, Yosuke and Wilkinson, Adam C and Buettner, Florian and Macaulay, Iain C and Jawaid, Wajid and Diamanti, Evangelia and Nishikawa, Shin-Ichi and Piterman, Nir and Kouskoff, Valerie and Theis, Fabian J and Fisher, Jasmin and Göttgens, Berthold},
  title     = {Decoding the regulatory network of early blood development from single-cell gene expression measurements},
  volume    = {33},
  issn      = {1546-1696},
  url       = {https://doi.org/10.1038/nbt.3154},
  doi       = {10.1038/nbt.3154},
  number    = {3},
  journal   = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  year      = {2015},
  month     = {feb},
  pages     = {269--276},
}

@article{Moon2019,
  author    = {Moon, Kevin R. and van Dijk, David and Wang, Zheng and Gigante, Scott and Burkhardt, Daniel B. and Chen, William S. and Yim, Kristina and Elzen, Antonia van den and Hirn, Matthew J. and Coifman, Ronald R. and Ivanova, Natalia B. and Wolf, Guy and Krishnaswamy, Smita},
  title     = {Visualizing structure and transitions in high-dimensional biological data},
  volume    = {37},
  issn      = {1546-1696},
  url       = {https://doi.org/10.1038/s41587-019-0336-3},
  doi       = {10.1038/s41587-019-0336-3},
  number    = {12},
  journal   = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  year      = {2019},
  month     = {dec},
  pages     = {1482--1492},
}

@article{Muraro2016,
  author    = {Muraro, Mauro J. and Dharmadhikari, Gitanjali and Gr\"{u}n, Dominic and Groen, Nathalie and Dielen, Tim and Jansen, Erik and van Gurp, Leon and Engelse, Marten A. and Carlotti, Francoise and de Koning, Eelco J.P. and van Oudenaarden, Alexander},
  title     = {A Single-Cell Transcriptome Atlas of the Human Pancreas},
  volume    = {3},
  issn      = {2405-4712},
  url       = {https://doi.org/10.1016/j.cels.2016.09.002},
  doi       = {10.1016/j.cels.2016.09.002},
  number    = {4},
  journal   = {Cell Systems},
  publisher = {Elsevier BV},
  year      = {2016},
  month     = {oct},
  pages     = {385--394.e3},
}

@article{Nowotschin2019,
  author    = {Nowotschin, Sonja and Setty, Manu and Kuo, Ying-Yi and Liu, Vincent and Garg, Vidur and Sharma, Roshan and Simon, Claire S. and Saiz, Nestor and Gardner, Rui and Boutet, Stéphane C. and Church, Deanna M. and Hoodless, Pamela A. and Hadjantonakis, Anna-Katerina and Pe’er, Dana},
  title     = {The emergent landscape of the mouse gut endoderm at single-cell resolution},
  volume    = {569},
  issn      = {1476-4687},
  url       = {https://doi.org/10.1038/s41586-019-1127-1},
  doi       = {10.1038/s41586-019-1127-1},
  number    = {7756},
  journal   = {Nature},
  publisher = {Springer Science and Business Media LLC},
  year      = {2019},
  month     = {apr},
  pages     = {361--367},
}

@article{Ntranos2019,
  author    = {Ntranos, Vasilis and Yi, Lynn and Melsted, Páll and Pachter, Lior},
  title     = {A discriminative learning approach to differential expression analysis for single-cell RNA-seq},
  volume    = {16},
  issn      = {1548-7105},
  url       = {https://doi.org/10.1038/s41592-018-0303-9},
  doi       = {10.1038/s41592-018-0303-9},
  number    = {2},
  journal   = {Nature Methods},
  publisher = {Springer Science and Business Media LLC},
  year      = {2019},
  month     = {jan},
  pages     = {163--166},
}

@article{Paul2015,
  author    = {Paul, Franziska and Arkin, Ya’ara and Giladi, Amir and Jaitin, Diego Adhemar and Kenigsberg, Ephraim and Keren-Shaul, Hadas and Winter, Deborah and Lara-Astiaso, David and Gury, Meital and Weiner, Assaf and David, Eyal and Cohen, Nadav and Lauridsen, Felicia Kathrine Bratt and Haas, Simon and Schlitzer, Andreas and Mildner, Alexander and Ginhoux, Florent and Jung, Steffen and Trumpp, Andreas and Porse, Bo Torben and Tanay, Amos and Amit, Ido},
  title     = {Transcriptional Heterogeneity and Lineage Commitment in Myeloid Progenitors},
  volume    = {163},
  issn      = {0092-8674},
  url       = {https://doi.org/10.1016/j.cell.2015.11.013},
  doi       = {10.1016/j.cell.2015.11.013},
  number    = {7},
  journal   = {Cell},
  publisher = {Elsevier BV},
  year      = {2015},
  month     = {dec},
  pages     = {1663--1677},
}

@misc{Pedersen2012,
  author       = {Pedersen, Brent},
  title        = {combat.py},
  year         = {2012},
  publisher    = {GitHub},
  journal      = {GitHub repository},
  url          = {https://github.com/brentp/combat.py},
  howpublished = {\url{https://github.com/brentp/combat.py}},
}

@article{Pedregosa2011,
  author    = {Pedregosa, Fabian and Varoquaux, Gaël 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 Vanderplas, Jake and Passos, Alexandre and Cournapeau, David and Brucher, Matthieu and Perrot, Matthieu and Duchesnay, Édouard},
  title     = {Scikit-learn: Machine Learning in Python},
  year      = {2011},
  publisher = {JMLR.org},
  volume    = {12},
  number    = {null},
  issn      = {1532-4435},
  journal   = {Journal of Machine Learning Research},
  month     = {nov},
  pages     = {2825--2830},
  numpages  = {6},
}

@article{Plass2018,
  author    = {Plass, Mireya and Solana, Jordi and Wolf, F. Alexander and Ayoub, Salah and Misios, Aristotelis and Glažar, Petar and Obermayer, Benedikt and Theis, Fabian J. and Kocks, Christine and Rajewsky, Nikolaus},
  title     = {Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics},
  volume    = {360},
  issn      = {1095-9203},
  url       = {https://doi.org/10.1126/science.aaq1723},
  doi       = {10.1126/science.aaq1723},
  number    = {6391},
  journal   = {Science},
  publisher = {American Association for the Advancement of Science (AAAS)},
  year      = {2018},
  month     = {may},
}

@article{Polanski2019,
  author    = {Polański, Krzysztof and Young, Matthew D and Miao, Zhichao and Meyer, Kerstin B and Teichmann, Sarah A and Park, Jong-Eun},
  editor    = {Berger, Bonnie},
  title     = {BBKNN: fast batch alignment of single cell transcriptomes},
  volume    = {36},
  issn      = {1367-4811},
  url       = {https://doi.org/10.1093/bioinformatics/btz625},
  doi       = {10.1093/bioinformatics/btz625},
  number    = {3},
  journal   = {Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  year      = {2019},
  month     = {aug},
  pages     = {964--965},
}

@article{Satija2015,
  author    = {Satija, Rahul and Farrell, Jeffrey A and Gennert, David and Schier, Alexander F and Regev, Aviv},
  doi       = {10.1038/nbt.3192},
  url       = {https://doi.org/10.1038/nbt.3192},
  year      = {2015},
  month     = {apr},
  publisher = {Springer Science and Business Media {LLC}},
  volume    = {33},
  number    = {5},
  pages     = {495--502},
  title     = {Spatial reconstruction of single-cell gene expression data},
  journal   = {Nature Biotechnology},
}

@article{Scialdone2015,
  author    = {Scialdone, Antonio and Natarajan, Kedar N. and Saraiva, Luis R. and Proserpio, Valentina and Teichmann, Sarah A. and Stegle, Oliver and Marioni, John C. and Buettner, Florian},
  title     = {Computational assignment of cell-cycle stage from single-cell transcriptome data},
  volume    = {85},
  issn      = {1046-2023},
  url       = {https://doi.org/10.1016/j.ymeth.2015.06.021},
  doi       = {10.1016/j.ymeth.2015.06.021},
  journal   = {Methods},
  publisher = {Elsevier BV},
  year      = {2015},
  month     = {sep},
  pages     = {54--61},
}

@article{Segerstolpe2016,
  author    = {Segerstolpe, Åsa and Palasantza, Athanasia and Eliasson, Pernilla and Andersson, Eva-Marie and Andréasson, Anne-Christine and Sun, Xiaoyan and Picelli, Simone and Sabirsh, Alan and Clausen, Maryam and Bjursell, Magnus K. and Smith, David M. and Kasper, Maria and Ämmälä, Carina and Sandberg, Rickard},
  title     = {Single-Cell Transcriptome Profiling of Human Pancreatic Islets in Health and Type 2 Diabetes},
  volume    = {24},
  issn      = {1550-4131},
  url       = {https://doi.org/10.1016/j.cmet.2016.08.020},
  doi       = {10.1016/j.cmet.2016.08.020},
  number    = {4},
  journal   = {Cell Metabolism},
  publisher = {Elsevier BV},
  year      = {2016},
  month     = {oct},
  pages     = {593--607},
}

@article{Setty2016,
  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},
  title     = {Wishbone identifies bifurcating developmental trajectories from single-cell data},
  volume    = {34},
  issn      = {1546-1696},
  url       = {https://doi.org/10.1038/nbt.3569},
  doi       = {10.1038/nbt.3569},
  number    = {6},
  journal   = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  year      = {2016},
  month     = {may},
  pages     = {637--645},
}

@article{Setty2019,
  author    = {Setty, Manu and Kiseliovas, Vaidotas and Levine, Jacob and Gayoso, Adam and Mazutis, Linas and Pe’er, Dana},
  title     = {Characterization of cell fate probabilities in single-cell data with Palantir},
  volume    = {37},
  issn      = {1546-1696},
  url       = {https://doi.org/10.1038/s41587-019-0068-4},
  doi       = {10.1038/s41587-019-0068-4},
  number    = {4},
  journal   = {Nature Biotechnology},
  publisher = {Springer Science and Business Media LLC},
  year      = {2019},
  month     = {mar},
  pages     = {451--460},
}

@article{Stuart2019,
  author    = {Stuart, Tim and Butler, Andrew and Hoffman, Paul and Hafemeister, Christoph and Papalexi, Efthymia and Mauck, William M. and Hao, Yuhan and Stoeckius, Marlon and Smibert, Peter and Satija, Rahul},
  title     = {Comprehensive Integration of Single-Cell Data},
  volume    = {177},
  issn      = {0092-8674},
  url       = {https://doi.org/10.1016/j.cell.2019.05.031},
  doi       = {10.1016/j.cell.2019.05.031},
  number    = {7},
  journal   = {Cell},
  publisher = {Elsevier BV},
  year      = {2019},
  month     = {jun},
  pages     = {1888--1902.e21},
}

@article{Tarashansky2019,
  author    = {Tarashansky, Alexander J and Xue, Yuan and Li, Pengyang and Quake, Stephen R and Wang, Bo},
  title     = {Self-assembling manifolds in single-cell RNA sequencing data},
  volume    = {8},
  issn      = {2050-084X},
  url       = {https://doi.org/10.7554/eLife.48994},
  doi       = {10.7554/elife.48994},
  journal   = {eLife},
  publisher = {eLife Sciences Publications, Ltd},
  year      = {2019},
  month     = {sep},
}

@misc{Traag2017,
  author    = {Traag, Vincent},
  doi       = {10.5281/ZENODO.35117},
  url       = {https://zenodo.org/record/35117},
  title     = {louvain-igraph: v0.5.3},
  publisher = {Zenodo},
  year      = {2015},
  copyright = {Open Access},
}

@article{Traag2019,
  author    = {Traag, V. A. and Waltman, L. and van Eck, N. J.},
  title     = {From Louvain to Leiden: guaranteeing well-connected communities},
  volume    = {9},
  issn      = {2045-2322},
  url       = {https://doi.org/10.1038/s41598-019-41695-z},
  doi       = {10.1038/s41598-019-41695-z},
  number    = {1},
  journal   = {Scientific Reports},
  publisher = {Springer Science and Business Media LLC},
  year      = {2019},
  month     = {mar},
}

@misc{Ulyanov2016,
  author       = {Ulyanov, Dmitry},
  title        = {Multicore-TSNE},
  year         = {2016},
  publisher    = {GitHub},
  journal      = {GitHub repository},
  url          = {https://github.com/DmitryUlyanov/Multicore-TSNE},
  howpublished = {\url{https://github.com/DmitryUlyanov/Multicore-TSNE}},
}

@article{Wang2016,
  author    = {Wang, Yue J. and Golson, Maria L. and Schug, Jonathan and Traum, Daniel and Liu, Chengyang and Vivek, Kumar and Dorrell, Craig and Naji, Ali and Powers, Alvin C. and Chang, Kyong-Mi and Grompe, Markus and Kaestner, Klaus H.},
  title     = {Single-Cell Mass Cytometry Analysis of the Human Endocrine Pancreas},
  volume    = {24},
  issn      = {1550-4131},
  url       = {https://doi.org/10.1016/j.cmet.2016.09.007},
  doi       = {10.1016/j.cmet.2016.09.007},
  number    = {4},
  journal   = {Cell Metabolism},
  publisher = {Elsevier BV},
  year      = {2016},
  month     = {oct},
  pages     = {616--626},
}

@misc{Waskom2016,
  author    = {Waskom, Michael and Botvinnik, Olga and {Drewokane} and Hobson, Paul and {, David} and Halchenko, Yaroslav and Lukauskas, Saulius and Cole, John B. and Warmenhoven, Jordi and De Ruiter, Julian and Hoyer, Stephan and Vanderplas, Jake and Villalba, Santi and Kunter, Gero and Quintero, Eric and Martin, Marcel and Miles, Alistair and Meyer, Kyle and Augspurger, Tom and Yarkoni, Tal and Bachant, Pete and Williams, Mike and Evans, Constantine and Fitzgerald, Clark and {, Brian} and Wehner, Daniel and Hitz, Gregory and Ziegler, Erik and Qalieh, Adel and Lee, Antony},
  doi       = {10.5281/ZENODO.54844},
  url       = {https://zenodo.org/record/54844},
  title     = {seaborn: v0.7.1 (June 2016)},
  publisher = {Zenodo},
  year      = {2016},
  copyright = {Open Access},
}

@article{Weinreb2017,
  author    = {Weinreb, Caleb and Wolock, Samuel and Klein, Allon M},
  editor    = {Berger, Bonnie},
  title     = {SPRING: a kinetic interface for visualizing high dimensional single-cell expression data},
  volume    = {34},
  issn      = {1367-4811},
  url       = {https://doi.org/10.1093/bioinformatics/btx792},
  doi       = {10.1093/bioinformatics/btx792},
  number    = {7},
  journal   = {Bioinformatics},
  publisher = {Oxford University Press (OUP)},
  year      = {2017},
  month     = {dec},
  pages     = {1246--1248},
}

@article{Wittmann2009,
  author    = {Wittmann, Dominik M and Krumsiek, Jan and Saez-Rodriguez, Julio and Lauffenburger, Douglas A and Klamt, Steffen and Theis, Fabian J},
  title     = {Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling},
  volume    = {3},
  issn      = {1752-0509},
  url       = {https://doi.org/10.1186/1752-0509-3-98},
  doi       = {10.1186/1752-0509-3-98},
  number    = {1},
  journal   = {BMC Systems Biology},
  publisher = {Springer Science and Business Media LLC},
  year      = {2009},
  month     = {sep},
}

@article{Wolf2018,
  author  = {Wolf, F. Alexander and Angerer, Philipp and Theis, Fabian J.},
  title   = {SCANPY: large-scale single-cell gene expression data analysis},
  journal = {Genome Biology},
  year    = {2018},
  month   = {feb},
  day     = {06},
  volume  = {19},
  number  = {1},
  pages   = {15},
  issn    = {1474-760X},
  doi     = {10.1186/s13059-017-1382-0},
  url     = {https://doi.org/10.1186/s13059-017-1382-0},
}

@article{Wolf2019,
  author    = {Wolf, F. Alexander and Hamey, Fiona K. and Plass, Mireya and Solana, Jordi and Dahlin, Joakim S. and Göttgens, Berthold and Rajewsky, Nikolaus and Simon, Lukas and Theis, Fabian J.},
  title     = {PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells},
  volume    = {20},
  issn      = {1474-760X},
  url       = {https://doi.org/10.1186/s13059-019-1663-x},
  doi       = {10.1186/s13059-019-1663-x},
  number    = {1},
  journal   = {Genome Biology},
  publisher = {Springer Science and Business Media LLC},
  year      = {2019},
  month     = {mar},
}

@article{Wolock2019,
  author    = {Wolock, Samuel L. and Lopez, Romain and Klein, Allon M.},
  doi       = {10.1016/j.cels.2018.11.005},
  url       = {https://doi.org/10.1016/j.cels.2018.11.005},
  year      = {2019},
  month     = {apr},
  publisher = {Elsevier {BV}},
  volume    = {8},
  number    = {4},
  pages     = {281--291.e9},
  title     = {Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data},
  journal   = {Cell Systems},
}

@article{Zheng2017,
  author    = {Zheng, Grace X. Y. 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 Gregory, Mark T. and Shuga, Joe and Montesclaros, Luz and Underwood, Jason G. and Masquelier, Donald A. and Nishimura, Stefanie Y. and Schnall-Levin, Michael and Wyatt, Paul W. and Hindson, Christopher M. and Bharadwaj, Rajiv and Wong, Alexander and Ness, Kevin D. and Beppu, Lan W. and Deeg, H. Joachim and McFarland, Christopher and Loeb, Keith R. and Valente, William J. and Ericson, Nolan G. and Stevens, Emily A. and Radich, Jerald P. and Mikkelsen, Tarjei S. and Hindson, Benjamin J. and Bielas, Jason H.},
  doi       = {10.1038/ncomms14049},
  url       = {https://doi.org/10.1038/ncomms14049},
  year      = {2017},
  month     = {jan},
  publisher = {Springer Science and Business Media {LLC}},
  volume    = {8},
  number    = {1},
  title     = {Massively parallel digital transcriptional profiling of single cells},
  journal   = {Nature Communications},
}

@article{Zunder2015,
  author    = {Zunder, Eli R. and Lujan, Ernesto and Goltsev, Yury and Wernig, Marius and Nolan, Garry P.},
  title     = {A Continuous Molecular Roadmap to iPSC Reprogramming through Progression Analysis of Single-Cell Mass Cytometry},
  volume    = {16},
  issn      = {1934-5909},
  url       = {https://doi.org/10.1016/j.stem.2015.01.015},
  doi       = {10.1016/j.stem.2015.01.015},
  number    = {3},
  journal   = {Cell Stem Cell},
  publisher = {Elsevier BV},
  year      = {2015},
  month     = {mar},
  pages     = {323--337},
}

@article{vanDerMaaten2008,
  author  = {van der Maaten, Laurens and Hinton, Geoffrey},
  title   = {Visualizing Data using t-SNE},
  journal = {Journal of Machine Learning Research},
  year    = {2008},
  volume  = {9},
  number  = {86},
  pages   = {2579--2605},
  url     = {http://jmlr.org/papers/v9/vandermaaten08a.html},
}

@article{vanDijk2018,
  author    = {van Dijk, David and Sharma, Roshan and Nainys, Juozas and Yim, Kristina and Kathail, Pooja and Carr, Ambrose J. and Burdziak, Cassandra and Moon, Kevin R. and Chaffer, Christine L. and Pattabiraman, Diwakar and Bierie, Brian and Mazutis, Linas and Wolf, Guy and Krishnaswamy, Smita and Pe’er, Dana},
  title     = {Recovering Gene Interactions from Single-Cell Data Using Data Diffusion},
  volume    = {174},
  issn      = {0092-8674},
  url       = {https://doi.org/10.1016/j.cell.2018.05.061},
  doi       = {10.1016/j.cell.2018.05.061},
  number    = {3},
  journal   = {Cell},
  publisher = {Elsevier BV},
  year      = {2018},
  month     = {jul},
  pages     = {716--729.e27},
}