@article{ruddle2009secondary,
  title={Secondary lymphoid organs: responding to genetic and environmental cues in ontogeny and the immune response},
  author={Ruddle, Nancy H and Akirav, Eitan M},
  journal={The Journal of Immunology},
  volume={183},
  number={4},
  pages={2205--2212},
  year={2009},
  publisher={Am Assoc Immnol}
}

@article{nave2001morphology,
  title={Morphology and immunology of the human palatine tonsil},
  author={Nave, Heike and Gebert, Andreas and Pabst, Reinhard},
  journal={Anatomy and embryology},
  volume={204},
  number={5},
  pages={367--373},
  year={2001},
  publisher={Springer}
}

@article{de2015dynamics,
  title={Dynamics of B cells in germinal centres},
  author={De Silva, Nilushi S and Klein, Ulf},
  journal={Nature reviews immunology},
  volume={15},
  number={3},
  pages={137--148},
  year={2015},
  publisher={Nature Publishing Group UK London}
}

@article{regev2018human,
  title={The human cell atlas white paper},
  author={Regev, Aviv and Teichmann, Sarah and Rozenblatt-Rosen, Orit and Stubbington, Michael and Ardlie, Kristin and Amit, Ido and Arlotta, Paola and Bader, Gary and Benoist, Christophe and Biton, Moshe and others},
  journal={arXiv preprint arXiv:1810.05192},
  year={2018}
}

@article{wagner2016revealing,
  title={Revealing the vectors of cellular identity with single-cell genomics},
  author={Wagner, Allon and Regev, Aviv and Yosef, Nir},
  journal={Nature biotechnology},
  volume={34},
  number={11},
  pages={1145--1160},
  year={2016},
  publisher={Nature Publishing Group US New York}
}

@article{hao2021integrated,
  title={Integrated analysis of multimodal single-cell data},
  author={Hao, Yuhan and Hao, Stephanie and Andersen-Nissen, Erica and Mauck III, William M and Zheng, Shiwei and Butler, Andrew and Lee, Maddie J and Wilk, Aaron J and Darby, Charlotte and Zager, Michael and others},
  journal={Cell},
  volume={184},
  number={13},
  pages={3573--3587},
  year={2021},
  publisher={Elsevier}
}

@article{mereu2020benchmarking,
  title={Benchmarking single-cell RNA-sequencing protocols for cell atlas projects},
  author={Mereu, Elisabetta and Lafzi, Atefeh and Moutinho, Catia and Ziegenhain, Christoph and McCarthy, Davis J and {\'A}lvarez-Varela, Adri{\'a}n and Batlle, Eduard and Gr{\"u}n, Dominic and Lau, Julia K and Boutet, St{\'e}phane C and others},
  journal={Nature biotechnology},
  volume={38},
  number={6},
  pages={747--755},
  year={2020},
  publisher={Nature Publishing Group}
}

@article{korsunsky2019fast,
  title={Fast, sensitive and accurate integration of single-cell data with Harmony},
  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},
  journal={Nature methods},
  volume={16},
  number={12},
  pages={1289--1296},
  year={2019},
  publisher={Nature Publishing Group}
}

@article{stuart2021single,
  title={Single-cell chromatin state analysis with Signac},
  author={Stuart, Tim and Srivastava, Avi and Madad, Shaista and Lareau, Caleb A and Satija, Rahul},
  journal={Nature methods},
  volume={18},
  number={11},
  pages={1333--1341},
  year={2021},
  publisher={Nature Publishing Group US New York}
}

@article{sturm2020scirpy,
  title={Scirpy: a Scanpy extension for analyzing single-cell T-cell receptor-sequencing data},
  author={Sturm, Gregor and Szabo, Tamas and Fotakis, Georgios and Haider, Marlene and Rieder, Dietmar and Trajanoski, Zlatko and Finotello, Francesca},
  journal={Bioinformatics},
  volume={36},
  number={18},
  pages={4817--4818},
  year={2020},
  publisher={Oxford University Press}
}
