@article{Virshup_2023,
  doi       = {10.1038/s41587-023-01733-8},
  url       = {https://doi.org/10.1038%2Fs41587-023-01733-8},
  year      = 2023,
  month     = {apr},
  publisher = {Springer Science and Business Media {LLC}},
  author    = {Isaac Virshup and Danila Bredikhin and Lukas Heumos and Giovanni Palla and Gregor Sturm and Adam Gayoso and Ilia Kats and Mikaela Koutrouli and Philipp Angerer and Volker Bergen and Pierre Boyeau and Maren Büttner and Gokcen Eraslan and David Fischer and Max Frank and Justin Hong and Michal Klein and Marius Lange and Romain Lopez and Mohammad Lotfollahi and Malte D. Luecken and Fidel Ramirez and Jeffrey Regier and Sergei Rybakov and Anna C. Schaar and Valeh Valiollah Pour Amiri and Philipp Weiler and Galen Xing and Bonnie Berger and Dana Pe'er and Aviv Regev and Sarah A. Teichmann and Francesca Finotello and F. Alexander Wolf and Nir Yosef and Oliver Stegle and Fabian J. Theis and},
  title     = {The scverse project provides a computational ecosystem for single-cell omics data analysis},
  journal   = {Nature Biotechnology}
}
@article{uieda2020,
  title     = {{Pooch}: {A} friend to fetch your data files},
  author    = {Leonardo Uieda and Santiago Soler and R{\'{e}}mi Rampin and Hugo van Kemenade and Matthew Turk and Daniel Shapero and Anderson Banihirwe and John Leeman},
  year      = {2020},
  doi       = {10.21105/joss.01943},
  url       = {https://doi.org/10.21105/joss.01943},
  month     = jan,
  publisher = {The Open Journal},
  volume    = {5},
  number    = {45},
  pages     = {1943},
  journal   = {Journal of Open Source Software}
}
@article{triana_single-cell_2021,
	title = {Single-cell proteo-genomic reference maps of the hematopoietic system enable the purification and massive profiling of precisely defined cell states},
	volume = {22},
	copyright = {2021 The Author(s)},
	issn = {1529-2916},
	url = {https://www.nature.com/articles/s41590-021-01059-0},
	doi = {10.1038/s41590-021-01059-0},
	abstract = {Single-cell genomics technology has transformed our understanding of complex cellular systems. However, excessive cost and a lack of strategies for the purification of newly identified cell types impede their functional characterization and large-scale profiling. Here, we have generated high-content single-cell proteo-genomic reference maps of human blood and bone marrow that quantitatively link the expression of up to 197 surface markers to cellular identities and biological processes across all main hematopoietic cell types in healthy aging and leukemia. These reference maps enable the automatic design of cost-effective high-throughput cytometry schemes that outperform state-of-the-art approaches, accurately reflect complex topologies of cellular systems and permit the purification of precisely defined cell states. The systematic integration of cytometry and proteo-genomic data enables the functional capacities of precisely mapped cell states to be measured at the single-cell level. Our study serves as an accessible resource and paves the way for a data-driven era in cytometry.},
	language = {en},
	number = {12},
	urldate = {2024-11-10},
	journal = {Nature Immunology},
	author = {Triana, Sergio and Vonficht, Dominik and Jopp-Saile, Lea and Raffel, Simon and Lutz, Raphael and Leonce, Daniel and Antes, Magdalena and Hernández-Malmierca, Pablo and Ordoñez-Rueda, Diana and Ramasz, Beáta and Boch, Tobias and Jann, Johann-Christoph and Nowak, Daniel and Hofmann, Wolf-Karsten and Müller-Tidow, Carsten and Hübschmann, Daniel and Alexandrov, Theodore and Benes, Vladimir and Trumpp, Andreas and Paulsen, Malte and Velten, Lars and Haas, Simon},
	month = dec,
	year = {2021},
    publisher = {Nature Publishing Group},
	keywords = {/unread, Gene expression analysis, Haematopoiesis, Haematopoietic stem cells, Leukaemia},
	pages = {1577--1589},
}
