@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}
}

# ResolVI
@article{ergen2025resolvi,
  title={ResolVI-addressing noise and bias in spatial transcriptomics},
  author={Ergen, Can and Yosef, Nir},
  journal={bioRxiv},
  pages={2025--01},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}

# scVI
@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 US New York}
}

# scANVI
@article{xu2021probabilistic,
  title={Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models},
  author={Xu, Chenling and Lopez, Romain and Mehlman, Edouard and Regier, Jeffrey and Jordan, Michael I and Yosef, Nir},
  journal={Molecular systems biology},
  volume={17},
  number={1},
  pages={e9620},
  year={2021}
}

# scVIVA
@article{levy2025scviva,
  title={scVIVA: a probabilistic framework for representation of cells and their environments in spatial transcriptomics},
  author={Levy, Nathan and Ingelfinger, Florian and Bakulin, Artemii and Cinnirella, Giacomo and Boyeau, Pierre and Nadler, Boaz and Ergen, Can and Yosef, Nir},
  journal={bioRxiv},
  pages={2025--06},
  year={2025},
  publisher={Cold Spring Harbor Laboratory}
}

# scPoli
@article{de2023population,
  title={Population-level integration of single-cell datasets enables multi-scale analysis across samples},
  author={De Donno, Carlo and Hediyeh-Zadeh, Soroor and Moinfar, Amir Ali and Wagenstetter, Marco and Zappia, Luke and Lotfollahi, Mohammad and Theis, Fabian J},
  journal={Nature Methods},
  volume={20},
  number={11},
  pages={1683--1692},
  year={2023},
  publisher={Nature Publishing Group US New York}
}

# scArches
@article{lotfollahi2022mapping,
  title={Mapping single-cell data to reference atlases by transfer learning},
  author={Lotfollahi, Mohammad and Naghipourfar, Mohsen and Luecken, Malte D and Khajavi, Matin and B{\"u}ttner, Maren and Wagenstetter, Marco and Avsec, {\v{Z}}iga and Gayoso, Adam and Yosef, Nir and Interlandi, Marta and others},
  journal={Nature biotechnology},
  volume={40},
  number={1},
  pages={121--130},
  year={2022},
  publisher={Nature Publishing Group US New York}
}

# Harmony
@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 US New York}
}

# LIGER
@article{welch2019single,
  title={Single-cell multi-omic integration compares and contrasts features of brain cell identity},
  author={Welch, Joshua D and Kozareva, Velina and Ferreira, Ashley and Vanderburg, Charles and Martin, Carly and Macosko, Evan Z},
  journal={Cell},
  volume={177},
  number={7},
  pages={1873--1887},
  year={2019},
  publisher={Elsevier}
}

# scanorama
@article{hie2019efficient,
  title={Efficient integration of heterogeneous single-cell transcriptomes using Scanorama},
  author={Hie, Brian and Bryson, Bryan and Berger, Bonnie},
  journal={Nature biotechnology},
  volume={37},
  number={6},
  pages={685--691},
  year={2019},
  publisher={Nature Publishing Group US New York}
}

# scIB metrics
@article{luecken2022benchmarking,
  title={Benchmarking atlas-level data integration in single-cell genomics},
  author={Luecken, Malte D and B{\"u}ttner, Maren and Chaichoompu, Kridsadakorn and Danese, Anna and Interlandi, Marta and M{\"u}ller, Michaela F and Strobl, Daniel C and Zappia, Luke and Dugas, Martin and Colom{\'e}-Tatch{\'e}, Maria and others},
  journal={Nature methods},
  volume={19},
  number={1},
  pages={41--50},
  year={2022},
  publisher={Nature Publishing Group US New York}
}

# scvi-tools library (general)
@article{gayoso2022python,
  title={A Python library for probabilistic analysis of single-cell omics data},
  author={Gayoso, Adam and Lopez, Romain and Xing, Galen and Boyeau, Pierre and Valiollah Pour Amiri, Valeh and Hong, Justin and Wu, Katherine and Jayasuriya, Michael and Mehlman, Edouard and Langevin, Maxime and others},
  journal={Nature biotechnology},
  volume={40},
  number={2},
  pages={163--166},
  year={2022},
  publisher={Nature Publishing Group US New York}
}

# scanpy
@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}
}
