% spatialvi-tools BibTeX References
% Maintained by: Ori Kronfeld
% Last updated: 2026-03-24
% Sources: scvi-tools/docs/references.bib + standard packages

% =============================================================================
% Core Models
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@article{Levy25,
  title = {scVIVA: a probabilistic framework for representation of cells and their environments in spatial transcriptomics},
  author = {Nathan Levy and Florian Ingelfinger and Artemii Bakulin and Giacomo Cinnirella and Pierre Boyeau and Boaz Nadler and Can Ergen and Nir Yosef},
  doi = {10.1101/2025.06.01.657182},
  year = {2025},
  month = jun,
  journal = {biorxiv},
  publisher = {Cold Spring Harbor Laboratory}
}

@article{Lopez22,
  title = {DestVI identifies continuums of cell types in spatial transcriptomics data},
  author = {Romain Lopez and Baoguo Li and Hadas Keren-Shaul and Pierre Boyeau and Merav Kedmi and David Pilzer and Adam Jelinski and Ido Yofe and Eyal David and Allon Wagner and Yoseph Addadi and Ofra Golani and Franca Ronchese and Michael I. Jordan and Ido Amit and Nir Yosef},
  doi = {10.1038/s41587-022-01272-8},
  year = {2022},
  month = apr,
  journal = {Nature Biotechnology},
  publisher = {Nature Publishing Group}
}

@article{Ergen25,
  title = {ResolVI - addressing noise and bias in spatial transcriptomics},
  author = {Can Ergen and Nir Yosef},
  doi = {10.1101/2025.01.20.634005},
  year = {2025},
  month = jan,
  journal = {biorxiv},
  publisher = {Cold Spring Harbor Laboratory}
}

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% Foundation: scvi-tools
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@article{Gayoso22,
  title = {A Python library for probabilistic analysis of single-cell omics data},
  author = {Adam Gayoso and Romain Lopez and Galen Xing and Pierre Boyeau and Valeh Valiollah Pour Amiri and Justin Hong and Katherine Wu and Michael Jayasuriya and Edouard Mehlman and Maxime Langevin and Yining Liu and Jules Samaran and Gabriel Misrachi and Achille Nazaret and Oscar Clivio and Chenling Xu and Tal Ashuach and Mariano Gabitto and Mohammad Lotfollahi and Valentine Svensson and Eduardo da Veiga Beltrame and Vitalii Kleshchevnikov and Carlos Talavera-L{\'{o}}pez and Lior Pachter and Fabian J. Theis and Aaron Streets and Michael I. Jordan and Jeffrey Regier and Nir Yosef},
  doi = {10.1038/s41587-021-01206-w},
  year = {2022},
  month = feb,
  journal = {Nature Biotechnology},
  volume = {40},
  number = {2},
  pages = {163--166},
  publisher = {Nature Publishing Group}
}

@article{Lopez18,
  title = {Deep generative modeling for single-cell transcriptomics},
  author = {Romain Lopez and Jeffrey Regier and Michael B. Cole and Michael I. Jordan and Nir Yosef},
  doi = {10.1038/s41592-018-0229-2},
  year = {2018},
  month = nov,
  journal = {Nature Methods},
  volume = {15},
  number = {12},
  pages = {1053--1058},
  publisher = {Nature Publishing Group}
}

% =============================================================================
% scverse Ecosystem
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@article{Virshup24,
  title = {The scverse project provides a computational ecosystem for single-cell omics data analysis},
  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 Branchetti and others},
  doi = {10.1038/s41587-023-01733-8},
  journal = {Nature Biotechnology},
  volume = {42},
  pages = {333--336},
  year = {2024},
  publisher = {Nature Publishing Group}
}

@article{Palla22,
  title = {Squidpy: a scalable framework for spatial omics analysis},
  author = {Giovanni Palla and Hannah Spitzer and Michal Klein and David Fischer and Anna Christina Schaar and Louis Benedikt Kuemmerle and Sergei Rybakov and Ignacio Leonardo Ibarra and Olle Holmberg and Isaac Virshup and Mohammad Lotfollahi and Sabrina Richter and Fabian J. Theis},
  doi = {10.1038/s41592-021-01358-2},
  journal = {Nature Methods},
  volume = {19},
  pages = {171--178},
  year = {2022},
  publisher = {Nature Publishing Group}
}

@article{Wolf18,
  title = {{SCANPY}: large-scale single-cell gene expression data analysis},
  author = {F. Alexander Wolf and Philipp Angerer and Fabian J. Theis},
  doi = {10.1186/s13059-017-1382-0},
  journal = {Genome Biology},
  volume = {19},
  pages = {15},
  year = {2018},
  publisher = {BioMed Central}
}

@comment{SpatialData — add full citation when published; currently preprint
  Marconato24: SpatialData: an open and universal data framework for spatial omics
  doi: 10.1038/s41592-024-02212-x, Nature Methods, 2024}

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% Deep Learning Frameworks
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@inproceedings{Paszke19,
  title = {{PyTorch}: An Imperative Style, High-Performance Deep Gradient Computing Library},
  author = {Adam Paszke and Sam Gross and Francisco Massa and Adam Lerer and James Bradbury and Gregory Chanan and Trevor Killeen and Zeming Lin and Natalia Gimelshein and Luca Antiga and Alban Desmaison and Andreas Kopf and Edward Yang and Zachary DeVito and Martin Raison and Alykhan Tejani and Sasank Chilamkurthy and Benoit Steiner and Lu Fang and Junjie Bai and Soumith Chintala},
  booktitle = {Advances in Neural Information Processing Systems},
  volume = {32},
  year = {2019},
}

@misc{Falcon19,
  author = {William Falcon and {The PyTorch Lightning Team}},
  title = {{PyTorch Lightning}},
  year = {2019},
  url = {https://github.com/Lightning-AI/pytorch-lightning},
  note = {GitHub repository},
}

@article{Bingham19,
  title = {Pyro: Deep Universal Probabilistic Programming},
  author = {Eli Bingham and Jonathan P. Chen and Martin Jankowiak and Fritz Obermeyer and Neeraj Pradhan and Theofanis Karaletsos and Rohit Singh and Paul Szerlip and Paul Horsfall and Noah D. Goodman},
  journal = {Journal of Machine Learning Research},
  volume = {20},
  number = {28},
  pages = {1--6},
  year = {2019},
  url = {http://jmlr.org/papers/v20/18-403.html},
}

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% GPU Acceleration
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@misc{RAPIDS,
  author = {{NVIDIA Corporation}},
  title = {{RAPIDS}: GPU Data Science},
  year = {2018},
  url = {https://rapids.ai},
  note = {cuML (GPU machine learning) and cuGraph (GPU graph analytics)},
}

% =============================================================================
% Future External Models (tracked for later integration)
% =============================================================================

@article{Andersson20,
  title = {Single-cell and spatial transcriptomics enables probabilistic inference of cell type topography},
  author = {Alma Andersson and Joseph Bergenstråhle and Michaela Asp and Ludvig Bergenstråhle and Aleksandra Jurek and José Fernández Navarro and Joakim Lundeberg},
  doi = {10.1038/s42003-020-01247-y},
  year = {2020},
  month = oct,
  journal = {Communications Biology},
  volume = {3},
  number = {1},
  publisher = {Nature Publishing Group}
}

@article{Biancalani21,
  title = {Deep learning and alignment of spatially resolved single-cell transcriptomes with Tangram},
  author = {Tommaso Biancalani and Gabriele Scalia and Lorenzo Buffoni and Raghav Avasthi and Ziqing Lu and Aman Sanger and Nerim Tokcan and Charles R. Vanderburg and Åsa Segerstolpe and Meng Zhang and Inbal Avraham-Davidi and Sanja Vickovic and Mor Nitzan and Sai Ma and Ayshwarya Subramanian and Michal Lipinski and Jason Buenrostro and Nik Bear Brown and Duccio Fanelli and Xiaowei Zhuang and Evan Z. Macosko and Aviv Regev},
  journal = {Nature Methods},
  volume = {18},
  number = {11},
  pages = {1352--1362},
  year = {2021},
  publisher = {Nature Publishing Group}
}

@article{Kleshchevnikov22,
  title = {Cell2location maps fine-grained cell types in spatial transcriptomics},
  author = {Vitalii Kleshchevnikov and Artem Shmatko and Emma Dann and Alexander Aivazidis and Hamish W. King and Tong Li and Artem Lomakin and Malte D. Luecken and Alexander T. Dilthey and Gord Fishell and Signe De Schepper and Niklas J. Savill and Mohammad Lotfollahi and Ivo G. Gut and Oliver Stegle and Omer Ali Bayraktar and Fabian J. Theis},
  doi = {10.1038/s41587-021-01139-4},
  journal = {Nature Biotechnology},
  volume = {40},
  pages = {661--671},
  year = {2022},
  publisher = {Nature Publishing Group}
}