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@article{Maynard2021Mar,
	author = {Maynard, Kristen R. and Collado-Torres, Leonardo and Weber, Lukas M. and Uytingco, Cedric and Barry, Brianna K. and Williams, Stephen R. and Catallini, Joseph L. and Tran, Matthew N. and Besich, Zachary and Tippani, Madhavi and Chew, Jennifer and Yin, Yifeng and Kleinman, Joel E. and Hyde, Thomas M. and Rao, Nikhil and Hicks, Stephanie C. and Martinowich, Keri and Jaffe, Andrew E.},
	title = {{Transcriptome-scale spatial gene expression in the human dorsolateral prefrontal cortex}},
	journal = {Nat Neurosci},
	volume = {24},
	pages = {425--436},
	year = {2021},
	month = mar,
	issn = {1546-1726},
	publisher = {Nature Publishing Group},
	doi = {10.1038/s41593-020-00787-0}
}

@article{Amezquita2020Feb,
	author = {Amezquita, Robert A. and Lun, Aaron T. L. and Becht, Etienne and Carey, Vince J. and Carpp, Lindsay N. and Geistlinger, Ludwig and Marini, Federico and Rue-Albrecht, Kevin and Risso, Davide and Soneson, Charlotte and Waldron, Levi and Pag{\ifmmode\grave{e}\else\`{e}\fi}s, Herv{\ifmmode\acute{e}\else\'{e}\fi} and Smith, Mike L. and Huber, Wolfgang and Morgan, Martin and Gottardo, Raphael and Hicks, Stephanie C.},
	title = {{Orchestrating single-cell analysis with Bioconductor}},
	journal = {Nat Methods},
	volume = {17},
	pages = {137--145},
	year = {2020},
	month = feb,
	issn = {1548-7105},
	publisher = {Nature Publishing Group},
	doi = {10.1038/s41592-019-0654-x}
}

@article{Righelli2022Jun,
	author = {Righelli, Dario and Weber, Lukas M. and Crowell, Helena L. and Pardo, Brenda and Collado-Torres, Leonardo and Ghazanfar, Shila and Lun, Aaron T. L. and Hicks, Stephanie C. and Risso, Davide},
	title = {{SpatialExperiment: infrastructure for spatially-resolved transcriptomics data in R using Bioconductor}},
	journal = {Bioinformatics},
	volume = {38},
	number = {11},
	pages = {3128--3131},
	year = {2022},
	month = jun,
	issn = {1367-4803},
	publisher = {Oxford Academic},
	doi = {10.1093/bioinformatics/btac299}
}

@article{McCarthy2017Apr,
	author = {McCarthy, Davis J. and Campbell, Kieran R. and Lun, Aaron T. L. and Wills, Quin F.},
	title = {{Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R}},
	journal = {Bioinformatics},
	volume = {33},
	number = {8},
	pages = {1179--1186},
	year = {2017},
	month = apr,
	issn = {1367-4803},
	publisher = {Oxford Academic},
	doi = {10.1093/bioinformatics/btw777}
}

@Manual{ggspavis2023Apr,
    title = {ggspavis: Visualization functions for spatially resolved transcriptomics data},
    author = {Lukas M. Weber and Helena L. Crowell},
    year = {2022},
    note = {R package version 1.4.0},
    url = {https://github.com/lmweber/ggspavis},
  }

@article{Lun2016Oct,
	author = {Lun, Aaron T. L. and McCarthy, Davis J. and Marioni, John C.},
	title = {{A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor}},
	journal = {F1000Research},
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	number = {2122},
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	year = {2016},
	month = oct,
	publisher = {F1000Research},
	doi = {10.12688/f1000research.9501.2}
}

@article{Li2022Jan,
	author = {Li, Yijun and Stanojevic, Stefan and He, Bing and Jing, Zheng and Huang, Qianhui and Kang, Jian and Garmire, Lana X.},
	title = {{Benchmarking Computational Integration Methods for Spatial Transcriptomics Data}},
	journal = {bioRxiv},
	pages = {2021.08.27.457741},
	year = {2022},
	month = jan,
	publisher = {Cold Spring Harbor Laboratory},
	eprint = {2021.08.27.457741},
	url = {https://doi.org/10.1101/2021.08.27.457741}
}

@misc{Moran1950Jun,
	title = {{Notes on Continuous Stochastic Phenomena on JSTOR}},
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	note = {[Online; accessed 10. Apr. 2023]},
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}

@misc{Geary1954Nov,
	title = {{The Contiguity Ratio and Statistical Mapping on JSTOR}},
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	note = {[Online; accessed 10. Apr. 2023]},
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}

@article{Zhu2021Dec,
	author = {Zhu, Jiaqiang and Sun, Shiquan and Zhou, Xiang},
	title = {{SPARK-X: non-parametric modeling enables scalable and robust detection of spatial expression patterns for large spatial transcriptomic studies}},
	journal = {Genome Biol},
	volume = {22},
	number = {1},
	pages = {1--25},
	year = {2021},
	month = dec,
	issn = {1474-760X},
	publisher = {BioMed Central},
	doi = {10.1186/s13059-021-02404-0}
}

@article{Sun2020Feb,
	author = {Sun, Shiquan and Zhu, Jiaqiang and Zhou, Xiang},
	title = {{Statistical analysis of spatial expression patterns for spatially resolved transcriptomic studies}},
	journal = {Nat Methods},
	volume = {17},
	pages = {193--200},
	year = {2020},
	month = feb,
	issn = {1548-7105},
	publisher = {Nature Publishing Group},
	doi = {10.1038/s41592-019-0701-7}
}

@article{Svensson2018May,
	author = {Svensson, Valentine and Teichmann, Sarah A. and Stegle, Oliver},
	title = {{SpatialDE: identification of spatially variable genes}},
	journal = {Nat Methods},
	volume = {15},
	pages = {343--346},
	year = {2018},
	month = may,
	issn = {1548-7105},
	publisher = {Nature Publishing Group},
	doi = {10.1038/nmeth.4636}
}

@article{McInnes2018Feb,
	author = {McInnes, Leland and Healy, John and Melville, James},
	title = {{UMAP: Uniform Manifold Approximation and Projection for Dimension Reduction}},
	journal = {arXiv},
	year = {2018},
	month = feb,
	eprint = {1802.03426},
	doi = {10.48550/arXiv.1802.03426}
}

@incollection{Keogh2017Apr,
	author = {Keogh, Eamonn and Mueen, Abdullah},
	title = {{Curse of Dimensionality}},
	booktitle = {{Encyclopedia of Machine Learning and Data Mining}},
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	pages = {314--315},
	year = {2017},
	month = apr,
	publisher = {Springer, Boston, MA},
	address = {Boston, MA, USA},
	doi = {10.1007/978-1-4899-7687-1_192}
}

@article{Hao2021Jun,
	author = {Hao, Yuhan and Hao, Stephanie and Andersen-Nissen, Erica and Mauck, William M. and Zheng, Shiwei and Butler, Andrew and Lee, Maddie J. and Wilk, Aaron J. and Darby, Charlotte and Zager, Michael and Hoffman, Paul and Stoeckius, Marlon and Papalexi, Efthymia and Mimitou, Eleni P. and Jain, Jaison and Srivastava, Avi and Stuart, Tim and Fleming, Lamar M. and Yeung, Bertrand and Rogers, Angela J. and McElrath, Juliana M. and Blish, Catherine A. and Gottardo, Raphael and Smibert, Peter and Satija, Rahul},
	title = {{Integrated analysis of multimodal single-cell data}},
	journal = {Cell},
	volume = {184},
	number = {13},
	pages = {3573--3587.e29},
	year = {2021},
	month = jun,
	issn = {0092-8674},
	publisher = {Elsevier},
	doi = {10.1016/j.cell.2021.04.048}
}

@article{GUILLIAMS2022379,
title = {Spatial proteogenomics reveals distinct and evolutionarily conserved hepatic macrophage niches},
journal = {Cell},
volume = {185},
number = {2},
pages = {379-396.e38},
year = {2022},
issn = {0092-8674},
doi = {https://doi.org/10.1016/j.cell.2021.12.018},
url = {https://www.sciencedirect.com/science/article/pii/S0092867421014811},
author = {Martin Guilliams and Johnny Bonnardel and Birthe Haest and Bart Vanderborght and Camille Wagner and Anneleen Remmerie and Anna Bujko and Liesbet Martens and Tinne Thoné and Robin Browaeys and Federico F. {De Ponti} and Bavo Vanneste and Christian Zwicker and Freya R. Svedberg and Tineke Vanhalewyn and Amanda Gonçalves and Saskia Lippens and Bert Devriendt and Eric Cox and Giuliano Ferrero and Valerie Wittamer and Andy Willaert and Suzanne J.F. Kaptein and Johan Neyts and Kai Dallmeier and Peter Geldhof and Stijn Casaert and Bart Deplancke and Peter {ten Dijke} and Anne Hoorens and Aude Vanlander and Frederik Berrevoet and Yves {Van Nieuwenhove} and Yvan Saeys and Wouter Saelens and Hans {Van Vlierberghe} and Lindsey Devisscher and Charlotte L. Scott},
keywords = {liver, atlas, spatial transcriptomics, CITE-seq, proteogenomic, across species, multi-omic, lipid-associated macrophage, Kupffer cell, NAFLD},
abstract = {Summary
The liver is the largest solid organ in the body, yet it remains incompletely characterized. Here we present a spatial proteogenomic atlas of the healthy and obese human and murine liver combining single-cell CITE-seq, single-nuclei sequencing, spatial transcriptomics, and spatial proteomics. By integrating these multi-omic datasets, we provide validated strategies to reliably discriminate and localize all hepatic cells, including a population of lipid-associated macrophages (LAMs) at the bile ducts. We then align this atlas across seven species, revealing the conserved program of bona fide Kupffer cells and LAMs. We also uncover the respective spatially resolved cellular niches of these macrophages and the microenvironmental circuits driving their unique transcriptomic identities. We demonstrate that LAMs are induced by local lipid exposure, leading to their induction in steatotic regions of the murine and human liver, while Kupffer cell development crucially depends on their cross-talk with hepatic stellate cells via the evolutionarily conserved ALK1-BMP9/10 axis.}
}

@article{Avis1985,
author = {Avis, David and Horton, Joe},
title = {REMARKS ON THE SPHERE OF INFLUENCE GRAPH},
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volume = {440},
number = {1},
pages = {323-327},
doi = {https://doi.org/10.1111/j.1749-6632.1985.tb14563.x},
url = {https://nyaspubs.onlinelibrary.wiley.com/doi/abs/10.1111/j.1749-6632.1985.tb14563.x},
eprint = {https://nyaspubs.onlinelibrary.wiley.com/doi/pdf/10.1111/j.1749-6632.1985.tb14563.x},
year = {1985}
}

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	author = {Matula, David W. and Sokal, Robert R.},
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}

@article{Toussaint1980Jan,
	author = {Toussaint, Godfried T.},
	title = {{The relative neighbourhood graph of a finite planar set}},
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	publisher = {Pergamon},
	doi = {10.1016/0031-3203(80)90066-7}
}

@article{Gollini2015Feb,
	author = {Gollini, Isabella and Lu, Binbin and Charlton, Martin and Brunsdon, Christopher and Harris, Paul},
	title = {{GWmodel: An R Package for Exploring Spatial Heterogeneity Using Geographically Weighted Models}},
	journal = {J Stat Soft},
	volume = {63},
	pages = {1--50},
	year = {2015},
	month = feb,
	issn = {1548-7660},
	doi = {10.18637/jss.v063.i17}
}

@article{Harris2011Oct,
	author = {Harris, Paul and Brunsdon, Chris and Charlton, Martin},
	title = {{Geographically weighted principal components analysis}},
	journal = {International Journal of Geographical Information Science},
	volume = {25},
	number = {10},
	pages = {1717--1736},
	year = {2011},
	month = oct,
	issn = {1365-8816},
	publisher = {Taylor {\&} Francis},
	doi = {10.1080/13658816.2011.554838}
}

@article{vandermaaten08,
  author  = {Laurens van der Maaten and Geoffrey Hinton},
  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}
}