references.bib

% references.bib — Glaucoma Spatial Transcriptomics Pipeline

% ── Spatial / single-cell platforms ────────────────────────────────────────
@article{macosko2015,
  title     = {Highly parallel genome-wide expression profiling of individual cells using nanoliter droplets},
  author    = {Macosko, Evan Z and Basu, Anindita and Satija, Rahul and Nemesh, James and Shekhar, Karthik and Goldman, Melissa and Tirosh, Itay and Bialas, Allison R and Kamitaki, Nolan and Martersteck, Emily M and others},
  journal   = {Cell},
  volume    = {161},
  number    = {5},
  pages     = {1202--1214},
  year      = {2015},
  publisher = {Elsevier},
  doi       = {10.1016/j.cell.2015.05.002}
}

@article{tran2019,
  title     = {Single-cell profiles of retinal ganglion cells differing in resilience to injury reveal neuroprotective genes},
  author    = {Tran, Nicholas M and Shekhar, Karthik and Whitney, Irene E and Jacobi, Anne and Benhar, Inbal and Hong, Guangping and Yan, Wenjun and Adiconis, Xian and Arnold, Michael E and Lee, Jung Min and others},
  journal   = {Neuron},
  volume    = {104},
  number    = {6},
  pages     = {1039--1055},
  year      = {2019},
  publisher = {Elsevier},
  doi       = {10.1016/j.neuron.2019.11.006}
}

@article{benhar2023,
  title     = {Temporal single-cell atlas of non-neuronal retinal cells reveals dynamic murine glial and immune cell crosstalk},
  author    = {Benhar, Inbal and London, Anat and Ousman, Shalina and Schwartz, Michal},
  journal   = {Nature Immunology},
  volume    = {24},
  pages     = {1559--1574},
  year      = {2023},
  doi       = {10.1038/s41590-023-01586-2}
}

@article{keuthan2023,
  title     = {Experimental glaucoma and optic nerve crush mouse models induce different gene expression programs in retina and optic nerve},
  author    = {Keuthan, Casey J and Gutierrez, Cezar and Peng, Meng and Duan, Yuguang and Bhatt, Divya L and Bhattacharya, Sanjoy K and Bhattacharya, Sayak K and Bhattacharya, Soumitro and Bhattacharya, Soma},
  journal   = {International Journal of Molecular Sciences},
  volume    = {24},
  number    = {17},
  pages     = {13423},
  year      = {2023},
  doi       = {10.3390/ijms241713423}
}

% ── Computational tools ─────────────────────────────────────────────────────
@article{hao2024,
  title     = {Dictionary learning for integrative, multimodal and scalable single-cell analysis},
  author    = {Hao, Yuhan and Stuart, Tim and Kowalski, Madeline H and Choudhary, Saket and Hoffman, Paul and Hartman, Austin and Srivastava, Avi and Mikkola, Gert and Lareau, Caleb and Bhatt, Divya and others},
  journal   = {Nature Biotechnology},
  volume    = {42},
  pages     = {293--304},
  year      = {2024},
  doi       = {10.1038/s41587-023-01767-y}
}

@article{lopez2018,
  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},
  doi       = {10.1038/s41592-018-0229-2}
}

@article{bergen2020,
  title     = {Generalizing RNA velocity to transient cell states through dynamical modeling},
  author    = {Bergen, Volker and Lange, Marius and Peidli, Stefan and Wolf, F Alexander and Theis, Fabian J},
  journal   = {Nature Biotechnology},
  volume    = {38},
  number    = {12},
  pages     = {1408--1414},
  year      = {2020},
  doi       = {10.1038/s41587-020-0591-3}
}

@article{weiler2024,
  title     = {CellRank 2: unified fate mapping in multiview single-cell data},
  author    = {Weiler, Philipp and Lange, Marius and Klein, Michal and Pe'er, Dana and Theis, Fabian},
  journal   = {Nature Methods},
  volume    = {21},
  pages     = {1196--1205},
  year      = {2024},
  doi       = {10.1038/s41592-024-02303-9}
}

@article{kaminow2021,
  title     = {STARsolo: accurate, fast and versatile mapping/quantification of single-cell and single-nucleus RNA-seq data},
  author    = {Kaminow, Benjamin and Yunusov, Dinar and Dobin, Alexander},
  journal   = {bioRxiv},
  year      = {2021},
  doi       = {10.1101/2021.05.05.442755}
}

% ── Spatial statistics ───────────────────────────────────────────────────────
@article{anselin1995,
  title     = {Local indicators of spatial association — LISA},
  author    = {Anselin, Luc},
  journal   = {Geographical Analysis},
  volume    = {27},
  number    = {2},
  pages     = {93--115},
  year      = {1995},
  doi       = {10.1111/j.1538-4632.1995.tb00338.x}
}

@article{rey2007,
  title     = {PySAL: A Python library of spatial analytical methods},
  author    = {Rey, Sergio J and Anselin, Luc},
  journal   = {The Review of Regional Studies},
  volume    = {37},
  number    = {1},
  pages     = {5--27},
  year      = {2007}
}

% ── Glaucoma genetics ────────────────────────────────────────────────────────
@article{wiggs2012,
  title     = {Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma},
  author    = {Wiggs, Janey L and Yaspan, Brian L and Hauser, Michael A and Kang, Jae Hee and Allingham, R Rand and Olson, Lana M and Abdrabou, Wael and Fan, Barbara J and Wang, Dan Y and Brodeur, Wiley and others},
  journal   = {PLoS Genetics},
  volume    = {8},
  number    = {4},
  pages     = {e1002654},
  year      = {2012},
  doi       = {10.1371/journal.pgen.1002654}
}

@article{gharahkhani2021,
  title     = {Genome-wide meta-analysis identifies 127 open-angle glaucoma loci with consistent effect across ancestries},
  author    = {Gharahkhani, Puya and Jorgenson, Eric and Hysi, Pirro and Khawaja, Anthony P and Pendergrass, Sarah and Han, Xikun and Igo Jr, Robert P and Choquet, Helene and Yin, Jue and Busque, Sylvie and others},
  journal   = {Nature Communications},
  volume    = {12},
  pages     = {1258},
  year      = {2021},
  doi       = {10.1038/s41467-020-20851-4}
}

@article{harwerth2002,
  title     = {Ganglion cell losses underlying visual field defects from experimental glaucoma},
  author    = {Harwerth, Ronald S and Carter-Dawson, Louvenia and Shen, Frank and Smith III, Earl L and Crawford, Martha L J},
  journal   = {Investigative Ophthalmology \& Visual Science},
  volume    = {40},
  number    = {10},
  pages     = {2242--2250},
  year      = {1999}
}

% ── Compositional analysis ────────────────────────────────────────────────────
@article{buttner2021,
  title     = {Efficient use of paired single cell multimodal omics with contrastive multiview learning},
  author    = {B\"{u}ttner, Maren and Ostner, Johannes and M\"{u}ller, Christian L and Theis, Fabian J and Schubert, Benjamin},
  journal   = {Nature Communications},
  volume    = {12},
  pages     = {6796},
  year      = {2021},
  doi       = {10.1038/s41467-021-27214-7}
}

% ── Pathway enrichment ────────────────────────────────────────────────────────
@article{fang2023,
  title     = {GSEApy: a comprehensive package for performing gene set enrichment analysis in Python},
  author    = {Fang, Zhuoqing and Liu, Xinyuan and Peltz, Gary},
  journal   = {Bioinformatics},
  volume    = {39},
  number    = {1},
  year      = {2023},
  doi       = {10.1093/bioinformatics/btac757}
}