References#

[AFB+18]

Anna Alemany, Maria Florescu, Chloé S. Baron, Josi Peterson-Maduro, and Alexander van Oudenaarden. Whole-organism clone tracing using single-cell sequencing. Nature, 556(7699):108–112, April 2018. doi:10.1038/nature25969.

[BVD+22]

Rachel C. Bandler, Ilaria Vitali, Ryan N. Delgado, May C. Ho, Elena Dvoretskova, Josue S. Ibarra Molinas, Paul W. Frazel, Maesoumeh Mohammadkhani, Robert Machold, Sophia Maedler, Shane A. Liddelow, Tomasz J. Nowakowski, Gord Fishell, and Christian Mayer. Single-cell delineation of lineage and genetic identity in the mouse brain. Nature, 601(7893):404–409, January 2022. doi:10.1038/s41586-021-04237-0.

[BPK+19]

Ninib Baryawno, Dariusz Przybylski, Monika S. Kowalczyk, Youmna Kfoury, Nicolas Severe, Karin Gustafsson, Konstantinos D. Kokkaliaris, Francois Mercier, Marcin Tabaka, Matan Hofree, Danielle Dionne, Ani Papazian, Dongjun Lee, Orr Ashenberg, Ayshwarya Subramanian, Eeshit Dhaval Vaishnav, Orit Rozenblatt-Rosen, Aviv Regev, and David T. Scadden. A Cellular Taxonomy of the Bone Marrow Stroma in Homeostasis and Leukemia. Cell, 177(7):1915–1932.e16, June 2019. doi:10.1016/j.cell.2019.04.040.

[BYS+23]

Seoyeon Bok, Alisha R. Yallowitz, Jun Sun, Jason McCormick, Michelle Cung, Lingling Hu, Sarfaraz Lalani, Zan Li, Branden R. Sosa, Tomas Baumgartner, Paul Byrne, Tuo Zhang, Kyle W. Morse, Fatma F. Mohamed, Chunxi Ge, Renny T. Franceschi, Randy T. Cowling, Barry H. Greenberg, David J. Pisapia, Thomas A. Imahiyerobo, Shenela Lakhani, M. Elizabeth Ross, Caitlin E. Hoffman, Shawon Debnath, and Matthew B. Greenblatt. A multi-stem cell basis for craniosynostosis and calvarial mineralization. Nature, 621(7980):804–812, September 2023. doi:10.1038/s41586-023-06526-2.

[DHT+22]

Emma Dann, Neil C. Henderson, Sarah A. Teichmann, Michael D. Morgan, and John C. Marioni. Differential abundance testing on single-cell data using k-nearest neighbor graphs. Nature Biotechnology, 40(2):245–253, February 2022. doi:10.1038/s41587-021-01033-z.

[DYM+18]

Shawon Debnath, Alisha R. Yallowitz, Jason McCormick, Sarfaraz Lalani, Tuo Zhang, Ren Xu, Na Li, Yifang Liu, Yeon Suk Yang, Mark Eiseman, Jae-Hyuck Shim, Meera Hameed, John H. Healey, Mathias P. Bostrom, Dan Avi Landau, and Matthew B. Greenblatt. Discovery of a periosteal stem cell mediating intramembranous bone formation. Nature, 562(7725):133–139, October 2018. doi:10.1038/s41586-018-0554-8.

[DMT21]

Zachary J. DeBruine, Karsten Melcher, and Timothy J. Triche. Fast and robust non-negative matrix factorization for single-cell experiments. September 2021. doi:10.1101/2021.09.01.458620.

[DS23]

Silvia Domcke and Jay Shendure. A reference cell tree will serve science better than a reference cell atlas. Cell, 186(6):1103–1114, March 2023. doi:10.1016/j.cell.2023.02.016.

[HJC+23]

Wenpin Hou, Zhicheng Ji, Zeyu Chen, E. John Wherry, Stephanie C. Hicks, and Hongkai Ji. A statistical framework for differential pseudotime analysis with multiple single-cell RNA-seq samples. Nature Communications, 14(1):7286, November 2023. doi:10.1038/s41467-023-42841-y.

[LXLY22]

Qiwen Li, Ruoshi Xu, Kexin Lei, and Quan Yuan. Insights into skeletal stem cells. Bone Research, 10(1):1–17, October 2022. doi:10.1038/s41413-022-00235-8.

[LNL+22]

Mohammad Lotfollahi, Mohsen Naghipourfar, Malte D. Luecken, Matin Khajavi, Maren Büttner, Marco Wagenstetter, Žiga Avsec, Adam Gayoso, Nir Yosef, Marta Interlandi, Sergei Rybakov, Alexander V. Misharin, and Fabian J. Theis. Mapping single-cell data to reference atlases by transfer learning. Nature Biotechnology, 40(1):121–130, January 2022. doi:10.1038/s41587-021-01001-7.

[MO21]

Toshihide Mizoguchi and Noriaki Ono. The diverse origin of bone-forming osteoblasts. Journal of Bone and Mineral Research, 36(8):1432–1447, 2021. doi:10.1002/jbmr.4410.

[NSK+19]

Sonja Nowotschin, Manu Setty, Ying-Yi Kuo, Vincent Liu, Vidur Garg, Roshan Sharma, Claire S. Simon, Nestor Saiz, Rui Gardner, Stéphane C. Boutet, Deanna M. Church, Pamela A. Hoodless, Anna-Katerina Hadjantonakis, and Dana Pe'er. The emergent landscape of the mouse gut endoderm at single-cell resolution. Nature, 569(7756):361–367, May 2019. doi:10.1038/s41586-019-1127-1.

[OGR+22]

Sehyun Oh, Ludwig Geistlinger, Marcel Ramos, Daniel Blankenberg, Marius van den Beek, Jaclyn N. Taroni, Vincent J. Carey, Casey S. Greene, Levi Waldron, and Sean Davis. GenomicSuperSignature facilitates interpretation of RNA-seq experiments through robust, efficient comparison to public databases. Nature Communications, 13(1):3695, June 2022. doi:10.1038/s41467-022-31411-3.

[SCS18]

Wouter Saelens, Robrecht Cannoodt, and Yvan Saeys. A comprehensive evaluation of module detection methods for gene expression data. Nature Communications, 9(1):1090, March 2018. doi:10.1038/s41467-018-03424-4.

[SJD+21]

Kishor K. Sivaraj, Hyun-Woo Jeong, Backialakshmi Dharmalingam, Dagmar Zeuschner, Susanne Adams, Michael Potente, and Ralf H. Adams. Regional specialization and fate specification of bone stromal cells in skeletal development. Cell Reports, July 2021. doi:10.1016/j.celrep.2021.109352.

[SRF+18]

Kelly Street, Davide Risso, Russell B. Fletcher, Diya Das, John Ngai, Nir Yosef, Elizabeth Purdom, and Sandrine Dudoit. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics, 19(1):1–16, December 2018. doi:10.1186/s12864-018-4772-0.

[Tut98]

Albert Henry Tuttle. The Principles of Histology, Descriptive and Practical: Book I. Descriptive Histology. University of Virginia, Anderson Bros., 1898.

[WWC+18]

Daniel E. Wagner, Caleb Weinreb, Zach M. Collins, James A. Briggs, Sean G. Megason, and Allon M. Klein. Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo. Science (New York, N.Y.), 360(6392):981–987, June 2018. doi:10.1126/science.aar4362.

[XLM+21]

Chenling Xu, Romain Lopez, Edouard Mehlman, Jeffrey Regier, Michael I Jordan, and Nir Yosef. Probabilistic harmonization and annotation of single-cell transcriptomics data with deep generative models. Molecular Systems Biology, 17(1):e9620, January 2021. doi:10.15252/msb.20209620.

[YLL+24]

Guixin Yuan, Xixi Lin, Ying Liu, Matthew B Greenblatt, and Ren Xu. Skeletal stem cells in bone development, homeostasis, and disease. Protein & Cell, 15(8):559–574, August 2024. doi:10.1093/procel/pwae008.

[ZYT+20]

Leilei Zhong, Lutian Yao, Robert J Tower, Yulong Wei, Zhen Miao, Jihwan Park, Rojesh Shrestha, Luqiang Wang, Wei Yu, Nicholas Holdreith, Xiaobin Huang, Yejia Zhang, Wei Tong, Yanqing Gong, Jaimo Ahn, Katalin Susztak, Nathanial Dyment, Mingyao Li, Fanxin Long, Chider Chen, Patrick Seale, and Ling Qin. Single cell transcriptomics identifies a unique adipose lineage cell population that regulates bone marrow environment. eLife, 9:e54695, April 2020. doi:10.7554/eLife.54695.

[RouxdBezieuxVandBergeSD24]

Hector Roux de Bézieux, Koen Van den Berge, Kelly Street, and Sandrine Dudoit. Trajectory inference across multiple conditions with condiments. Nature Communications, 15(1):833, January 2024. doi:10.1038/s41467-024-44823-0.

[VandBergeRouxdBezieuxS+20]

Koen Van den Berge, Hector Roux de Bézieux, Kelly Street, Wouter Saelens, Robrecht Cannoodt, Yvan Saeys, Sandrine Dudoit, and Lieven Clement. Trajectory-based differential expression analysis for single-cell sequencing data. Nature Communications, 11(1):1201, March 2020. doi:10.1038/s41467-020-14766-3.