References#
Junedh M Amrute, Xin Luo, Vinay Penna, Steven Yang, Tracy Yamawaki, Sikander Hayat, Andrea Bredemeyer, In-Hyuk Jung, Farid F Kadyrov, Gyu Seong Heo, and others. Targeting immune–fibroblast cell communication in heart failure. Nature, pages 1–11, 2024. URL: https://www.nature.com/articles/s41586-024-08008-5.
Mariano I Gabitto, Kyle J Travaglini, Victoria M Rachleff, Eitan S Kaplan, Brian Long, Jeanelle Ariza, Yi Ding, Joseph T Mahoney, Nick Dee, Jeff Goldy, and others. Integrated multimodal cell atlas of alzheimer’s disease. Nature Neuroscience, pages 1–18, 2024. URL: https://www.nature.com/articles/s41593-024-01774-5#data-availability.
Shijie Hao, Xiaojia Zhu, Zhi Huang, Qianqian Yang, Hean Liu, Yan Wu, Yafeng Zhan, Yu Dong, Chao Li, He Wang, Elize Haasdijk, Zihan Wu, Shenglong Li, Haotian Yan, Lijing Zhu, Shiyong Guo, Zefang Wang, Aojun Ye, Youning Lin, Luman Cui, Xing Tan, Huanlin Liu, Mingli Wang, Jing Chen, Yanqing Zhong, Wensi Du, Guangling Wang, Tingting Lai, Mengdi Cao, Tao Yang, Yuanfang Xu, Ling Li, Qian Yu, Zhenkun Zhuang, Ying Xia, Ying Lei, Yingjie An, Mengnan Cheng, Yun Zhao, Lei Han, Yue Yuan, Xinxiang Song, Yumo Song, Liqin Gu, Chang Liu, Xiumei Lin, Ruiqi Wang, Zhifeng Wang, Yang Wang, Shenyu Li, Huanhuan Li, Jingjing Song, Mengni Chen, Wanqiu Zhou, Nini Yuan, Suhong Sun, Shiwen Wang, Yu Chen, Mingyuan Zheng, Jiao Fang, Ruiyi Zhang, Shuzhen Zhang, Qinwen Chai, Jiabing Liu, Wu Wei, Jie He, Haibo Zhou, Yangang Sun, Zhen Liu, Chuanyu Liu, Jianhua Yao, Zhifeng Liang, Xun Xu, Muming Poo, Chengyu Li, Chris I. De Zeeuw, Zhiming Shen, Zhiyong Liu, Longqi Liu, Shiping Liu, Yidi Sun, and Cirong Liu. Cross-species single-cell spatial transcriptomic atlases of the cerebellar cortex. Science, 385(6716):eado3927, 2024. URL: https://www.science.org/doi/abs/10.1126/science.ado3927, doi:10.1126/science.ado3927.
Yuhan Hao, Stephanie Hao, Erica Andersen-Nissen, William M Mauck, Shiwei Zheng, Andrew Butler, Maddie J Lee, Aaron J Wilk, Charlotte Darby, Michael Zager, and Others. Integrated analysis of multimodal single-cell data. Cell, 184(13):3573–3587, 2021. URL: https://www.cell.com/cell/fulltext/S0092-8674(21)00583-3.
Velina Kozareva, Caroline Martin, Tomas Osorno, Stephanie Rudolph, Chong Guo, Charles Vanderburg, Naeem Nadaf, Aviv Regev, Wade G Regehr, and Evan Macosko. A transcriptomic atlas of mouse cerebellar cortex comprehensively defines cell types. Nature, 598(7879):214–219, 2021. URL: https://www.nature.com/articles/s41586-021-03220-z.
Jin Li, Jongsu Choi, Xuesen Cheng, Justin Ma, Shahil Pema, Joshua R Sanes, Graeme Mardon, Benjamin J Frankfort, Nicholas M Tran, Yumei Li, and others. Comprehensive single-cell atlas of the mouse retina. Iscience, 2024. URL: https://www.cell.com/iscience/fulltext/S2589-0042(24)01138-6.
Jin Li, Jun Wang, Ignacio L Ibarra, Xuesen Cheng, Malte D Luecken, Jiaxiong Lu, Aboozar Monavarfeshani, Wenjun Yan, Yiqiao Zheng, Zhen Zuo, and others. Integrated multi-omics single cell atlas of the human retina. Research Square, 2023. URL: https://www.researchsquare.com/article/rs-3471275/v1.
Malte Luecken, Daniel Burkhardt, Robrecht Cannoodt, Christopher Lance, Aditi Agrawal, Hananeh Aliee, Ann Chen, Louise Deconinck, Angela Detweiler, Alejandro Granados, Shelly Huynh, Laura Isacco, Yang Kim, Dominik Klein, BONY DE KUMAR, Sunil Kuppasani, Heiko Lickert, Aaron McGeever, Joaquin Melgarejo, Honey Mekonen, Maurizio Morri, Michaela Müller, Norma Neff, Sheryl Paul, Bastian Rieck, Kaylie Schneider, Scott Steelman, Michael Sterr, Daniel Treacy, Alexander Tong, Alexandra-Chloe Villani, Guilin Wang, Jia Yan, Ce Zhang, Angela Pisco, Smita Krishnaswamy, Fabian Theis, and Jonathan M Bloom. A sandbox for prediction and integration of dna, rna, and proteins in single cells. In J. Vanschoren and S. Yeung, editors, Proceedings of the Neural Information Processing Systems Track on Datasets and Benchmarks, volume 1. 2021. URL: https://openreview.net/forum?id=gN35BGa1Rt.
Stefan Salcher, Gregor Sturm, Lena Horvath, Gerold Untergasser, Christiane Kuempers, Georgios Fotakis, Elisa Panizzolo, Agnieszka Martowicz, Manuel Trebo, Georg Pall, and others. High-resolution single-cell atlas reveals diversity and plasticity of tissue-resident neutrophils in non-small cell lung cancer. Cancer cell, 40(12):1503–1520, 2022. URL: https://www.cell.com/cancer-cell/fulltext/S1535-6108(22)00499-8.
Lisa Sikkema, Ciro Ramírez-Suástegui, Daniel C Strobl, Tessa E Gillett, Luke Zappia, Elo Madissoon, Nikolay S Markov, Laure-Emmanuelle Zaragosi, Yuge Ji, Meshal Ansari, and others. An integrated cell atlas of the lung in health and disease. Nature medicine, 29(6):1563–1577, 2023. URL: https://www.nature.com/articles/s41591-023-02327-2.
Kimberly Siletti, Rebecca Hodge, Alejandro Mossi Albiach, Ka Wai Lee, Song-Lin Ding, Lijuan Hu, Peter Lönnerberg, Trygve Bakken, Tamara Casper, Michael Clark, and others. Transcriptomic diversity of cell types across the adult human brain. Science, 382(6667):eadd7046, 2023. URL: https://www.science.org/doi/10.1126/science.add7046.
Andy GX Zeng, Ilaria Iacobucci, Sayyam Shah, Amanda Mitchell, Gordon Wong, Suraj Bansal, David Chen, Qingsong Gao, Hyerin Kim, James A Kennedy, and others. Single-cell transcriptional atlas of human hematopoiesis reveals genetic and hierarchy-based determinants of aberrant aml differentiation. Blood Cancer Discovery, pages 1–18, 2025. URL: https://aacrjournals.org/bloodcancerdiscov/article/6/4/307/763153/Single-cell-Transcriptional-Atlas-of-Human.
Zehao Zhang, Chloe Schaefer, Weirong Jiang, Ziyu Lu, Jasper Lee, Andras Sziraki, Abdulraouf Abdulraouf, Brittney Wick, Maximilian Haeussler, Zhuoyan Li, Gesmira Molla, Rahul Satija, Wei Zhou, and Junyue Cao. A panoramic view of cell population dynamics in mammalian aging. Science, 0(0):eadn3949, 2024. URL: https://www.science.org/doi/abs/10.1126/science.adn3949, doi:10.1126/science.adn3949.
Lei Zhao, Zhongqi Li, Joaquim SL Vong, Xinyi Chen, Hei-Ming Lai, Leo YC Yan, Junzhe Huang, Samuel KH Sy, Xiaoyu Tian, Yu Huang, and others. Pharmacologically reversible zonation-dependent endothelial cell transcriptomic changes with neurodegenerative disease associations in the aged brain. Nature Communications, 11(1):4413, 2020. URL: https://www.nature.com/articles/s41467-020-18249-3#Sec10.
Kaiyi Zhu, Jaroslav Bendl, Samir Rahman, James M Vicari, Claire Coleman, Tereza Clarence, Ovaun Latouche, Nadejda M Tsankova, Aiqun Li, Kristen J Brennand, and others. Multi-omic profiling of the developing human cerebral cortex at the single-cell level. Science Advances, 9(41):eadg3754, 2023. URL: https://www.science.org/doi/10.1126/sciadv.adg3754.