Dissecting cell identity via network inference and in silico gene perturbation
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DOI: 10.1038/s41586-022-05688-9
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- Xiaoning Qi & Lianhe Zhao & Chenyu Tian & Yueyue Li & Zhen-Lin Chen & Peipei Huo & Runsheng Chen & Xiaodong Liu & Baoping Wan & Shengyong Yang & Yi Zhao, 2024. "Predicting transcriptional responses to novel chemical perturbations using deep generative model for drug discovery," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Hao Li & Zebei Han & Yu Sun & Fu Wang & Pengzhen Hu & Yuang Gao & Xuemei Bai & Shiyu Peng & Chao Ren & Xiang Xu & Zeyu Liu & Hebing Chen & Yang Yang & Xiaochen Bo, 2024. "CGMega: explainable graph neural network framework with attention mechanisms for cancer gene module dissection," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
- Gregory Farber & Yanhan Dong & Qiaozi Wang & Mitesh Rathod & Haofei Wang & Michelle Dixit & Benjamin Keepers & Yifang Xie & Kendall Butz & William J. Polacheck & Jiandong Liu & Li Qian, 2024. "Direct conversion of cardiac fibroblasts into endothelial-like cells using Sox17 and Erg," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
- Kathryn Weinand & Saori Sakaue & Aparna Nathan & Anna Helena Jonsson & Fan Zhang & Gerald F. M. Watts & Majd Al Suqri & Zhu Zhu & Deepak A. Rao & Jennifer H. Anolik & Michael B. Brenner & Laura T. Don, 2024. "The chromatin landscape of pathogenic transcriptional cell states in rheumatoid arthritis," Nature Communications, Nature, vol. 15(1), pages 1-25, December.
- Peizhuo Wang & Xiao Wen & Han Li & Peng Lang & Shuya Li & Yipin Lei & Hantao Shu & Lin Gao & Dan Zhao & Jianyang Zeng, 2023. "Deciphering driver regulators of cell fate decisions from single-cell transcriptomics data with CEFCON," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
- Mingsen Li & Huizhen Guo & Bofeng Wang & Zhuo Han & Siqi Wu & Jiafeng Liu & Huaxing Huang & Jin Zhu & Fengjiao An & Zesong Lin & Kunlun Mo & Jieying Tan & Chunqiao Liu & Li Wang & Xin Deng & Guigang L, 2024. "The single-cell transcriptomic atlas and RORA-mediated 3D epigenomic remodeling in driving corneal epithelial differentiation," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
- Shilu Zhang & Saptarshi Pyne & Stefan Pietrzak & Spencer Halberg & Sunnie Grace McCalla & Alireza Fotuhi Siahpirani & Rupa Sridharan & Sushmita Roy, 2023. "Inference of cell type-specific gene regulatory networks on cell lineages from single cell omic datasets," Nature Communications, Nature, vol. 14(1), pages 1-25, December.
- Xiaoying Wang & Maoteng Duan & Jingxian Li & Anjun Ma & Gang Xin & Dong Xu & Zihai Li & Bingqiang Liu & Qin Ma, 2024. "MarsGT: Multi-omics analysis for rare population inference using single-cell graph transformer," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
- Nicolas Ledru & Parker C. Wilson & Yoshiharu Muto & Yasuhiro Yoshimura & Haojia Wu & Dian Li & Amish Asthana & Stefan G. Tullius & Sushrut S. Waikar & Giuseppe Orlando & Benjamin D. Humphreys, 2024. "Predicting proximal tubule failed repair drivers through regularized regression analysis of single cell multiomic sequencing," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Yingtong Hou & Bo Lin & Tianyi Xu & Juan Jiang & Shuli Luo & Wanna Chen & Xinwen Chen & Yuanqi Wang & Guanrui Liao & Jianping Wang & Jiayuan Zhang & Xuyang Li & Xiao Xiang & Yubin Xie & Ji Wang & Sui , 2024. "The neurotransmitter calcitonin gene-related peptide shapes an immunosuppressive microenvironment in medullary thyroid cancer," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Fangfang Yan & Akiko Suzuki & Chihiro Iwaya & Guangsheng Pei & Xian Chen & Hiroki Yoshioka & Meifang Yu & Lukas M. Simon & Junichi Iwata & Zhongming Zhao, 2024. "Single-cell multiomics decodes regulatory programs for mouse secondary palate development," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
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