GiniClust3: a fast and memory-efficient tool for rare cell type identification by Rui Dong, Guo-Cheng Yuan

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SpatialDWLS: accurate deconvolution of spatial transcriptomic data by Rui Dong, Guo-Cheng Yuan

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GiniClust2: a cluster-aware, weighted ensemble clustering method for cell-type detection by Daphne Tsoucas, Guo-Cheng Yuan

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RECCIPE: A new framework assessing localized cell-cell interaction on gene expression in multicellular ST data by Weiping Ma, Xiaoyu Song, Xiaoyu Song, Guo-Cheng Yuan, Guo-Cheng Yuan, Pei Wang, Pei Wang

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RESCUE: imputing dropout events in single-cell RNA-sequencing data by Sam Tracy, Guo-Cheng Yuan, Ruben Dries

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Passing messages between biological networks to refine predicted interactions. by Kimberly Glass, Curtis Huttenhower, John Quackenbush, Guo-Cheng Yuan

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Identifying quantitatively differential chromosomal compartmentalization changes and their biological significance from Hi-C data using DARIC by Yan Kai, Nan Liu, Stuart H. Orkin, Guo-Cheng Yuan

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CUT&RUNTools: a flexible pipeline for CUT&RUN processing and footprint analysis by Qian Zhu, Nan Liu, Stuart H. Orkin, Guo-Cheng Yuan

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Modeling the dynamics of bivalent histone modifications. by Wai Lim Ku, Michelle Girvan, Guo-Cheng Yuan, Francesco Sorrentino, Edward Ott

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Revealing the Critical Regulators of Cell Identity in the Mouse Cell Atlas by Shengbao Suo, Qian Zhu, Assieh Saadatpour, Lijiang Fei, Guoji Guo, Guo-Cheng Yuan

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Accurate estimation of cell-type composition from gene expression data by Daphne Tsoucas, Rui Dong, Haide Chen, Qian Zhu, Guoji Guo, Guo-Cheng Yuan

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Chromatin signature of widespread monoallelic expression by Anwesha Nag, Virginia Savova, Ho-Lim Fung, Alexander Miron, Guo-Cheng Yuan, Kun Zhang, Alexander A Gimelbrant

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Mapping human pluripotent stem cell differentiation pathways using high throughput single-cell RNA-sequencing by Xiaoping Han, Haide Chen, Daosheng Huang, Huidong Chen, Lijiang Fei, Chen Cheng, He Huang, Guo-Cheng Yuan, Guoji Guo

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Serum-Based Culture Conditions Provoke Gene Expression Variability in Mouse Embryonic Stem Cells as Revealed by Single-Cell Analysis by Guoji Guo, Luca Pinello, Xiaoping Han, Shujing Lai, Li Shen, Ta-Wei Lin, Keyong Zou, Guo-Cheng Yuan, Stuart H. Orkin

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Distinct niche structures and intrinsic programs of fallopian tube and ovarian surface epithelial cells by Guyu Qin, Eun-Sil Park, Xueqing Chen, Sen Han, Dongxi Xiang, Fang Ren, Gang Liu, Huidong Chen, Guo-Cheng Yuan, Zhe Li

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Matrin3 mediates differentiation through stabilizing chromatin loop-domain interactions and YY1 mediated enhancer-promoter interactions by Tianxin Liu, Qian Zhu, Yan Kai, Trevor Bingham, Stacy Wang, Hye Ji Cha, Stuti Mehta, Thorsten M. Schlaeger, Guo-Cheng Yuan, Stuart H. Orkin

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The landscape of human tissue and cell type specific expression and co-regulation of senescence genes by Peng Xu, Minghui Wang, Won-min Song, Qian Wang, Guo-Cheng Yuan, Peter H. Sudmant, Habil Zare, Zhidong Tu, Miranda E. Orr, Bin Zhang

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Inner nuclear protein Matrin-3 coordinates cell differentiation by stabilizing chromatin architecture by Hye Ji Cha, Özgün Uyan, Yan Kai, Tianxin Liu, Qian Zhu, Zuzana Tothova, Giovanni A. Botten, Jian Xu, Guo-Cheng Yuan, Job Dekker, Stuart H. Orkin

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Mapping the evolving landscape of super-enhancers during cell differentiation by Yan Kai, Bin E. Li, Ming Zhu, Grace Y. Li, Fei Chen, Yingli Han, Hye Ji Cha, Stuart H. Orkin, Wenqing Cai, Jialiang Huang, Guo-Cheng Yuan

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Author Correction: Massively parallel in vivo CRISPR screening identifies RNF20/40 as epigenetic regulators of cardiomyocyte maturation by Nathan J. VanDusen, Julianna Y. Lee, Weiliang Gu, Catalina E. Butler, Isha Sethi, Yanjiang Zheng, Justin S. King, Pingzhu Zhou, Shengbao Suo, Yuxuan Guo, Qing Ma, Guo-Cheng Yuan, William T. Pu

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