Circulation | Suppression of the Prostaglandin I2–Type 1 Interferon Axis Induces Extramedullary Hematopoiesis to Promote Cardiac Repair After Myocardial Infarction.

Huizhen Lv, Chenchen Wang, Zening Liu, Meixi Quan, Kan Li, Fanglin Gou, Xuelian Shi, Qian Liu, Ying Yu, Ping Zhu, Hui Cheng, Tao Cheng, Ding Ai. 2025.

Blood | Heterogeneity of high-potency multilineage hematopoietic stem cells and identification of 'Super' transplantability.

Fang Dong , Sen Zhang , Caiying Zhu , Zining Yang , Lisha Wang , Yao Ma, Jiayi Lu, Xialin Li, Xiaofang Wang, Nini Wang, Shanshan Zhang, Miner Xie, Jinhong Wang, Xiaobing Zhang, Yawei Zheng, Shihui Ma, Hideo Ema, Hui Cheng, Sha Hao, Toshio Suda, Yu Lan, Bing Liu, Ping Zhu , Junren Chen , Tao Cheng . 2025.

Cell Stem Cell | An erythroid-biased FOShi hematopoietic multipotent progenitor subpopulation contributes to adaptation to chronic hypoxia.

Weili Liu , Xiaoru Zhang , Jinhua Liu , Lingling Pu , Lanlan Ai, Hongbao Xu, Guangrui Wang, Ding Wang, Xiaona Song, Yingnan Zhang, Ling Zhang, Jie Gao, Xiaoling Cheng, Xinxing Wang, Jingyuan Tong, Xiaowei Xie, Fang Dong, Yingchi Zhang, Ping Zhu , Zhaoli Chen , Peng Wu , Lihong Shi . 2025.

Blood | Single-cell epigenetic and clonal analysis decodes disease progression in pediatric acute myeloid leukemia.

Boyu Cui , Lanlan Ai , Minghui Lei , Yongjuan Duan , Chao Tang, Jingliao Zhang, Yan Gao, Xuan Li, Caiying Zhu, Yingchi Zhang, Xiaofan Zhu, Tomoya Isobe, Wenyu Yang , Berthold Göttgens , Ping Zhu . 2024.

Blood | The ATF4-RPS19BP1 axis modulates ribosome biogenesis to promote erythropoiesis.

Zhaofeng Zheng , Shangda Yang , Fanglin Gou , Chao Tang , Zhaoru Zhang , Quan Gu, Guohuan Sun, Penglei Jiang, Nini Wang, Xiangnan Zhao, Junnan Kang, Yifei Wang, Yicheng He, Meng Yang, Ting Lu, Shihong Lu, Pengxu Qian , Ping Zhu , Hui Cheng , Tao Cheng . 2024.

Nature Communications | Discovery and characterization of potent pan-variant SARS-CoV-2 neutralizing antibodies from individuals with Omicron breakthrough infection.

Yu Guo , Guangshun Zhang , Qi Yang , Xiaowei Xie , Yang Lu , Xuelian Cheng , Hui Wang , Jingxi Liang , Jielin Tang , Yuxin Gao , Hang Shang, Jun Dai, Yongxia Shi, Jiaxi Zhou, Jun Zhou, Hangtian Guo, Haitao Yang, Jianwei Qi, Lijun Liu, Shihui Ma, Biao Zhang, Qianyu Huo, Yi Xie, Junping Wu, Fang Dong, Song Zhang, Zhiyong Lou, Yan Gao, Zidan Song, Wenming Wang, Zixian Sun, Xiaoming Yang , Dongsheng Xiong , Fengjiang Liu , Xinwen Chen , Ping Zhu , Ximo Wang , Tao Cheng , Zihe Rao . 2023.

Immunity | Multi-omics blood atlas reveals unique features of immune and platelet responses to SARS-CoV-2 Omicron breakthrough infection.

Hong Wang , Cuicui Liu , Xiaowei Xie , Mingming Niu , Yingrui Wang , Xuelian Cheng , Biao Zhang , Dong Zhang, Mengyao Liu, Rui Sun, Yezi Ma, Shihui Ma, Huijun Wang, Guoqing Zhu, Yang Lu, Baiming Huang, Pei Su, Xiaoyuan Chen, Jingjing Zhao, Hongtao Wang, Long Shen, Lixia Fu, Qianqian Huang, Yang Yang, He Wang, Chunlong Wu, Weigang Ge, Chen Chen, Qianyu Huo, Qingping Wang, Ying Wang, Li Geng, Yan Xie, Yi Xie, Lijun Liu, Jianwei Qi, Huaiyong Chen, Junping Wu, Erlie Jiang, Wentao Jiang, Ximo Wang , Zhongyang Shen , Tiannan Guo , Jiaxi Zhou , Ping Zhu , Tao Cheng . 2023.

Dev Cell | Temporal molecular program of human hematopoietic stem and progenitor cells after birth.

Yawen Zhang , Xiaowei Xie , Yaojing Huang , Mengyao Liu, Qiaochuan Li, Jianming Luo, Yunyan He, Xiuxiu Yin, Shihui Ma, Wenbin Cao, Shulian Chen, Jun Peng, Jiaojiao Guo, Wen Zhou, Hongbo Luo, Fang Dong, Hui Cheng, Sha Hao, Linping Hu , Ping Zhu , Tao Cheng . 2022.

Development | DNA methylation safeguards the generation of hematopoietic stem and progenitor cells by repression of Notch signaling.

Yan Li , Chao Tang , Fan Liu, Caiying Zhu, Feng Liu, Ping Zhu , Lu Wang . 2022 vol. 149 (10).

Blood Science | Single-cell analysis of transcription factor regulatory networks reveals molecular basis for subtype-specific dysregulation in acute myeloid leukemia.

Ruixia Sun , Lina Sun , Xiaowei Xie, Peng Wu , Lu Wang , Ping Zhu . 2022 vol. 4 (2) p. 65.

Cell Discovery | Decoding the pathogenesis of Diamond-Blackfan Anemia using single-cell RNA-seq.

Bingrui Wang , Chenchen Wang , Yang Wan , Jie Gao , Yige Ma, Yingnan Zhang, Jingyuan Tong, Yingchi Zhang, Jinhua Liu, Lixian Chang, Changlu Xu, Biao Shen, Yumei Chen, Erlie Jiang, Ryo Kurita, Yukio Nakamura, Kim-Chew Lim, James Douglas Engel, Jiaxi Zhou, Tao Cheng , Xiaofan Zhu , Ping Zhu , Lihong Shi . 2022 vol. 8 (1) pp. 1-19.

Blood Science | SIEVE: identifying robust single cell variable genes for single-cell RNA sequencing data.

Yinan Zhang , Xiaowei Xie, Peng Wu , Ping Zhu . March, 2021.

Blood | Single-cell transcriptomics dissects hematopoietic cell destruction and T cell engagement in aplastic anemia.

Caiying Zhu , Yu Lian , Chenchen Wang , Peng Wu , Xuan Li , Yan Gao, Sibin Fan, Lanlan Ai, Liwei Fang, Hong Pan, Tao Cheng , Jun Shi , Ping Zhu . March, 2021.

Cell Stem Cell | Hematopoietic Stem Cell Heterogeneity Is Linked to the Initiation and Therapeutic Response of Myeloproliferative Neoplasms.

Jingyuan Tong, Ting Sun, Shihui Ma, Yanhong Zhao, Mankai Ju, Yuchen Gao, Ping Zhu, Puwen Tan, Rongfeng Fu, Anqi Zhang, Ding Wang, Di Wang, Zhijian Xiao, Jiaxi Zhou, Renchi Yang, Stephen J Loughran, Juan Li, Anthony R Green, Emery H Bresnick, Dong Wang, Tao Cheng, Lei Zhang, and Lihong Shi. vol. 28 (3) pp. 502-513.e6, 2021.

Sci China Life Sci | Single-cell transcriptomes of peripheral blood cells indicate and elucidate severity of COVID-19.

Xiaowei Xie , Xuelian Cheng , GaoXiang Wang , Biao Zhang , Mengyao Liu, Liting Chen, Hui Cheng, Sha Hao, Jianfeng Zhou , Ping Zhu , Tao Cheng . February, 2021.

Cell | COVID-19 immune features revealed by a large-scale single cell transcriptome atlas.

Xianwen Ren, Wen Wen, Xiaoying Fan, Wenhong Hou, Bin Su, Pengfei Cai, Jiesheng Li, Yang Liu, Fei Tang, Fan Zhang, Yu Yang, Jiangping He, Wenji Ma, Jingjing He, Pingping Wang, ..., Lai Wei, Xiu-Wu Bian, Xindong Liu, Tao Cheng, Xiangpan Li, Pingsen Zhao, Fu-Sheng Wang, Hongyang Wang, Bing Su, Zheng Zhang, Kun Qu, Xiaoqun Wang, Jiekai Chen, Ronghua Jin, Zemin Zhang. February, 2021.

National Science Review | The Single-cell Transcriptome Landscape of Human Blood Cells.

Xiaowei Xie , Mengyao Liu , Yawen Zhang , Bingrui Wang, Caiying Zhu, Chenchen Wang, Qing Li, Yingying Huo, Jiaojiao Guo, Changlu Xu, Linping Hu, Aiming Pang, Shihui Ma, Lina Wang, Wenbin Cao, Shulian Chen, Qiuling Li, Sudong Zhang, Xueying Zhao, Wen Zhou, Hongbo Luo, Guoguang Zheng, Erlie Jiang, Sizhou Feng, Lixiang Chen, Xiuli An, Lihong Shi, Hui Cheng, Sha Hao , Ping Zhu , Tao Cheng . August, 2020.

Nature Cell Biology | Differentiation of transplanted haematopoietic stem cells tracked by single cell transcriptomic analysis.

Fang Dong , Sha Hao , Sen Zhang , Caiying Zhu , Hui Cheng , Zining Yang, Fiona K. Hamey, Xiaofang Wang, Ai Gao, Fengjiao Wang, Yun Gao, Ji Dong, Chenchen Wang, Jinyong Wang, Yu Lan, Bing Liu, Hideo Ema, Fuchou Tang, Berthold Gottgens , Ping Zhu , Tao Cheng . March, 2020.

Bone Marrow Transplantation | PDGFB-expressing mesenchymal stem cells improve human hematopoietic stem cell engraftment in immunodeficient mice.

Xiuxiu Yin, Linping Hu, Yawen Zhang, Caiying Zhu, Hui Cheng, Xiaowei Xie, Ming Shi, Ping Zhu, Xueying Zhao, Wanqiu Chen, Lu Zhang, Cameron Arakaki, Sha Hao, Mei Wang, Wenbin Cao, Shihui Ma, Xiao-Bing Zhang, Tao Cheng. 55, 1029–1040, 2020.

Bioinformatics | Using Local Alignment to Enhance Single Cell Bisulfite Sequencing Data Efficiency.

Peng Wu , Yan Gao, Weilong Guo, Ping Zhu . 35 (18): 3273-3278, 2019.

Science | Single-cell multiomics sequencing and analyses of human colorectal cancer.

Shuhui Bian, Yu Hou, Xin Zhou, Xianlong Li, Jun Yong, Yicheng Wang, Wendong Wang, Jia Yan, Boqiang Hu, Hongshan Guo, Jilian Wang, Shuai Gao, Yunuo Mao, Ji Dong, Ping Zhu, Dianrong Xiu, Liying Yan, Lu Wen, Jie Qiao, Fuchou Tang, Wei Fu. 362(6418):1060-1063, 2018.

Nature Genetics | Single-cell DNA methylome sequencing of human preimplantation embryos.

Ping Zhu , Hongshan Guo , Yixin Ren , Yu Hou , Ji Dong, Rong Li, Ying Lian, Xiaoying Fan, Boqiang Hu, Yun Gao, Xiaoye Wang, Yuan Wei, Ping Liu, Jie Yan, Xiulian Ren, Peng Yuan, Yifeng Yuan, Zhiqiang Yan, Lu Wen, Liying Yan , Jie Qiao , Fuchou Tang . 50(1):12-19, 2018.

Bioinformatics | CGmapTools improves the precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.

Weilong Guo , Ping Zhu , Matteo Pellegrini, Michael Q Zhang, Xiangfeng Wang, Zhongfu Ni. 34(3):381-387, 2018.

Nature Communications | 3D genome of multiple myeloma reveals spatial genome disorganization associated with copy number variations.

Pengze Wu, Tingting Li, Ruifeng Li, Lumeng Jia, Ping Zhu, Yifang Liu, Qing Chen, Daiwei Tang, Yuezhou Yu, Cheng Li. 8(1):1937, 2017.

Cell Res | Single-cell multi-omics sequencing of mouse early embryos and embryonic stem cells.

Fan Guo, Lin Li, Jingyun Li, Xinglong Wu, Boqiang Hu, Ping Zhu, Lu Wen, Fuchou Tang. 27(8):967-988, 2017.

Nature | Tracing haematopoietic stem cell formation at single-cell resolution.

Fan Zhou , Xianlong Li , Weili Wang , Ping Zhu , Jie Zhou , Wenyan He , Meng Ding, Fuyin Xiong, Xiaona Zheng, Zhuan Li, Yanli Ni, Xiaohuan Mu, Lu Wen, Tao Cheng, Yu Lan, Weiping Yuan , Fuchou Tang , Bing Liu . 533(7604):487-492, 2016.

Cell Res | Single-cell triple omics sequencing reveals genetic, epigenetic, and transcriptomic heterogeneity in hepatocellular carcinomas.

Yu Hou, Huahu Guo, Chen Cao, Xianlong Li, Boqiang Hu, Ping Zhu, Xinglong Wu, Lu Wen, Fuchou Tang, Yanyi Huang, and Jirun Peng. 26(3):304-319, 2016.

PLoS ONE | Characterization of Genomic Variants Associated with Scout and Recruit Behavioral Castes in Honey Bees Using Whole-Genome Sequencing.

Bruce R Southey, Ping Zhu, Morgan K Carr-Markell, Zhengzheng S Liang, Amro Zayed, Ruiqiang Li, Gene E Robinson, Sandra L Rodriguez-Zas. 11(1):e0146430, 2016.

Nature Chemical Biology | Chemical pulldown reveals dynamic pseudouridylation of the mammalian transcriptome.

Xiaoyu Li , Ping Zhu , Shiqing Ma , Jinghui Song, Jinyi Bai, Fangfang Sun, Chengqi Yi . 11(8):592-597, 2015.

Cell | The Transcriptome and DNA Methylome Landscapes of Human Primordial Germ Cells.

Fan Guo, Liying Yan, Hongshan Guo, Lin Li, Boqiang Hu, Yangyu Zhao, Jun Yong, Yuqiong Hu, Xiaoye Wang, Yuan Wei, Wei Wang, Rong Li, Jie Yan, Xu Zhi, Yan Zhang, Hongyan Jin, Wenxin Zhang, Yu Hou, Ping Zhu, Jingyun Li, Ling Zhang, Sirui Liu, Yixin Ren, Xiaohui Zhu, Lu Wen, Yi Qin Gao, Fuchou Tang, Jie Qiao. 161(6):1437-1452, 2015.

Nature Protocols | Profiling DNA methylome landscapes of mammalian cells with single-cell reduced-representation bisulfite sequencing.

Hongshan Guo , Ping Zhu , Fan Guo, Xianlong Li, Xinglong Wu, Xiaoying Fan, Lu Wen , Fuchou Tang . 10(5):645-659, 2015.

Science | Suppression of endogenous gene silencing by bidirectional cytoplasmic RNA decay in Arabidopsis.

Xinyan Zhang, Ying Zhu, Xiaodan Liu, Xinyu Hong, Yang Xu, Ping Zhu, Yang Shen, Huihui Wu, Yusi Ji, Xing Wen, Chen Zhang, Qiong Zhao, Yichuan Wang, Jian Lu, Hongwei Guo. 348(6230):120-123, 2015.

Cell Res | Correction of a genetic disease by CRISPR-Cas9-mediated gene editing in mouse spermatogonial stem cells.

Yuxuan Wu, Hai Zhou, Xiaoying Fan, Ying Zhang, Man Zhang, Yinghua Wang, Zhenfei Xie, Meizhu Bai, Qi Yin, Dan Liang, Wei Tang, Jiaoyang Liao, Chikai Zhou, Wujuan Liu, Ping Zhu, Hongshan Guo, Hong Pan, Chunlian Wu, Huijuan Shi, Ligang Wu, Fuchou Tang, Jinsong Li. 25:67-79, 2015.

Cell Stem Cell | Active and Passive Demethylation of Male and Female Pronuclear DNA in the Mammalian Zygote.

Fan Guo, Xianlong Li, Dan Liang, Tong Li, Ping Zhu, Hongshan Guo, Xinglong Wu, Lu Wen, Tian-Peng Gu, Boqiang Hu, Colum P Walsh, Jinsong Li, Fuchou Tang, Guo-Liang Xu. 15:447-458, 2014.

Nature | The DNA methylation landscape of human early embryos.

Hongshan Guo , Ping Zhu , Liying Yan , Rong Li , Boqiang Hu, Ying Lian, Jie Yan, Xiulian Ren, Shengli Lin, Junsheng Li, Xiaohu Jin, Xiaodan Shi, Ping Liu, Xiaoye Wang, Wei Wang, Yuan Wei, Xianlong Li, Fan Guo, Xinglong Wu, Xiaoying Fan, Jun Yong, Lu Wen, Sunney X Xie, Fuchou Tang , Jie Qiao . 511(7511):606-610, 2014.

Genome Biology | Whole-genome analysis of 5-hydroxymethylcytosine and 5-methylcytosine at base resolution in the human brain.

Lu Wen, Xianlong Li, Liying Yan, Yuexi Tan, Rong Li, Yangyu Zhao, Yan Wang, Jingcheng Xie, Yan Zhang, Chunxiao Song, Miao Yu, Xiaomeng Liu, Ping Zhu, Xiaoyu Li, Yu Hou, Hongshan Guo, Xinglong Wu, Chuan He, Ruiqiang Li, Fuchou Tang, Jie Qiao. 15:R49, 2014.

Genome Res | Single-cell methylome landscapes of mouse embryonic stem cells and early embryos analyzed using reduced representation bisulfite sequencing.

Hongshan Guo , Ping Zhu , Xinglong Wu, Xianlong Li, Lu Wen, Fuchou Tang , Jie Qiao . 23(12):2126-2135, 2013.

Nucl Acids Res | MimoDB 2.0: a mimotope database and beyond.

Jian Huang, Beibei Ru, Ping Zhu, Fulei Nie, Jun Yang, Xuyang Wang, Ping Dai, Hao Lin, Feng-Biao Guo, and Nini Rao. 40(D1):D271-D277, 2012.

Science | Probing Meiotic Recombination and Aneuploidy of Single Sperm Cells by Whole-Genome Sequencing.

Sijia Lu, Chenghang Zong, Wei Fan, Mingyu Yang, Jinsen Li, Alec R Chapman, Ping Zhu, Xuesong Hu, Liya Xu, Liying Yan, Fan Bai, Jie Qiao, Fuchou Tang, Ruiqiang Li, and X Sunney Xie. 338(6114):1627-1630, 2012.