Beijing Insitute of Genomics

1. Tongnian Gu#, Siqi Zhao#, Yishuang Pia, Weizhong Chena, Chuanyuan Chenb,c, Qian Liud, Min Lid, Dali Han *, and Quanjiang Ji* .Highly Efficient Base Editing in Staphylococcus aureus Using an Engineered CRISPR RNA-guided Cytidine Deaminase. Chemical Science (2018 Accepted, DIO: 10.1039/C8SC00637G. http://pubs.rsc.org/en/Content/ArticleLanding/2018/SC/C8SC00637G#! divAbstract)


2.Xin Tian#, Baofa Sun#, Chuanyuan Chen#, Chunchun Gao#, Ji Zhang#, Xingyu Lu#, Linchen Wang, Xiangnan Li, Yurong Xing, Ruijuan Liu, Xiao Han, Zheng Qi, Xiaojian Zhang, Chuan He, Dali Han*, Yun-Gui Yang*, Quancheng Kan*. Circulating tumor DNA 5-hydroxymethylcytosine as a novel diagnostic biomarker for esophageal cancer. Cell Research. (2018 Accepted, DIO: 10.1038/s41422-018-0014x,  https://www.ncbi.nlm.nih.gov/pubmed/?term=29467383)


3.Qing Dai* ∙ Sharon Moshitch-Moshkovitz* ∙ Dali Han* ∙ Nitzan Kol ∙ Ninette Amariglio ∙ Gideon Rechavi ∙ Dan Dominissini ∙ Chuan He. Nm-seq maps 2'-O-methylation sites in human mRNA with base precision. Nature Methods. 2017, doi:10.1038/nmeth.4294 


4.Dali Han* ∙ Xingyu Lu* ∙ Alan H. Shih* ∙ Ji Nie ∙ Qiancheng You ∙ Meng Michelle Xu ∙ Ari M. Melnick ∙ Ross L. Levine ∙ Chuan He. A highly sensitive and robust method for genome-wide 5hmC profiling of rare cell populations. Molecular Cell. 2016, 63, 711–719 

5.Bo Xia* ∙ Dali Han* ∙ Xingyu Lu* ∙ Zhaozhu Sun ∙ Ankun Zhou ∙ Qiangzong Yin ∙ Hu Zeng∙ Menghao Liu ∙ Xiang Jiang ∙ Wei Xie ∙ Chuan He ∙ Chengqi Yi. Bisulfite-free, Base-resolution analysis of 5-formylcytosine at the genome scale. Nature Methods 2015, 12, 1047-1050 

6.Xingyu Lu*∙ Dali Han* ∙ Zhao Boxuan Simen* ∙ ChunXiao Song ∙ LiSheng Zhang ∙ Louis C Doré ∙ Chuan He. Base-resolution maps of     5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics. Cell Research 2015, 25, 386-389

7.Fange Liu ∙ Wesley Clark ∙ Guanzheng Luo ∙ Xiaoyun Wang ∙ Ye Fu ∙ Jiangbo Wei ∙ Xiao Wang ∙ Ziyang Hao ∙ Qing Dai ∙ Guanqun Zheng ∙ Honghui Ma ∙ Dali Han ∙ Molly Evans ∙ Arne Klungland ∙ Tao Pan ∙ Chuan He. ALKBH1-mediated tRNA demethylation regulates translation. Cell 2016, 167, 816-828

8.Dan Dominissini ∙ Sigrid Nachtergaele ∙ Sharon Moshitch-Moshkovitz ∙ Eyal Peer ∙ Nitzan Kol, Moshe Shay Ben-Haim ∙ Qing Dai ∙ Ayelet Di Segni ∙ Mali Salmon-Divon ∙ Wesley C. Clark, Guanqun Zheng ∙ Tao Pan ∙ Oz Solomon ∙ Eran Eyal ∙ Vera Hershkovitz ∙ Dali Han ∙ Louis C. Doré ∙ Ninette Amariglio ∙ Gideon Rechavi ∙ Chuan He. The dynamic N-1-methyladenosine methylome in eukaryotic messenger RNA. Nature 2016, 530, 441-446

9.Jianzhao Liu ∙ Yuanxiang Zhu ∙ Guan-Zheng Luo ∙ Xinxia Wang ∙ Yanan Yue ∙ Xiaona Wang ∙ Xin Zong ∙ Kai Chen ∙ Hang Yin ∙ Ye Fu ∙ Dali Han ∙ Yizhen Wang ∙ Dahua Chen ∙ Chuan He. Abundant DNA 6mA methylation during early embryogenesis of zebrafish and pig. Nature communications 2016, 7, 13052

10.Xiao Wang ∙ Boxuan Simen Zhao ∙ Ian A Roundtree ∙ Zhike Lu ∙ Dali Han ∙ Honghui Ma ∙ Xiaocheng Weng ∙ Kai Chen ∙ Hailing Shi ∙ Chuan He. N-6-methyladenosine Modulates Messenger RNA Translation Efficiency. Cell 2015, 161, 1388-1399

11.Ye Fu ∙ Guanzheng Luo ∙ Kai Chen ∙ Xin Deng ∙ Miao Yu ∙ Dali Han ∙ Ziyang Hao ∙ Jianzhao Liu ∙ Xingyu Lu ∙ Louis C Doré ∙ Xiaocheng Weng ∙ Quanjiang Ji ∙ Laurens Mets ∙ Chuan He. N-6-Methyldeoxyadenosine Marks Active Transcription Start Sites in Chlamydomonas. Cell 2015, 161, 879-892

12.Jing Wang ∙ Cheng Luo ∙ Changliang Shan ∙ Qiancheng You ∙ Junyan Lu ∙ Shannon Elf ∙ Yu Zhou ∙ Yi Wen ∙ Jan L. Vinkenborg ∙ Jun Fan ∙ Heebum Kang ∙ Ruiting Lin ∙ Dali Han ∙ Yuxin Xie, Jason Karpus ∙ Shijie Chen ∙ Shisheng Ouyang ∙ Chihao Luan ∙ Naixia Zhang ∙ Hong Ding, Maarten Merkx ∙ Hong Liu ∙ Jing Chen ∙ Hualiang Jiang ∙ Chuan He. Inhibition of human copper trafficking by a small molecule significantly attenuates cancer cell proliferation. Nature Chemistry 2015, 7, 968-979

13.Qing Dai ∙ Paul J Sanstead ∙ Chunte Sam Peng ∙ Dali Han ∙ Chuan He ∙ Andrei Tokmakoff. Weakened N3 hydrogen bonding by 5-formylcytosine and 5-carboxylcytosine reduces their base-pairing stability. ACS chemical biology 2015, 11, 470-477

 14.Kai Chen ∙ Zhike Lu ∙ Xiao Wang ∙ Ye Fu ∙ GuanZheng Luo ∙ Nian Liu ∙ Dali Han ∙ Dan Dominissini ∙ Qing Dai ∙ Tao Pan ∙ Chuan He. High-Resolution N-6-Methyladenosine (m6A) Map Using Photo-Crosslinking-Assisted m6A Sequencing. Angewandte Chemie International Edition in English 2015, 54, 1587-1590

15.Ming Su* ∙ Dali Han* ∙ Jerome BoydKirkup ∙ Xiaoming Yu ∙ JingDong J Han. Evolution of Alu Elements toward Enhancers. Cell Reports 2014, 7, 376-385 

16.Jianzhao Liu* ∙ Yanan Yue* ∙ Dali Han ∙ Xiao Wang ∙ Ye Fu ∙ Liang Zhang ∙ Guifang Jia ∙ Miao Yu ∙ Zhike Lu ∙ Xin Deng ∙ Qing Dai ∙ Weizhong Chen ∙ Chuan He. A METTL3-METTL14 complex mediates mammalian nuclear RNA N-6-adenosine methylation. Nature Chemical Biology 2014, 10, 93-95

16.Xiao Wang ∙ Zhike Lu ∙ Adrian Gomez ∙ Gary C Hon ∙ Yanan Yue ∙ Dali Han ∙ Ye Fu ∙ Marc Parisien ∙ Qing Dai ∙ Guifang Jia ∙ Bing Ren ∙ Tao Pan ∙ Chuan He. N-6-methyladenosine-dependent regulation of messenger RNA stability. Nature 2014  505, 117-120

17.Yixing Han* ∙ Dali Han* ∙ Zheng Yan ∙ Jerome D BoydKirkup ∙ Christopher D Green ∙ Philipp Khaitovich ∙ JingDong J Han. Stress-associated H3K4 methylation accumulates during postnatal development and aging of rhesus macaque brain. Aging cell 2012, 11, 1055-1064  

 18.Chunyu Jin ∙ Jing Li ∙ Christopher D Green ∙ Xiaoming Yu ∙ Xia Tang ∙ Dali Han ∙ Bo Xian ∙ Dan Wang ∙ Xinxin Huang ∙ Xiongwen Cao ∙ Zheng Yan ∙ Lei Hou ∙ Jiancheng Liu ∙ Nicholas Shukeir ∙ Philipp Khaitovich ∙ Charlie D Chen ∙ Hong Zhang ∙ Thomas Jenuwein ∙ JingDong J Han. Histone Demethylase UTX1-Regulates C. elegans Life Span by Targeting the Insulin/IGF-1 Signaling Pathway. Cell metabolism 2011, 14, 161-172

19.Yi Liu* ∙ Dali Han* ∙ Yixing Han* ∙ Zheng Yan ∙ Bin Xie ∙ Jing Li ∙ Nan Qiao ∙ Haiyang Hu ∙ Philipp Khaitovich ∙ Yuan Gao ∙ JingDong J Han. Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Nucleic Acids Research 2011, 39, 1408-1418