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Yingying Zeng#, Yaqiang Cao#, Rivka Sukenik Halevy#, Picard Nguyen, Denghui Liu, Xiaoli Zhang, Nadav Ahituv* and Jing-Dong J. Han*. Characterization of functional transposable element enhancers in acute myeloid leukemia. Sci China Life Sci, 2020 May;63(5):675-687.
Yaqiang Cao#, Zhaoxiong Chen#, Xingwei Chen#, Daosheng Ai#, Guoyu Chen, Joseph McDermott, Yi Huang, Xiaoxiao Guo, Jing-Dong J Han*. Accurate loop calling for 3D genomic data with cLoops. Bioinformatics, 2020 Feb 1;36(3):666-675.
Xiaoyang Dou#, Jerome Boyd-Kirkup#, Joseph McDermott#, Xiaoli Zhang#, Fang Li, Bowen Rong, Rui Zhang, Bisi Miao, Peilin Chen, Hao Cheng, Jianhuang Xue, David Bennett, Jiemin Wong, Fei Lan and Jing-Dong J. Han*. The strand-biased mitochondrial DNA methylome and its regulation by DNMT3A. Genome Res, 2019 Oct;29(10):1622-1634.
Guangdun Peng#*, Shengbao Suo#, Guizhong Cui#, Fang Yu#, Ran Wang, Jun Chen, Shirui Chen, Zhiwen Liu, Guoyu Chen, Yun Qian, Patrick P. L. Tam, Jing-Dong J. Han* and Naihe Jing*. Molecular architecture of lineage allocation and tissue organization in early mouse embryo. Nature, 2019 Aug;572(7770):528-532.
Yuanyuan Xue#, Denghui Liu#, Guizhong Cui, Yanyan Ding, Daosheng Ai, Suwei Gao, Yifan Zhang, Shengbao Suo, Xiaohan Wang, Peng Lv, Chunyu Zhou, Yizhou Li, Xingwei Chen, Guangdun Peng, Naihe Jing, Jing-Dong J. Han* and Feng Liu*. A 3D Atlas of Hematopoietic Stem and Progenitor Cell Expansion by Multi-dimensional RNA-Seq Analysis. Cell Rep, 2019 Apr 30;27(5):1567-1578.e5.
Xingwei Chen#, Chi Xu#, Shengjun Hong#, Xian Xia, Yaqiang Cao, Joseph McDermott, Yongling Mu and Jing-Dong J. Han*. Immune Cell Types and Secreted Factors Contributing to Inflammation-to-Cancer Transition and Immune Therapy Response. Cell Rep, 2019 Feb 12;26(7):1965-1977.e4.
Yaqiang Cao#, Guoyu Chen#, Gang Wu#, Xiaoli Zhang#, Joseph McDermott, Xingwei Chen, Chi Xu, Quanlong Jiang, Zhaoxiong Chen, Yingying Zeng, Daosheng Ai, Yi Huang and Jing-Dong J. Han*. Widespread roles of enhancer-like transposable elements in cell identity and long-range genomic interactions. Genome Res, 2019 Jan;29(1):40-52.
Chi Xu#, Daosheng Ai#, Shengbao suo, Xingwei Chen, Yizhen Yan, Yaqiang Cao, Na Sun, Weizhong Chen, Joseph McDermott, Shiqiang Zhang, Yingying Zeng, Jing-Dong J. Han*. Accurate Drug Repositioning through Non-tissue-Specific Core Signatures from Cancer Transcriptomes. Cell Rep, 2018 Oct 9;25(2):523-535.e5.
Clayton E. Friedman, Quan Nguyen, Samuel W. Lukowski, Abbigail Helfer, Han Sheng Chiu, Jason Miklas, Shiri Levy, Shengbao Suo, Jing-Dong Jackie Han, Pierre Osteil, Guangdun Peng, Naihe Jing, Greg J. Baillie, Anne Senabouth, Angelika N. Christ, Timothy J. Bruxner, Charles E. Murry, Emily S. Wong, Jun Ding, Yuliang Wang, James Hudson, Hannele Ruohola-Baker, Ziv Bar-Joseph, Patrick P.L. Tam, Joseph E. Powell* and Nathan J. Palpant*. Single-Cell Transcriptomic Analysis of Cardiac Differentiation from Human PSCs Reveals HOPX-Dependent Cardiomyocyte Maturation. Cell Stem Cell, 2018 Oct 4;23(4):586-598.e8.
Guangdun Peng, Jing-Dong J. Han*. Regulatory network characterization in development: challenges and opp ortunities. F1000 Research, 2018 Sep 17;7. pii: F1000 Faculty Rev-1477.
Xian Xia, Jing-Dong J. Han*. Systems Biology in Aging Research. Adv Exp Med Biol, 2018;1086:1-15.
Weizhong Chen#, Yi Liu#, Shanshan Zhu, Guoyu Chen, Jing-Dong J. Han*. Inter-nucleosomal communication between histone modifications for nucleosome phasing. PLoS Comput Biol, 2018 Sep 6;14(9):e1006416.
Denghui Liu#, Xinyi Wang#, Dajian He#, Chunli Sun#, Xiechao He, Lanzhen Yan, Yizhou Li, Jing-Dong J. Han*, Ping Zheng*. Single cell RNA-sequencing reveals the existence of na？ve and primed pluripotency in pre-implantation rhesus monkey embryos. Genome Res, 2018 Oct;28(10):1481-1493.
Hao Cheng#, Hongwen Xuan#, Christopher D. Green, Yixing Han, Na Sun, Hongjie Shen, Joseph McDermott, David Bennett, Fei Lan and Jing-Dong J. Han*. Repression of human and mouse brain inflammaging transcriptome by broad gene-body histone hyperacetylation. Proc Natl Acad Sci U S A, 2018 Jul 17;115(29):7611-7616.
Xian Xia#, Quanlong Jiang#, Joseph McDermott, Jing-Dong J. Han*. Aging and Alzheimer's disease: Comparison and Associations from Molecular to Systems Levels. Aging Cell, 2018 Oct;17(5):e12802.
Na Sun#, Xiaoming Yu#, Fang Li#, Denghui Liu, Shengbao Suo, Weiyang Chen, Shirui Chen, Lu Song, Christopher D. Green, Joseph McDermott, Qin Shen, Naihe Jing and Jing-Dong J. Han. Inference of differentiation time for single cell transcriptomes using cell population reference data. Nature Commun, 2017 Nov 30;8(1):1856.
Xinyi Wang#, Denghui Liu#, Dajian He, Shengbao Suo, Xian Xia, Xiechao He, Jing-Dong J. Han*, Ping Zheng*. Transcriptome analyses of rhesus monkey preimplantation embryos reveal a reduced capacity for DNA double-strand break repair in primate oocytes and early embryos. Genome Res, 2017 Apr;27(4):567-579.
Guangdun Peng#, Shengbao Suo#, Jun Chen#, Weiyang Chen, Chang Liu, Fang Yu, Ran Wang, Shirui Chen, Na Sun, Guizhong Cui, Lu Song, Patrick P.L. Tam, Jing-Dong J. Han*, Naihe Jing*. Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo. Dev Cell, 2016 Mar 21;36(6):681-697.
Lei Hou, Dan Wang, Di Chen, Yi Liu, Yue Zhang, Hao Cheng, Chi Xu, Na Sun, Joseph McDermott, William B. Mair and Jing-Dong J. Han*. A Systems Approach to Reverse Engineer Lifespan Extension by Dietary Restriction. Cell Metab, 2016 Mar 8;23(3):529-540.
Yi Huang, Xiaoming Yu, Na Sun, Nan Qiao, Yaqiang Cao, Jerome D. Boyd-Kirkup, Qin Shen, Jing-Dong J Han. Single-cell level spatial gene expression in the embryonic neural differentiation niche. Genome Res, 2015 Apr;25(4):570-581.
Weiyang Chen, Wei Qian, Gang Wu, Weizhong Chen, Bo Xian, Xingwei Chen, Yaqiang Cao, Christopher D Green, Fanghong Zhao, Kun Tang and Jing-Dong J. Han*. Three-dimensional human facial morphologies as robust aging markers. Cell Res, 2015;25:574-587.
(highlighted by Nature Press Release, Science News, New Scientists, The Guardian, Daily Mail and NewsWeek, etc).
Weizhong Chen, Yi Liu, Shanshan Zhu, Christopher D. Green, Gang Wei, Jing-Dong J. Han*, Improved Nucleosome Positioning Algorithm iNPS for Accurate Nucleosome Positioning from Sequencing Data. Nat Commun, 2014 Sep 18;5:4909.
Ming Su, Dali Han, Jerome D Boyd-Kirkup, Xiaoming Yu and Jing-Dong J Han*. Evolution of Alu towards enhancers. Cell Rep, 2014,7(2):376-385.
Jin’e Li, Yi Liu, Min Liu and Jing-Dong J Han*. Functional dissection of regulatory models using gene expression data of deletion mutants. PLoS Genetics, 2013;9(9):e1003757.
Wei Zhang, Yi Liu, Na Sun, Dan Wang, Jerome Boyd-Kirkup, Xiaoyang Dou, Jing-Dong J Han*. Integrating Genomic, Epigenomic and Transcriptomic Features Reveals Modular Signatures Underlying Poor Prognosis in Ovarian Cancer. Cell Rep, 2013;4(3):542-553.
Yi Liu, Nan Qiao, Shanshan Zhu, Ming Su, Na Sun, Jerome Boyd-Kirkup, Jing-Dong J. Han*. A novel Bayesian network inference algorithm for integrative analysis of heterogeneous deep sequencing data. Cell Res, 2013 Mar;23(3):440-443.
Zhou B, Yang L, Li SF, Huang JL, Chen HY, Hou L, Wang JB, Green CD, Yan Z, Huang X, Zhu L, Xiao HS, Liu Y*, Han J-D.J*. Midlife Gene Expressions Identify Modulators of Aging through Dietary Interventions. Proc Natl Acad Sci U S A, 2012 May 8;109(19):E1201-E1209.
Jin C, Li J, Green CD, Yu X, Tang X, Han D, Xian Bo, Wang D, Huang X, Cao X, Yan ., Hou L, Liu J, Shukeir N, Khaitovich P, Chen CD, Zhang H, Jenuwein T and Han J-D.J*. Histone demethylase UTX-1 regulates C. elegans life span by targeting the insulin/IGF-1 signaling pathway. Cell Metab, 2011 Aug 3;14(2):161-172.
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