Research interests:

Our research focuses on the structure and dynamic inference of molecular networks，using a combination of large-scale experiments and computational analysis to probe the networks and to integrate functional interaction data in order to explore the design principles of the networks and to find how the complex phenotypes, such as aging, cancer and stem cell development are regulated through molecular networks. 
Academic experiences:

2017-present: Center for Quantatitive Biology & Peking-Tsinghua Center for Life Sciences, Academy for Advanced Interdisciplinary Studies, Peking University, China,Investigator and Professor

2010 – present: CAS-MPG Partner Institute for Computational Biology,Director, Investigator and Professor

2005 – 2010 :Institute of Genetics and Developmental Biology, Chinese Academy of Sciences,Investigator and Professor

2002 –2005 :Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, Boston, MA,Research Fellow of Bioinformatics

2001 –2002:CQOS, Inc., Irvine, CA,Software Engineer

2000 –2001: Rare Medium, Inc., New York, NY,Software Engineer

1999 –2000:NorthStar Technologies, Inc., New York, NY,Software Engineer

1997 –1998:The Rockefeller University and Howard Hughes Medical Institute, New York, NY,Post-Doctoral Research Associate

Selected publications:

1.       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 & Jing-Dong J. Han. Inference of differentiation time for single cell transcriptomes using cell population reference data. Nature Communications. 2017 Nov 30;8(1):1856        

2.       Xinyi Wang^, Denghui Liu^, Dajian He, Shengbao Suo, Xian Xia, Xiechao He, Jing-Dong J. Han*, and 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 Research. 2017 Apr;27(4):567-579. doi: 10.1101/gr.198044.115. Epub 2017 Feb 21.

3.       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. Developmental Cell, 2016 Mar 21;36(6):681-97. doi: 10.1016/j.devcel.2016.02.020.

4.       Lei Hou, Dan Wang, Di Chen, Yi Liu, Yue Zhang, Hao Cheng, Chi Xu, Na Sun, Joseph McDermott, and William B. Mair and Jing-Dong J. Han*. A Systems Approach to Reverse Engineer Lifespan Extension by Dietary Restriction. Cell Metabolism, 2016, 8;23(3):529-40.

5.       Yi Huang, Xiaoming Yu, Na Sun, Nan Qiao, Yaqiang Cao, Jerome D. Boyd-Kirkup, Qin Shen, and Jing-Dong J Han. Single-cell level spatial gene expression in the embryonic neural differentiation niche. Genome Research. 2015 Apr;25(4):570-81.

6.       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 Research, 2015, 25:574-587 (highlighted by Nature Press Release, Science News, New Scientists, The Guardian, Daily Mail, and NewsWeek, etc).

7.       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, Nature Communications 2014, doi:10.1038/ncomms5909.

8.       Ming Su, Dali Han, Jerome D Boyd-Kirkup, Xiaoming Yu and Jing-Dong J Han*，Evolution of Alu towards enhancers, Cell Reports, 2014, 7(2): 376-385

9.       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.

10.    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 Reports, 2013, 4(3):542–553

11.    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 Research. 2013 Mar;23(3):440-3.

12.    Zhou, B., Yang, L., Li, S.F., Huang, J.L., Chen, H.Y., Hou, L., Wang, J.B., Green, C.D., Yan, Z., Huang, X., Zhu L., Xiao H.S., Liu Y. *, and Han J.D.J. * (2012). Midlife Gene Expressions Identify Modulators of Aging through Dietary Interventions, Proc Natl Acad Sci U S A. 8;109(19):E1201-9.

13.   Jin, C., Li, J., Green, C.D., Yu, X. , Tang, X, Han, D., Xian, Bo., Wang, D, Huang, X., Cao, X., Yan. Z., Hou, L., Liu, J., Shukeir, N., Khaitovich, P., Chen, C.D., Zhang, H., Jenuwein, T. and  Han, J.-D.J *, Histone Demethylase UTX-1 Regulates C. elegans Lifespan by Targeting Insulin/IGF-1 Signaling Pathway, Cell Metabolism, 2011, 14: 16