Yi Liu
Former Research Assistant
Email: yiliu@genetics.ac.cn
Experience
2009.7 - , Research Assistant, Dr. Jing-Dong Jackie Han's Laboratory.
2009, Ph.D., School of Electronics Engineering and Computer Science, Peking University.
2004, B.S., School of Physics, Peking University.
Research Focus
Currently: Reasoning and uncertainty modeling in System Biology, especially with epigenetics. Previously: Various problems in machine learning, information retrieval and 3D geometric processing.
Publications
Yi Liu*, Xu-Lei Wang, Hua-Yan Wang, Hongbin Zha, Hong Qin. Learning Robust Similarity Measures for 3D Partial Shape Retrieval. International Journal of Computer Vision (IJCV), 2010. (Featured News)
Xu-Lei Wang, Yi Liu*, Hongbin Zha*. Intrinsic Spin Images: A Subspace Decomposition Approach to Understanding 3D Deformable Shapes. Proceedings of Fifth International Symposium 3D Data Processing, Visualization and Transmission (3DPVT'10), 2010.
Yi Liu, Xu-Lei Wang, Hongbin Zha. 3D Partial Shape Retrieval based on Local Bag-of-Words Models. Acta Scientiarum Naturalium Universitatis Pekinensis, 2009.
Yi Liu, Xu-Lei Wang, Hongbin Zha. Dimension Amnesic Pyramid Match Kernel. The Twenty-Third AAAI Conference on Artificial Intelligence (AAAI), 2008. (Featured News)
Yadong Mu, Shuicheng Yan, Yi Liu, Tom Huang, Bingfeng Zhou. Discriminative Local Binary Patterns for Human Detection in Personal Album. IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), 2008.
Ying Shi, Hong Liu, Yi Liu, Hongbin Zha. Adaptive feature-spatial representation for Mean-shift tracker. ICIP, 2008
Yi Liu, Hongbin Zha, Hong Qin. Shape Topics: A Compact Representation and New Algorithms for 3D Partial Shape Retrieval. IEEE Computer Society Conference on Computer Vision and Pattern Recognition (CVPR), 2006.
Yi Liu, Hongbin Zha, Hong Qin. The Generalized Shape Distributions for Shape Matching and Analysis. IEEE International Conference on Shape Modeling and Applications (SMI), 2006.
Weibin Liu, Yusuke Uehara, Yi Liu, Jiantao Pu, Hao Yu, Daiki Masumoto, Hongbin Zha. 3DMIRACLES: 3D models retrieval and visualization engine. Conference on Visualization and Data Analysis 2005 (IS&T/SPIE Symposium on Electronic Imaging), 2005.
Weibin Liu, Yusuke Uehara, Hao Yu, Daiki Masumoto, Yi Liu, Jiantao Pu, Hongbin Zha. Interactive Visual Retrieval System for Large Scale 3D Models Database. Proceedings of the 11th International Multimedia Modelling Conference (MMM2005), 2005.
Yi Liu, Jiantao Pu, Guyu Xin, Hongbin Zha, Weibin Liu, Yusuke Uehara. A robust method for shape-based 3D model retrieval. 12th Pacific Conference on Computer Graphics and Applications (PG 2004), 2004.
Yi Liu, Jiantao Pu, Hongbin Zha, Weibin Liu, Yusuke Uehara. Thickness histogram and statistical harmonic representation for 3D model retrieval. Proceedings of 2nd International Symposium on 3D Data Processing, Visualization and Transmission (3DPVT 2004), 2004.
Pu Jiantao, Yi Liu, Xin Guyu, Zha hongbin, Weibin Liu, Yusuke Uehara. 3D model retrieval based on 2D slice similarity measurements. Proceedings of 2nd International Symposium on 3D Data Processing, Visualization and Transmission (3DPVT 2004), 2004.
- Zhengqing Yu^, Yong Zhou^, Kehang Mao^, Bo Pang^, Kai Wang, Tang Jin, Haonan Zheng, Haotian Zhai, Yiyang Wang, Xiaohan Xu, Hongxiao Liu, Yi Wang, Jing-Dong J. Han*. Thermal facial image analyses reveal quantitative hallmarks of aging and metabolic diseases. Cell Metabolism, July 2024.
- Yiyang Wang^, Yunyan Ye^, Shengyi Shi^, Kehang Mao, Haonan Zheng, Xuguang Chen, Hanting Yan, Yiming Lu, Yong Zhou, Weimin Ye, Jing Ye* and Jing-Dong J. Han*. Prediagnosis recognition of acute ischemic stroke by artificial intelligence from facial images. Aging Cell, Apr 2024.
- Wanyu Tao, Zhengqing Yu, Jing-Dong J. Han*. Single-cell senescence identification reveals senescence heterogeneity, trajectory, and modulators. Cell Metabolism, Apr 2024.
- Xinyu Yang, Runhan Li, Xindi Yang, Yong Zhou, Yi Liu, Jing-Dong J. Han*. Coordinate-wise monotonic transformations enable privacy-preserving age estimation with 3D face point cloud. Science China, Apr 2024.
- Dawei Meng,Shiqiang Zhang, Yuanfang Huang, Kehang Mao, Jing-Dong J. Han*. Application of AI in biological age prediction. Current Opinion in Structural Biology, Feb 2024.
- Xueqing Wang, Quanlong Jiang, Hongdao Zhang, Zhidong He, Yuanyuan Song, Yifan Chen, Na Tang, Yifei Zhou, Yiping Li, Adam Antebi, Ligang Wu, Jing-Dong J. Han*, Yidong Shen*. Nature Communications, Feb 2024.
- Jing-Dong J. Han*. The ticking of aging clocks. Trends in Endocrinology & Metabolism, Oct 2023.
- Yiyang Wang, Kehang Mao, Haotian Zhai and Jing-Dong J. Han*. Clinical application of facial aging clocks. Lancet Regional Health-Western Pacific, Jul 2023.
- Hongming Zhu^, Jiawei Chen^, Kangping Liu^, Lei Gao, Haiyan Wu, Liangliang Ma,Jieru Zhou, Zhongmin Liu*, Jing-Dong J. Han*. Human PBMC scRNA-seq–based aging clocks reveal ribosome to inflammation balance as a single-cell aging hallmark and super longevity. Science Advances, Jun 2023.
- Yuxuan Zhao^, Shiqiang Zhang^, Jian Xu, Yangyang Yu, Guangdun Peng,
Carlo Vittorio Cannistraci* and Jing-Dong J. Han*. Spatial Reconstruction of Oligo and Single Cells by De Novo Coalescent Embedding of Transcriptomic Networks. Advanced Science, Jun 2023.
- Jing-Dong J. Han*. LncRNAs: the missing link to senescence nuclear architecture. Trends in Biochemical Sciences, Apr 2023.
- Jiawei Chen^, Hao Xu^, Wanyu Tao, Zhaoxiong Chen, Yuxuan Zhao and Jing-Dong J. Han*. Transformer for one stop interpretable cell type annotation. Nature Communications, Jan 2023.
- Xiaoli Zhang^, Quanlong Jiang^, Jiyang Li^, Shiqiang Zhang^, Yaqiang Cao, Xian Xia, Donghong Cai, Jiaqi Tan, Jiekai Chen and Jing-Dong J. Han*. KCNQ1OT1 promotes genome-wide transposon repression by guiding RNA–DNA triplexes and HP1 binding. Nature Cell Biology, Oct 2022.
- Yusheng Cai^, Wei Song^, Jiaming Li^, Ying Jing^, Chuqian Liang^, Liyuan Zhang^, Xia Zhang^, Wenhui Zhang^, Beibei Liu^, Yongpan An^, Jingyi Li^, Baixue Tang^, Siyu Pei^, Xueying Wu^, Yuxuan Liu^, Cheng-Le Zhuang^, Yilin Ying^, Xuefeng Dou^, Yu Chen^, Fu-Hui Xiao^, Dingfeng Li^, Ruici Yang^, Ya Zhao^, Yang Wang^, Lihui Wang^, Yujing Li^, Shuai Ma*, Si Wang*, Xiaoyuan Song*, Jie Ren*, Liang Zhang*, Jun Wang*, Weiqi Zhang*, Zhengwei Xie*, Jing Qu*, Jianwei Wang*, Yichuan Xiao*, Ye Tian*, Gelin Wang*, Ping Hu*, Jing Ye*, Yu Sun*, Zhiyong Mao*, Qing-Peng Kong*, Qiang Liu*, Weiguo Zou*, Xiao-Li Tian*, Zhi-Xiong Xiao*, Yong Liu*, Jun-Ping Liu*, Moshi Song*, Jing-Dong J. Han* and Guang-Hui Liu*. The landscape of aging. Science China Life Sciences, Sep 2022.
- Shiqiang Zhang^, Wanyu Tao^ and Jing-Dong J. Han*. 3D chromatin structure changes during spermatogenesis and oogenesis. Computational and Structural Biotechnology Journal, May 2022.
- Xueqing Wang^, Quanlong Jiang^, Yuanyuan Song^, Zhidong He, Hongdao Zhang, Mengjiao Song, Xiaona Zhang, Yumin Dai, Oezlem Karalay, Christoph Dieterich, Adam Antebi, Ligang Wu*, Jing-Dong J. Han* and Yidong Shen*. Ageing induces tissue-specific transcriptomic changes in Caenorhabditis elegans. The EMBO Journal, Mar 2022.
- Yingying Zhao^, Hongwen Xuan^, Chao Shen, Peiyi Liu, Jing-Dong J. Han* and Wei Yu*. Immunosuppression Induced by Brain‑Specific HDAC6 Knockdown Improves Aging Performance in Drosophila melanogaster. Phenomics, Feb 2022.
- Guixian Liang^, Chunyu Zhou^, Xiangxiang Jiang^, Yifan Zhang, Baofeng Huang, Suwei Gao, Zhixin Kang, Dongyuan Ma, Fengchao Wang, Berthold Gottgens*, Hongmei Wang*, Jing-Dong J. Han* and Feng Liu*. De novo generation of macrophage from placenta-derived hemogenic endothelium. Developmental Cell, Jun 2021.
- Donghong Cai^ and Jing-Dong J. Han*. Aging-associated lncRNAs are evolutionarily conserved and participate in NFκB signaling. Nature Aging, May 2021.
- Xian Xia^, Yiyang Wang^, Zhengqing Yu, Jiawei Chen and Jing-Dong J. Han*. Assessing the rate of aging to monitor aging itself. Ageing Research Reviews, Apr 2021.
- Dawei Shi^, Xian Xia^, Aoyuan Cui^, Zhongxiang Xiong, Yizhen Yan, Jing Luo, Guoyu Chen, Yingying Zeng, Donghong Cai, Lei Hou, Joseph McDermott, Yu Li, Hong Zhang and Jing-Dong J. Han*. The precursor of PI(3,4,5)P3 alleviates aging by activating daf-18(Pten) and independent of daf-16. Nature Communications, Sep 2020.
- Xian Xia^, Xingwei Chen^, Gang Wu, Fang Li, Yiyang Wang, Yang Chen, Mingxu Chen, Xinyu Wang, Weiyang Chen, Bo Xian, Weizhong Chen, Yaqiang Cao, Chi Xu, Wenxuan Gong, Guoyu Chen, Donghong Cai, Wenxin Wei, Yizhen Yan, Kangping Liu, Nan Qiao, Xiaohui Zhao, Jin Jia, Wei Wang, Brian K. Kennedy, Kang Zhang, Carlo V. Cannistraci, Yong Zhou* and Jing-Dong J. Han*. Three-dimensional facial-image analysis to predict heterogeneity of the human ageing rate and the impact of lifestyle. Nature Metabolism, Sep 2020.
- Jiawei Chen^, Quanlong Jiang^, Xian Xia^, Kangping Liu^, Zhengqing Yu, Wanyu Tao, Wenxuan Gong and Jing-Dong J. Han*. Individual variation of the SARS-CoV-2 receptor ACE2 gene expression and regulation. Aging Cell, Jun 2020.
- 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. Science China Life Sciences, Mar 2020.
- 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 Research, Sep 2019.
- Yaqiang Cao^, Zhaoxiong Chen^, Xingwei Chen^, Daosheng Ai^, Guoyu Chen, Joseph McDermott, Yi Huang, Xiaoxiao Guo and Jing-Dong J. Han*. Accurate loop calling for 3D genomic data with cLoops. Bioinformatics, Aug 2019.
- 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, Aug 2019.
- 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 Reports, Apr 2019.
- 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 Reports, Feb 2019.
- 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 Research, Nov 2018.
- Chi Xu^, Daosheng Ai^, Shengbao suo, Xingwei Chen, Yizhen Yan, Yaqiang Cao, Na Sun, Weizhong Chen, Joseph McDermott, Shiqiang Zhang, Yingying Zeng and Jing-Dong J. Han*. Accurate Drug Repositioning through Non-tissue-Specific Core Signatures from Cancer Transcriptomes. Cell Reports, Oct 2018.
- Clayton E. Friedman^, Quan Nguyen^, Samuel W. Lukowski^, Abbigail Helfer, Han Sheng Chiu, Jason Miklas, Shiri Levy, Shengbao Suo, Jing-Dong J. 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, Oct 2018.
- Xian Xia and Jing-Dong J. Han*. Systems Biology in Aging Research. Advances in Experimental Medicine and Biology, Sep 2018.
- Guangdun Peng and Jing-Dong J. Han*. Regulatory network characterization in development: challenges and opportunities. F1000 Research, Sep 2018.
- Weizhong Chen^, Yi Liu^, Shanshan Zhu, Guoyu Chen and Jing-Dong J. Han*. Inter-nucleosomal communication between histone modifications for nucleosome phasing. PLoS Computational Biology, Sep 2018.
- Denghui Liu^, Xinyi Wang^, Dajian He^, Chunli Sun^, Xiechao He, Lanzhen Yan, Yizhou Li, Jing-Dong J. Han* and Ping Zheng*. Single cell RNA-sequencing reveals the existence of naïve and primed pluripotency in pre-implantation rhesus monkey embryos. Genome Research, Aug 2018.
- 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. PNAS, Jul 2018.
- Xian Xia^, Quanlong Jiang^, Joseph McDermott and Jing-Dong J. Han*. Aging and Alzheimer's disease: Comparison and Associations from Molecular to Systems Levels. Aging Cell, Jul 2018.
- 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 Communications, Nov 2017.
- Jing-Dong J. Han*, Lei Hou^, Na Sun^, Chi Xu, Joseph McDermott and Dan Wang. The system capacity view of aging and longevity. Quantitative Biology, Jun 2017.
- Xian Xia, Weiyang Chen, Joseph McDermott and Jing-Dong J. Han*. Molecular and phenotypic biomarkers of aging. F1000Research, Jun 2017.
- Davina Derous, Sharon E. Mitchell, Cara L. Green, Yingchun Wang, Jing-Dong J. Han, Luonan Chen, Daniel E.L. Promislow, David Lusseau, Alex Douglas and John R. Speakman*. The Effects of Graded Levels of Calorie Restriction: X. Transcriptomic Responses of Epididymal Adipose Tissue. The Journals of Gerontology Series A, May 2017.
- Bo Shan^, Xiaoxia Wang^, Ying Wu^, Chi Xu, Zhixiong Xia, Jianli Dai, Mengle Shao, Feng Zhao, Shengqi He, Liu Yang, Mingliang Zhang, Fajun Nan, Jia Li, Jianmiao Liu, Jianfeng Liu, Weiping Jia, Yifu Qiu, Baoliang Song, Jing-Dong J. Han, Liangyou Rui, Sheng-Zhong Duan* and Yong Liu*. The metabolic ER stress sensor IRE1α suppresses alternative activation of macrophages and impairs energy expenditure in obesity. Nature Immunology, May 2017.
- Christopher D. Green^, Yi Huang^, Xiaoyang Dou^, Liu Yang, Yong Liu and Jing-Dong J. Han*. Impact of Dietary Interventions on Noncoding RNA Networks and mRNAs Encoding Chromatin-Related Factors. Cell Reports, Mar 2017.
- 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, Apr 2017.
- Jun Chen^, Shengbao Suo^, Patrick PL Tam, Jing-Dong J. Han*, Guangdun Peng* and Naihe Jing*. Spatial transcriptomic analysis of cryosectioned tissue samples with Geo-seq. Nature Protocols, Feb 2017.
- Dan Wang^, Lei Hou^, Shuhei Nakamura, Ming Su, Fang Li, Weiyang Chen, Yizhen Yan, Christopher D. Green, Di Chen, Hong Zhang, Adam Antebi and Jing-Dong J. Han*. LIN-28 balances longevity and germline stem cell number in Caenorhabditis elegans through let-7/AKT/DAF-16 axis. Aging Cell, Oct 2016.
- 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* and Naihe Jing*. Spatial Transcriptome for the Molecular Annotation of Lineage Fates and Cell Identity in Mid-gastrula Mouse Embryo. Developmental Cell, Mar 2016.
- 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 Metabolism, Mar 2016.
- Hao Cheng^, Xiaoyang Dou^ and Jing-Dong J. Han*. Understanding super-enhancers. Science China Life Sciences, Mar 2016.
- Weiyang Chen, Xian Xia, Yi Huang, Xingwei Chen and Jing-Dong J. Han*. Bioimaging for quantitative phenotype analysis. Methods, Feb 2016.
- Ming Su^, Xiaoyang Dou^, Hao Cheng^ and Jing-Dong J. Han*. Integrative Epigenomics. Computational and Statistical Epigenomics Translational Bioinformatics, Oct 2015.
- Lei Hou, Dan Wang, Hao Cheng, Bo Xian and Jing-Dong J Han. Handbook of the Biology of Aging (Eighth Edition) by Academic Press, Chapter 8: Systems Approaches to Understanding Aging. Oct 2015.
- Han Zhang^, Hao Cheng^, Qingqing Wang, Xianping Zeng, Yanfen Chen, Jin Yan, Yanran Sun, Xiaoxi Zhao, Weijing Li, Chao Gao, Wenyu Gong, Bei Li, Ruidong Zhang, Li Nan, Young Wu, Shilai Bao*, Jing-Dong J. Han* and Huyong Zheng*. An advanced fragment analysis-based individualized subtype classification of pediatric acute lymphoblastic leukemia. Scientific Reports, Jul 2015.
- 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, Mar 2015.
- 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, Jan 2015.
- Weizhong Chen^, Yi Liu^, Shanshan Zhu, Christopher D. Green, Gang Wei and Jing-Dong J. Han*. Improved nucleosome-positioning algorithm iNPS for accurate nucleosome positioning from sequencing data. Nature Communications, Sep 2014.
- Qingqing Zhu^, Lu Song^, Guangdun Peng, Na Sun, Jun Chen, Ting Zhang, Nengyin Sheng, Wei Tang, Cheng Qian, Yunbo Qiao, Ke Tang, Jing-Dong J. Han, Jinsong Li and Naihe Jing*. The transcription factor Pou3f1 promotes neural fate commitment via activation of neural lineage genes and inhibition of external signaling pathways. eLife, Jun 2014.
- Ming Su^, Dali Han^, Jerome Boyd-Kirkup, Xiaoming Yu and Jing-Dong J. Han*. Evolution of Alu Elements toward Enhancers. Cell Reports, Apr 2014.
- Nan Qiao^, Yi Huang^, Hammad Naveed, Christopher D. Green and Jing-Dong J. Han*. CoCiter: An Efficient Tool to Infer Gene Function by Assessing the Significance of Literature Co-Citation. PLoS One, Sep 2013.
- 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, Sep 2013.
- Hammad Naveed and Jing-Dong J. Han*. Structure-based protein-protein interaction networks and drug design. Quantitative Biology, Sep 2013.
- Wei Zhang^, Yi Liu^, Na Sun, Dan Wang, Jerome Boyd-Kirkup, Xiaoyang Dou and Jing-Dong J. Han*. Integrating Genomic, Epigenomic, and Transcriptomic Features Reveals Modular Signatures Underlying Poor Prognosis in Ovarian Cancer. Cell Reports, Aug 2013.
- Jerome D Boyd-Kirkup, Christopher D Green, Gang Wu, Dan Wang and Jing-Dong J. Han*. Epigenomics and the regulation of aging. Epigenomics, Apr 2013.
- Eirini Karamariti^, Andriana Margariti^, Bernhard Winkler, Xiaocong Wang, Xuechong Hong, Dilair Baban, Jiannis Ragoussis, Yi Huang, Jing-Dong J. Han, Mei Mei Wong, Can M. Sag, Ajay M. Shah, Yanhua Hu and Qingbo Xu*. Smooth Muscle Cells Differentiated from Reprogrammed Embryonic Lung Fibroblasts Through DKK3 Signalling are Potent for Tissue Engineering of Vascular Grafts. Circulation Research, Mar 2013.
- Li Yang, Gang Wei, Kun Tang, Christine Nardini and Jing-Dong J. Han*. Understanding human diseases with high-throughput quantitative measurement and analysis of molecular signatures. Science China Life Sciences, Mar 2013.
- Jialiang Huang^, Chaoqun Niu, Christopher D.Green, Lun Yang, Hongkang Mei* and Jing-Dong J. Han*. Systematic Prediction of Pharmacodynamic Drug-Drug Interactions through Protein-Protein-Interaction Network. PLoS Computational Biology, Mar 2013.
- Bo Xian^, Jie Shen^, Weiyang Chen^, Na Sun, Nan Qiao, Dongqing Jiang, Tao Yu, Yongfan Men, Zhijun Han, Yuhong Pang, Matt Kaeberlein, Yanyi Huang and Jing-Dong J. Han*. WormFarm: a quantitative control and measurement device toward automated Caenorhabditis elegans aging analysis. Aging Cell, Feb 2013.
- Yi Liu^, Nan Qiao^, Shanshan Zhu, Ming Su, Na Sun, Jerome Boyd-Kirkup and Jing-Dong J. Han*. A novel Bayesian network inference algorithm for integrative analysis of heterogeneous deep sequencing data. Cell Research, Jan 2013.
- Lei Hou, Jialiang Huang, Christopher D. Green, Jerome Boyd-Kirkup, Wei Zhang, Xiaoming Yu, Wenxuan Gong, Bing Zhou and Jing-Dong J. Han*. Systems Biology in Aging: Linking the Old and the Young. Current Genomics, Nov 2012.
- Yixing Han^, Dali Han^, Zheng Yan, Jerome D. Boyd-Kirkup, Christopher D. Green, Philipp Khaitovich and Jing-Dong J. Han*. Stress-associated H3K4 methylation accumulates during postnatal development and aging of Rhesus macaque brain. Aging Cell, Sep 2012.
- Andriana Margariti, Bernhard Winkler, Eirini Karamariti, Anna Zampetaki, Tsung-neng Tsai, Dilair Baban, Jiannis Ragoussis, Yi Huang, Jing-Dong J. Han, Lingfang Zeng, Yanhua Hu and Qingbo Xu*. Direct reprogramming of fibroblasts into endothelial cells capable of angiogenesis and reendothelialization in tissue-engineered vessels. PNAS, Aug 2012.
- Chenhuan Xu^, Xiaowen Lv^, Eric Z. Chen, Zhiying He, Borjigin Uyunbilig, Guangpeng Li, Yue Ma, Lijian Hui, Bin Xie, Yuan Gao, Xiaoyan Ding, Yiping Hu, Ping Hu*, Jing-Dong J. Han* and Xin Wang. Genome-wide roles of Foxa2 in directing liver specification. Journal of Molecular Cell Biology, Jun 2012.
- Jing-Dong J. Han*. An aging program at the systems level? Birth Defects Research Part C Embryo today: reviews, Jun 2012.
- Jian Xue^, Nan Qiao^, Wei Zhang, Ruo-Lin Cheng, Xiao-Qin Zhang, Yan-Yuan Bao, Yi-Peng Xu, Lin-Zhu Gu, Jing-Dong Jackie Han* and Chuan-Xi Zhang*. Dynamic Interactions between Bombyx mori Nucleopolyhedrovirus and Its Host Cells Revealed by Transcriptome Analysis. Journal of Virology, Jul 2012.
- Bing Zhou^, Liu Yang^, Shoufeng Li, Jialiang Huang, Haiyang Chen, Lei Hou, Jinbo Wang, Christopher D. Green, Zhen Yan, Xun Huang, Matt Kaeberlein, Li Zhu, Huasheng Xiao, Yong Liu* and Jing-Dong J. Han*. Midlife gene expressions identify modulators of aging through dietary interventions. PNAS, Apr 2012.
- Fang Chen^, Wei Zhang^, Yu Liang^, Jialiang Huang^, Kui Li^, Christopher D. Green^, Jiancheng Liu^, Guojie Zhang, Bing Zhou, Xin Yi, Wei Wang, Hang Liu, Xiaohong Xu, Feng Shen, Ning Qu, Yading Wang, Guoyi Gao, A. San, LuoSang JiangBai, Hua Sang, Xiangdong Fang, Karsten Kristiansen, Huanming Yang, Jun Wang*, Jing-Dong J. Han* and Jian Wang*. Transcriptome and Network Changes in Climbers at Extreme Altitudes. PLoS One, Feb 2012.
- Zhongwei Li^, Teng Fei^, Jianping Zhang, Gaoyang Zhu, Lu Wang, Danyu Lu, Xiaochun Chi, Yan Teng, Ning Hou, Xiao Yang, Hongquan Zhang, Jing-Dong J. Han and Ye-Guang Chen*. BMP4 Signaling Acts via Dual-Specificity Phosphatase 9 to Control ERK Activity in Mouse Embryonic Stem Cells. Cell Stem Cell, Feb 2012.
- Ting Mao^, Mengle Shao^, Yifu Qiu, Jialiang Huang, Yongliang Zhang, Bo Song, Qiong Wang, Lei Jiang, Yi+ Liu, Jing-Dong J. Han, Pengrong Cao, Jia Li, Xiang Gao, Liangyou Rui, Ling Qi, Wenjun Li and Yong Liu*. PKA phosphorylation couples hepatic inositol-requiring enzyme 1α to glucagon signaling in glucose metabolism. PNAS, Sep 2011.
- 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 and Jing-Dong J. Han*. Histone Demethylase UTX-1 Regulates C. elegans Life Span by Targeting the Insulin/IGF-1 Signaling Pathway. Cell Metabolism, Aug 2011.
- Jialiang Huang, Yi Liu, Wei Zhang, Hong Yu and Jing-Dong J. Han*. eResponseNet: a package prioritizing candidate disease genes through cellular pathways. Bioinformatics, Jun 2011.
- Ran Tao, Hua Chen, Chan Gao, Peng Xue, Fuquan Yang, Jing-Dong J. Han, Bing Zhou and Ye-Guang Chen*. Xbp1-mediated histone H4 deacetylation contributes to DNA double-strand break repair in yeast. Cell Research, Apr 2011.
- Christopher D. Green and Jing-Dong J. Han*. Epigenetic regulation by nuclear receptors. Epigenomics, Feb 2011.
- Teng Fei, Shanshan Zhu, Kai Xia, Jianping Zhang, Zhongwei Li, Jing-Dong J. Han* and Ye-Guang Chen*. Smad2 mediates Activin/Nodal signaling in mesendoderm differentiation of mouse embryonic stem cells. Cell Research, Nov 2010.
- Yi Liu^, Dali Han^, Yixing Han^, Zheng Yan, Bin Xie, Jing Li, Nan Qiao, Haiyang Hu, Philipp Khaitovich, Yuan Gao and Jing-Dong J. Han*. Ab initio identification of transcription start sites in the Rhesus macaque genome by histone modification and RNA-Seq. Nucleic Acids Research, Oct 2010.
- Hong Yu^, Jialiang Huang^, Nan Qiao, Christopher D Green and Jing-Dong J. Han*. Evaluating diabetes and hypertension disease causality using mouse phenotypes. BMC Systems Biology, Jul 2010.
- Jing-Dong J. Han. Cancer Systems Biology by Chapman & Hall/CRC Press, Chapter 2: Network biology, the framework of systems biology. May 2010.
- Yi Liu* and Jing-Dong J. Han*. Application of Bayesian networks on large-scale biological data. Frontiers in Biology, Apr 2010.
- Teng Fei^, Kai Xia^, Zhongwei Li`, Bing Zhou`, Shanshan Zhu`, Hua Chen, Jianping Zhang, Zhang Chen, Huasheng Xiao, Jing-Dong J. Han* and Ye-Guang Chen*. Genome-wide mapping of SMAD target genes reveals the role of BMP signaling in embryonic stem cell fate determination. Genome Research, Nov 2009.
- Zhigang Li^, Wei Zhang^, Minyuan Wu, Shanshan Zhu, Chao Gao, Lin Sun, Ruidong Zhang, Nan Qiao, Huiling Xue, Yamei Hu, Shilai Bao*, Huyong Zheng* and Jing-Dong J. Han*. Expression-based classification and regulatory networks of pediatric acute lymphoblastic leukemia. Blood, Sep 2009.
- Jing-Dong J. Han and Chris J. Needham. Biological Data Mining by Chapman & Hall/CRC Press, Chapter 18: Statistical analysis of biomolecular networks. Sep 2009.
- Jing-Dong J. Han*, Yi Liu^, Huiling Xue^, Kai Xia^, Hong Yu^, Shanshan Zhu^, Zhang Chen, Wei Zhang, Chunyu Jin, Bo Xian, Jing Li, Lei Hou, Yixing Han, Chaoqun Niu and Timothy C. Alcon. Developmental systems biology flourishing on new technologies. Journal of Genetics and Genomics, Oct 2008.
- Kai Xia^, Zheng Fu^, Lei Hou and Jing-Dong J. Han*. Impacts of protein-protein interaction domains on organism and network complexity. Genome Research, Aug 2008.
- Hong Yu^, Shanshan Zhu^, Bing Zhou^, Huiling Xue and Jing-Dong J. Han*. Inferring causal relationships among different histone modifications and gene expression. Genome Research, Jun 2008.
- Qian-Ru Li^, Anne-Ruxandra Carvunis^, Haiyuan Yu^, Jing-Dong J. Han^, Quan Zhong, Nicolas Simonis, Stanley Tam, Tong Hao, Niels J. Klitgord, Denis Dupuy, Danny Mou, Ilan Wapinski, Aviv Regev, David E Hill, Michael E. Cusick and Marc Vidal*. Revisiting the Saccharomyces cerevisiae predicted ORFeome. Genome Research, May 2008.
- Jing-Dong Jackie Han*. Understanding biological functions through molecular networks. Cell Research, Jan 2008.
- Huiling Xue^, Bo Xian^, Dong Dong, Kai Xia, Shanshan Zhu, Zhongnan Zhang, Lei Hou, Qingpeng Zhang, Yi Zhang and Jing-Dong J. Han*. A modular network model of aging. Molecular Systems Biology, Dec 2007.
- Dong Dong, Bing Zhou and Jing-Dong J. Han*. Comparing the biological coherence of network clusters identified by different detection algorithms. Chinese Science Bulletin, Nov 2007.
- Miguel Angel Pujana^, Jing-Dong J. Han^, Lea M Starita^, Kristen N Stevens^, Muneesh Tewari, Jin Sook Ahn, Gad Rennert, Vı́ctor Moreno, Tomas Kirchhoff , Bert Gold, Volker Assmann, Wael M ElShamy, Jean-François Rual, Douglas Levine, Laura S Rozek, Rebecca S Gelman, Kristin C Gunsalus, Roger A Greenberg, Bijan Sobhian, Nicolas Bertin, Kavitha Venkatesan, Nono Ayivi-Guedehoussou, Xavier Solé, Pilar Hernández, Conxi Lázaro, Katherine L Nathanson, Barbara L Weber, Michael E Cusick, David E Hill, Kenneth Offit, David M Livingston, Stephen B Gruber*, Jeffrey D Parvin* and Marc Vidal*. Network modeling links breast cancer susceptibility and centrosome dysfunction. Nature Genetics, Oct 2007.
- Qiang Wang, Zheng Huang, Huiling Xue, Chengcheng Jin, Xiu-Li Ju, Jing-Dong J. Han and Ye-Guang Chen*. MicroRNA miR-24 inhibits erythropoiesis by targeting activin type I receptor ALK4. Blood, Sep 2007.
- Nicolas Bertin^, Nicolas Simonis^, Denis Dupuy^, Michael E. Cusick, Jing-Dong J. Han, Hunter B. Fraser*, Frederick P. Roth* and Marc Vidal*. Confirmation of organized modularity in the yeast interactome. PLoS Biology, Jun 2007.
- Kai Xia^, Huiling Xue^, Dong Dong^, Shanshan Zhu^, Jiamu Wang, Qingpeng Zhang, Lei Hou, Hua Chen, Ran Tao, Zheng Huang, Zheng Fu, Ye-Guang Chen and Jing-Dong J. Han*. Identification of the Proliferation/Differentiation Switch in the Cellular Network of Multicellular Organisms. PLoS Computational Biology, Nov 2006.
- Kai Xia^, Dong Dong^ and Jing-Dong J. Han*. IntNetDB v1.0: An integrated protein-protein interaction network database generated by a probabilistic model. BMC Bioinformatics, Nov 2006.
- Jing Ma^, Qiang Wang^, Teng Fei, Jing-Dong Jackie Han and Ye-Guang Chen*. MCP-1 mediates TGF-beta-induced angiogenesis by stimulating vascular smooth muscle cell migration. Blood, Oct 2006.
- Denis Dupuy, Nicolas Bertin, Michael E. Cusick, Jing-Dong J. Han and Marc Vidal. Reply to Toward the complete interactome. Nature Biotechnology, Jun 2006.
- Xiaoping Wu^, Jing Ma^, Jing-Dong Han, Nanping Wang and Ye-Guang Chen*. Distinct regulation of gene expression in human endothelial cells by TGF-beta and its receptors. Microvascular Research, Jan 2006.
- Kristin C. Gunsalus^, Hui Ge^, Aaron J. Schetter^, Debra S. Goldberg^, Jing-Dong J. Han, Tong Hao, Gabriel F. Berriz, Nicolas Bertin, Jerry Huang, Ling-Shiang Chuang, Ning Li, Ramamurthy Mani, Anthony A. Hyman, Birte Sonnichsen, Christophe J. Echeverri, Frederick P. Roth*, Marc Vidal* and Fabio Piano*. Predictive models of molecular machines involved in Caenorhabditis elegans early embryogenesis. Nature, Aug 2005.
- Jing-Dong J. Han^, Denis Dupuy^, Nicolas Bertin, Michael E Cusick and Marc Vidal*. Effect of sampling on topology predictions of protein-protein interaction networks. Nature Biotechnology, Jul 2005.
- Jing-Dong J. Han, Nicolas Bertin, Tong Hao, Debra S. Goldberg, Gabriel F. Berriz, Lan V. Zhang, Denis Dupuy, Albertha J. M. Walhout, Michael E. Cusick, Frederick P. Roth and Marc Vidal*. Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature, Jun 2004.
- Haiyuan Yu, Nicholas M. Luscombe, Hao Xin Lu, Xiaowei Zhu, Yu Xia, Jing-Dong J. Han, Nicolas Bertin, Sambath Chung, Marc Vidal and Mark Gerstein*. Annotation Transfer Between Genomes: Protein-Protein Interologs and Protein-DNA Regulogs. Genome Research, Jun 2004.
- Siming Li^, Christopher M. Armstrong^, Nicolas Bertin^, Hui Ge^, Stuart Milstein^, Mike Boxem^, Pierre-Olivier Vidal ain^, Jing-Dong J. Han^, Alban Chesneau^, Tong Hao, Debra S. Goldberg, Ning Li, Monica Martinez, Jean-François Rual, Philippe Lamesch, Lai Xu, Muneesh Tewari, Sharyl L. Wong, Lan V. Zhang, Gabriel F. Berriz, Laurent Jacotot, Philippe Vaglio, Jerome Reboul, Tomoko Hirozane-Kishikawa, Qianru Li, Harrison W. Gabel, Ahmed Elewa, Bridget Baumgartner, Debra J. Rose, Haiyuan Yu, Stephanie Bosak, Reynaldo Sequerra, Andrew Fraser, Susan E. Mango, William M. Saxton, Susan Strome, Sander van den Heuvel, Fabio Piano, Jean Vandenhaute, Claude Sardet, Mark Gerstein, Lynn Doucette-Stamm, Kristin C. Gunsalus, J. Wade Harper, Michael E. Cusick, Frederick P. Roth, David E. Hill and Marc Vidal*. A Map of the Interactome Network of the Metazoan C. elegans. Science, Jan 2004.
- Xingang Zhao^, Jing-Dong Han^, Yuanheng Ning, Anming Meng and Yeguang Chen*. Bioinformatics analysis of putative gene products encoded in SARS-HCoV genome. Tsinghua Science and Technology, Aug 2003.
- Jing-Dong Han, Nicholas E. Baker and Charles S. Rubin*. Molecular Characterization of a Novel A Kinase Anchor Protein from Drosophila melanogaster. Journal of Biological Chemistry, Oct 1997.
- Jing-Dong Han and Charles S. Rubin*. Regulation of Cytoskeleton Organization and Paxillin Dephosphorylation by cAMP: STUDIES ON MURINE Y1 ADRENAL CELLS. Journal of Biological Chemistry, Nov 1996.