Dr. Yong Wang
王 勇 博士
Professor of Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences
研究员, 应用数学研究所, 数学与系统科学研究院, 中国科学院
Email: ywang@amss.ac.cn
Tel: +86(10)-82541372
WangLab: Welcome to visit my Optimization and Computational Systems Biology Lab
Vitae
Research Philosophy
- Think globally, act locally
- As simple as possible, but no simpler
- Hacker spirit
Research Interests
- Optimization
- Bioinformatics
- Systems biology
- Complex network
Selected Publications
- Yong Wang, Rui Jiang, and Wing Hung Wong.
Modeling the causal regulatory network by integrating chromatin accessibility and transcriptome data
National Science Review. 3(2),240-251, 2016.
- Meng Zou, Peng-Jun Zhang, Luonan Chen, Ya-Ping Tian, and Yong Wang.
Identifying joint biomarker panel from multiple level dataset by an optimization model
Biomarkers in Medicine. 10(6),567-575. 2016.
- Duren Zhana, Yong Wang.
A systematic method to identify modulation of transcriptional regulation via chromatin activity reveals regulatory network during mESC differentiation
Scientific Report. 6, 2016.
- Yongcui Wang, Nai-Yang Deng, Shi-Long Chen, and Yong Wang.
Computational probing protein-protein interactions targeting small molecules
Bioinformatics. 32: 226-234, 2016.
- Meng Zou, Zhaoqi Liu, Xiang-Sun Zhang, and Yong Wang.
NCC-AUC: an AUC optimization method to identify multi-biomarker panel for cancer prognosis from genomic and clinical data
Bioinformatics. 31 (20), 3330-3338, 2015.
- Meng Zou, Pengjun Zhang, Xin-Yu Wen, Luonan Chen, Yaping Tian, and Yong Wang.
A novel mixed integer programming for multi-biomarker panel identification by distinguishing malignant from benign colorectal tumors
Methods. Vol. 83, 3–17, 2015.
- Jingxue Xin, Xianwen Ren, Luonan Chen and Yong Wang.
Identifying network biomarkers based on protein-protein interactions and expression data
BMC Medical Genomics, 8(Suppl 2):S11， 2015
- Pengjun Zhang, Meng Zou, Xinyu Wen, Feng Gu, Juan Li, Gaixia Liu, Jingxiao Dong, Xinxin Deng, Jing Gao, Xiaolong Li, Xingwang Jia, Zhennan Dong, Luonan Chen, Yong Wang, Yaping Tian.
Development of Serum Parameters Panels for the Early Detection of Pancreatic Cancer
International Journal of Cancer, 134(11):2646-55, 2014.
- Lin Wang, Yong Wang, Qinghua Hu, Shao Li.
Systematic analysis of new drug indications by drug-gene-disease coherent subnetworks.
CPT: Pharmacometrics & Systems Pharmacology, 3, e146; 2014.
- Shao-Yan Sun, Tao Zeng, Zhi-Ping Liu, Yong Wang*, and Luonan Chen*.
Spatio-temporal analysis of type 2 diabetes mellitus based on differential expression networks.
Scientific Report, 3, 2268; 2013.
- Xianwen Ren, Yong Wang*, Xiang-Sun Zhang, and Qi Jin.
iPcc: a novel feature extraction method for accurate disease class discovery and prediction.
Nucleic Acids Research. 2013 Vol. 41, No. 4, e143.
- Yongcui Wang, Nai-Yang Deng, Shi-Long Chen, Yong Wang*.
Network predicting drug's anatomical therapeutic chemical code.
Bioinformatics, 2013 29: 1317-1324.
- Yong Wang.
Bioinformatics studies on induced pluripotent stem cell.
Current Bioinformatics, 2013, Vol. 8. No. 1. 80--87. PDF
- Xianwen Ren, Yong Wang*, Luonan Chen, Xiang-Sun Zhang, and Qi Jin.
ellipsoidFN: a tool for identifying a heterogeneous set of cancer biomarkers based on gene expressions
Nucleic Acids Research. 2013 41(4): e53.
- Duren Zhana, Yong Wang*, Shigeru Saito, Katsuhisa Horimoto.
Inferring Gene Regulatory Network for Cell Reprogramming
Proceedings of The 31th Chinese Control Conference (CCC), pp. 7437-7442, 2012. PDF
- Yong Wang*, Qiao-Feng Wu, Chen Chen, Ling-Yun Wu, Xian-Zhong Yan, Shu-Guang Yu, Xiang-Sun Zhang, and Fan-Rong Liang.
Revealing metabolite biomarkers for acupuncture treatment by linear programming based feature selection
BMC Systems Biology, 6(Suppl 1):S15， 2012.
- Xianwen Ren, Yong Wang*, Jiguang Wang and Xiang-Sun Zhang.
A unified computational model for revealing and predicting subtle subtypes of cancers
BMC Bioinformatics, 13:70, 2012.
- Ji-Guang Wang, Qiang Huang, Zhi-Ping Liu, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen.
NOA: a novel network ontology analysis method
Nucleic Acids Research, 39(13):e87, 2011.
- Yong Wang, Katsuhisa Horimoto, Luonan Chen.
An Integrated Pipeline for Gene Regulatory Network Inference
Proceedings of The 30th Chinese Control Conference (CCC), pp. 6593-6598, 2011. PDF
- Yong Wang, Eric Franzosa, Xiang-Sun Zhang, and Yu Xia.
Protein evolution in yeast transcription factor subnetworks
Nucleic Acids Research, 38(18): 5959–5969, 2010. PDF
- Yong Wang, Rui-Sheng Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen, and Yu Xia.
A Linear Programming Framework for Inferring Gene Regulatory Networks by Integrating Heterogeneous Data,
Chapter XIX in Computational Methodologies in Gene Regulatory Networks, Sanjoy Das, Doina Caragea, W. H. Hsu, Stephen M. Welch (eds.), IGI Global, 2009. PDF
- Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.
Evaluating protein similarity from coarse structures.
IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 6, No. 4, pp. 583-593, 2009. PDF
- Yong Wang, Xiang-Sun Zhang, and Yu Xia.
Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data.
Nucleic Acids Research, Vol. 37, No. 18, pp. 5943-5958, 2009. PDF
- Yong Wang, Xiang-Sun Zhang, and Luonan Chen.
A network biology study on circadian rhythm by integrating various omics data.
OMICS: A Journal of Integrative Biology, Vol. 13, No. 4, 2009. PDF
- Yong Wang and Yu Xia,
Condition specific subnetwork identification using an optimization model.
Lecture Notes in Operations Research, 9, pp. 329--336, 2008.
- Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, Luonan Chen.
Analysis on multi-domain cooperation for predicting protein-protein interactions.
BMC Bioinformatics, 8:391, 2007. PDF
- Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen.
Inferring transcriptional regulatory networks from high-throughput data.
Bioinformatics, Vol. 23, pp. 3056-3064, 2007. PDF
- Yong Wang, Trupti Joshi, Xiang-Sun. Zhang, Dong Xu and Luonan Chen.
Supervised Inference of Gene Regulatory Networks by Linear Programming.
Lecture Notes in Bioinformatics, Vol. 4115, pp. 551-561, 2006. PDF
- Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen.
Inferring gene regulatory networks from multiple microarray datasets.
Bioinformatics, 22(19):2413-2420, 2006. PDF
- Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen.
Exploring protein's optimal HP configurations by self-organizing mapping.
Journal of Bioinformatics and Computational Biology, Vol. 3, No. 2, pp. 385-400, 2005. PDF
- Full list of paper can be found Google Scholar or Here. Papers in bioinformatics and systems biology can be found in PubMed
Softwares
Links
| File | Last modified | Size |
|---|---|---|
| BMCBioinfo2007.pdf | 2011-01-09 17:14 | 423Kb |
| Bioinformatics2006.pdf | 2011-01-09 17:14 | 202Kb |
| Bioinformatics2007.pdf | 2011-01-09 17:14 | 414Kb |
| CMGRN2009.pdf | 2011-01-09 17:15 | 904Kb |
| CurrentBIO2013.pdf | 2013-06-09 01:40 | 729Kb |
| GRNiPSCCCC2012.pdf | 2012-10-17 11:33 | 696Kb |
| JBCB2005.pdf | 2011-01-09 17:19 | 248Kb |
| LNBI2006.pdf | 2011-01-09 17:15 | 296Kb |
| NAR2009.pdf | 2011-01-09 17:20 | 868Kb |
| NAR2010.pdf | 2011-01-09 17:19 | 514Kb |
| OMICS2009.pdf | 2011-01-09 17:15 | 753Kb |
| Pipeline.pdf | 2012-10-17 11:22 | 148Kb |
| TCBB2009.pdf | 2011-01-09 17:19 | 685Kb |
| Yong Wang Vitae Chinese.pdf | 2011-01-02 13:12 | 396Kb |
| Yong Wang Vitae.pdf | 2011-01-02 13:12 | 74Kb |
| Yong Wang Vitae Chinese.pdf | 2011-09-22 14:08 | 174Kb |
| Yong Wang Vitae Chinese2011.pdf | 2011-10-17 11:13 | 176Kb |
| Yong Wang Vitae.pdf | 2011-09-22 14:07 | 81Kb |
| Yong Wang Vitae2011.pdf | 2011-10-17 11:13 | 81Kb |
| YongWangVitae2011.pdf | 2011-10-17 11:16 | 81Kb |
| YongWangVitae2013.pdf | 2013-11-05 14:42 | 94Kb |
| YongWangVitaeChinese2011.pdf | 2011-10-17 11:15 | 176Kb |
| YongWangVitaeChinese2013.pdf | 2013-11-05 14:42 | 187Kb |
