Wiki source for YongWang
""<img src="images/users/yongwang.jpg" style="float: right; margin: 1.0%; padding: 0.5%;">""
====== Dr. Yong Wang======
====== 王 勇 博士 ======
Professor of [[http://www.amt.ac.cn Institute of Applied Mathematics]], [[http://www.amss.ac.cn Academy of Mathematics and Systems Science]], [[http://www.cas.ac.cn Chinese Academy of Sciences]]
研究员, [[http://www.amt.ac.cn 应用数学研究所]], [[http://www.amss.ac.cn 数学与系统科学研究院]], [[http://www.cas.ac.cn 中国科学院]]
Email: ""<a href="mailto:ywang@amss.ac.cn">ywang@amss.ac.cn</a>""
Tel: +86(10)-82541372
[[http://wanglab.amss.ac.cn WangLab: Welcome to visit my Optimization and Computational Systems Biology Lab]]
=== Vitae ===
~- {{files download="YongWangVitaeChinese2013.pdf" text="科研简历 （PDF）"}}
~- {{files download="YongWangVitae2013.pdf" text="Curriculum Vitae （PDF）"}}
""<img src="images/users/YongReasearchSummary.jpg" style="float: right; margin: 1.0%; padding: 0.5%;">""
=== 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===
~- **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**, Rui Jiang, and Wing Hung Wong. ---**[[http://nsr.oxfordjournals.org/content/early/2016/04/19/nsr.nww025 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 **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**. ---**[[https://www.ncbi.nlm.nih.gov/pubmed/27172589 Identifying joint biomarker panel from multiple level dataset by an optimization model]]**--- //Biomarkers in Medicine//. 10(6),567-575. 2016.
~- Duren Zhana, **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**. ---**[[http://www.nature.com/articles/srep22656 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 **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**. ---**[[http://http://bioinformatics.oxfordjournals.org/ Computational probing protein-protein interactions targeting small molecules]]**--- //Bioinformatics//. 32: 226-234, 2016.
~- **[[http://zhangroup.aporc.org/MengZou Meng Zou]]**, Zhaoqi Liu, **[[http://zhangroup.aporc.org/XiangsunZhang Xiang-Sun Zhang]]**, and **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**. ---**[[http://bioinformatics.oxfordjournals.org/content/early/2015/07/08/bioinformatics.btv374.full 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.
~- **[[http://zhangroup.aporc.org/MengZou Meng Zou]]**, Pengjun Zhang, Xin-Yu Wen, Luonan Chen, Yaping Tian, and **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**. ---**[[http://www.sciencedirect.com/science/article/pii/S1046202315002042 A novel mixed integer programming for multi-biomarker panel identification by distinguishing malignant from benign colorectal tumors]]**--- //Methods//. Vol. 83, 3–17, 2015.
~- **[[http://zhangroup.aporc.org/JinxueXin Jingxue Xin]]**, **[[http://zhangroup.aporc.org/XianwenRen Xianwen Ren]]**, Luonan Chen and **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**. ---**[[http://www.biomedcentral.com/1755-8794/8/S2/S11/abstract Identifying network biomarkers based on protein-protein interactions and expression data]]**--- //BMC Medical Genomics//, 8(Suppl 2):S11， 2015
~- Pengjun Zhang, **[[http://zhangroup.aporc.org/MengZou Meng Zou]]**, Xinyu Wen, Feng Gu, Juan Li, Gaixia Liu, Jingxiao Dong, Xinxin Deng, Jing Gao, Xiaolong Li, Xingwang Jia, Zhennan Dong, Luonan Chen, **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**, Yaping Tian. --- **[[http://onlinelibrary.wiley.com/doi/10.1002/ijc.28584/abstract Development of Serum Parameters Panels for the Early Detection of Pancreatic Cancer]]** --- //International Journal of Cancer//, 134(11):2646-55, 2014.
~- **[[http://zhangroup.aporc.org/LinWang Lin Wang]]**, **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**, Qinghua Hu, Shao Li. ---**[[http://www.nature.com/psp/journal/v3/n11/full/psp201444a.html 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*. --- ** [[http://www.nature.com/srep/2013/130724/srep02268/full/srep02268.html 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.--- ** [[http://nar.oxfordjournals.org/content/early/2013/06/12/nar.gkt343.full 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*. --- ** [[http://bioinformatics.oxfordjournals.org/content/early/2013/04/04/bioinformatics.btt158.long Network predicting drug's anatomical therapeutic chemical code. ]]**--- //Bioinformatics//, 2013 29: 1317-1324.
~- Yong Wang. --- ** [[http://www.ingentaconnect.com/content/ben/cbio/2013/00000008/00000001/art00013 Bioinformatics studies on induced pluripotent stem cell. ]]**--- //Current Bioinformatics//, 2013, Vol. 8. No. 1. 80--87. {{files download="CurrentBIO2013.pdf" text="PDF"}}
~- Xianwen Ren, Yong Wang*, Luonan Chen, Xiang-Sun Zhang, and Qi Jin.--- ** [[http://nar.oxfordjournals.org/content/41/4/e53.long 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. --- ** [[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6391257&tag=1 Inferring Gene Regulatory Network for Cell Reprogramming]]**---//Proceedings of The 31th Chinese Control Conference (CCC)//, pp. 7437-7442, 2012. {{files download="GRNiPSCCCC2012.pdf" text="PDF"}}
~- Yong Wang*, Qiao-Feng Wu, Chen Chen, Ling-Yun Wu, Xian-Zhong Yan, Shu-Guang Yu, Xiang-Sun Zhang, and Fan-Rong Liang.--- ** [[http://www.biomedcentral.com/1752-0509/6/S1/S15/abstract 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. ---**[[http://www.biomedcentral.com/1471-2105/13/70 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. ---**[[http://nar.oxfordjournals.org/content/early/2011/05/04/nar.gkr251 NOA: a novel network ontology analysis method]]**---//Nucleic Acids Research//, 39(13):e87, 2011.
~-Yong Wang, Katsuhisa Horimoto, Luonan Chen. ---**[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6001633&tag=1 An Integrated Pipeline for Gene Regulatory Network Inference]]**---//Proceedings of The 30th Chinese Control Conference (CCC)//, pp. 6593-6598, 2011. {{files download="Pipeline.pdf" text="PDF"}}
~- Yong Wang, Eric Franzosa, Xiang-Sun Zhang, and Yu Xia. ---**[[http://nar.oxfordjournals.org/content/38/18/5959 Protein evolution in yeast transcription factor subnetworks]]**--- //Nucleic Acids Research//, 38(18): 5959–5969, 2010. {{files download="NAR2010.pdf" text="PDF"}}
~- Yong Wang, Rui-Sheng Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen, and Yu Xia. --- **[[http://www.igi-global.com/reference/details.asp?ID=34877&v=tableOfContents 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. {{files download="CMGRN2009.pdf" text="PDF"}}
~- Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]].**--- //IEEE/ACM Transactions on Computational Biology and Bioinformatics,// Vol. 6, No. 4, pp. 583-593, 2009. {{files download="TCBB2009.pdf" text="PDF"}}
~- Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** [[http://nar.oxfordjournals.org/cgi/content/full/gkp625?ijkey=SRGbC88ZbnbWPme&keytype=ref Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data]].**--- //Nucleic Acids Research//, Vol. 37, No. 18, pp. 5943-5958, 2009. {{files download="NAR2009.pdf" text="PDF"}}
~- Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** [[http://www.liebertonline.com/doi/abs/10.1089/omi.2009.0040 A network biology study on circadian rhythm by integrating various omics data]].**--- //OMICS: A Journal of Integrative Biology,// Vol. 13, No. 4, 2009. {{files download="OMICS2009.pdf" text="PDF"}}
~- Yong Wang and Yu Xia,--- ** [[http://www.aporc.org/LNOR/9/OSB2008F42.pdf 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.--- **[[http://www.biomedcentral.com/1471-2105/8/391/abstract Analysis on multi-domain cooperation for predicting protein-protein interactions]].**--- //BMC Bioinformatics//, 8:391, 2007. {{files download="BMCBioinfo2007.pdf" text="PDF"}}
~- Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm465v1 Inferring transcriptional regulatory networks from high-throughput data]].**--- //Bioinformatics//, Vol. 23, pp. 3056-3064, 2007. {{files download="Bioinformatics2007.pdf" text="PDF"}}
~- Yong Wang, Trupti Joshi, Xiang-Sun. Zhang, Dong Xu and Luonan Chen.--- **[[http://www.springerlink.com/content/?k=Inference+of+Gene+Regulatory+Networks+by+Linear+Programming Supervised Inference of Gene Regulatory Networks by Linear Programming]].**--- Lecture Notes in Bioinformatics, Vol. 4115, pp. 551-561, 2006. {{files download="LNBI2006.pdf" text="PDF"}}
~- Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen.--- **[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/19/2413 Inferring gene regulatory networks from multiple microarray datasets]].**--- //Bioinformatics//, 22(19):2413-2420, 2006. {{files download="Bioinformatics2006.pdf" text="PDF"}}
~- Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen. --- **[[http://www.worldscinet.com/jbcb/03/0302/S0219720005001107.html Exploring protein's optimal HP configurations by self-organizing mapping]].**--- //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 2, pp. 385-400, 2005. {{files download="JBCB2005.pdf" text="PDF"}}
~- Full list of paper can be found [[http://scholar.google.com/citations?hl=en&user=M0fnh30AAAAJ Google Scholar]] or [[http://zhangroup.aporc.org/YongWang/files.xml?action=download&file=Yong+Wang+Vitae.pdf Here]]. Papers in bioinformatics and systems biology can be found in [[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=Yong+Wang+Academy+of+Mathematics+and+Systems+Science PubMed]]
=== Softwares ===
~- [[http://doc.aporc.org/wiki/GRNInfer GRNInfer: Gene Regulatory Network Inference by Integrating Multiple Datasets ]]
~- [[http://doc.aporc.org/wiki/GNTInfer GNTInfer Gene Regulatory Network and Drug Target Inference]]
~- [[http://doc.aporc.org/wiki/MDCInfer MDCInfer: Protein-Protein Interaction Prediction by Linear Programming]]
~- [[http://doc.aporc.org/wiki/MNAligner MNAligner: Network Alignment by Quadratic Programming]]
~- [[http://doc.aporc.org/wiki/Samo SAMO: Structure Alignment by Multi-objective Optimization model]]
~- [[http://app.aporc.org/NOA/ NOA: Network Ontology Analysis tool]]
~- [[http://doc.aporc.org/wiki/NetPredATC NetPredATC: Network Network Predicting Drug's ATC Code]]
=== Links ===
~- [[http://www.researcherid.com/rid/J-9193-2012 My Research ID]]
~- [[http://scholar.google.com/citations?hl=en&user=M0fnh30AAAAJ My Citation in Google]]
~- [[http://scholar.google.com Google Scholar]]
~- [[http://apps.newisiknowledge.com/UA_GeneralSearch.do ISI Web of Knowledge]]
~- [[http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]]
~- [[http://web.stanford.edu/group/wonglab/ Wonglab]]
~- [[http://intelligent.eic.osaka-sandai.ac.jp/ Chen Lab]]
~- [[http://xialab.bu.edu Yu Xia Lab]]
~- [[http://multimedia.mcb.harvard.edu/innerHi.swf Inner Life of the Cell]]
~- [[http://nook.cs.ucdavis.edu/~koehl/BioEbook/ Bio eBook]]
~- [[http://www.cbrc.jp/eng/organization/team_network.eng.html Prof. Horimoto's Team]]
~- [[http://people.gucas.ac.cn/~yongwang My Homepage in GUCAS]]
{{files}}
====== Dr. Yong Wang======
====== 王 勇 博士 ======
Professor of [[http://www.amt.ac.cn Institute of Applied Mathematics]], [[http://www.amss.ac.cn Academy of Mathematics and Systems Science]], [[http://www.cas.ac.cn Chinese Academy of Sciences]]
研究员, [[http://www.amt.ac.cn 应用数学研究所]], [[http://www.amss.ac.cn 数学与系统科学研究院]], [[http://www.cas.ac.cn 中国科学院]]
Email: ""<a href="mailto:ywang@amss.ac.cn">ywang@amss.ac.cn</a>""
Tel: +86(10)-82541372
[[http://wanglab.amss.ac.cn WangLab: Welcome to visit my Optimization and Computational Systems Biology Lab]]
=== Vitae ===
~- {{files download="YongWangVitaeChinese2013.pdf" text="科研简历 （PDF）"}}
~- {{files download="YongWangVitae2013.pdf" text="Curriculum Vitae （PDF）"}}
""<img src="images/users/YongReasearchSummary.jpg" style="float: right; margin: 1.0%; padding: 0.5%;">""
=== 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===
~- **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**, Rui Jiang, and Wing Hung Wong. ---**[[http://nsr.oxfordjournals.org/content/early/2016/04/19/nsr.nww025 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 **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**. ---**[[https://www.ncbi.nlm.nih.gov/pubmed/27172589 Identifying joint biomarker panel from multiple level dataset by an optimization model]]**--- //Biomarkers in Medicine//. 10(6),567-575. 2016.
~- Duren Zhana, **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**. ---**[[http://www.nature.com/articles/srep22656 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 **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**. ---**[[http://http://bioinformatics.oxfordjournals.org/ Computational probing protein-protein interactions targeting small molecules]]**--- //Bioinformatics//. 32: 226-234, 2016.
~- **[[http://zhangroup.aporc.org/MengZou Meng Zou]]**, Zhaoqi Liu, **[[http://zhangroup.aporc.org/XiangsunZhang Xiang-Sun Zhang]]**, and **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**. ---**[[http://bioinformatics.oxfordjournals.org/content/early/2015/07/08/bioinformatics.btv374.full 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.
~- **[[http://zhangroup.aporc.org/MengZou Meng Zou]]**, Pengjun Zhang, Xin-Yu Wen, Luonan Chen, Yaping Tian, and **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**. ---**[[http://www.sciencedirect.com/science/article/pii/S1046202315002042 A novel mixed integer programming for multi-biomarker panel identification by distinguishing malignant from benign colorectal tumors]]**--- //Methods//. Vol. 83, 3–17, 2015.
~- **[[http://zhangroup.aporc.org/JinxueXin Jingxue Xin]]**, **[[http://zhangroup.aporc.org/XianwenRen Xianwen Ren]]**, Luonan Chen and **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**. ---**[[http://www.biomedcentral.com/1755-8794/8/S2/S11/abstract Identifying network biomarkers based on protein-protein interactions and expression data]]**--- //BMC Medical Genomics//, 8(Suppl 2):S11， 2015
~- Pengjun Zhang, **[[http://zhangroup.aporc.org/MengZou Meng Zou]]**, Xinyu Wen, Feng Gu, Juan Li, Gaixia Liu, Jingxiao Dong, Xinxin Deng, Jing Gao, Xiaolong Li, Xingwang Jia, Zhennan Dong, Luonan Chen, **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**, Yaping Tian. --- **[[http://onlinelibrary.wiley.com/doi/10.1002/ijc.28584/abstract Development of Serum Parameters Panels for the Early Detection of Pancreatic Cancer]]** --- //International Journal of Cancer//, 134(11):2646-55, 2014.
~- **[[http://zhangroup.aporc.org/LinWang Lin Wang]]**, **[[http://zhangroup.aporc.org/YongWang Yong Wang]]**, Qinghua Hu, Shao Li. ---**[[http://www.nature.com/psp/journal/v3/n11/full/psp201444a.html 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*. --- ** [[http://www.nature.com/srep/2013/130724/srep02268/full/srep02268.html 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.--- ** [[http://nar.oxfordjournals.org/content/early/2013/06/12/nar.gkt343.full 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*. --- ** [[http://bioinformatics.oxfordjournals.org/content/early/2013/04/04/bioinformatics.btt158.long Network predicting drug's anatomical therapeutic chemical code. ]]**--- //Bioinformatics//, 2013 29: 1317-1324.
~- Yong Wang. --- ** [[http://www.ingentaconnect.com/content/ben/cbio/2013/00000008/00000001/art00013 Bioinformatics studies on induced pluripotent stem cell. ]]**--- //Current Bioinformatics//, 2013, Vol. 8. No. 1. 80--87. {{files download="CurrentBIO2013.pdf" text="PDF"}}
~- Xianwen Ren, Yong Wang*, Luonan Chen, Xiang-Sun Zhang, and Qi Jin.--- ** [[http://nar.oxfordjournals.org/content/41/4/e53.long 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. --- ** [[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6391257&tag=1 Inferring Gene Regulatory Network for Cell Reprogramming]]**---//Proceedings of The 31th Chinese Control Conference (CCC)//, pp. 7437-7442, 2012. {{files download="GRNiPSCCCC2012.pdf" text="PDF"}}
~- Yong Wang*, Qiao-Feng Wu, Chen Chen, Ling-Yun Wu, Xian-Zhong Yan, Shu-Guang Yu, Xiang-Sun Zhang, and Fan-Rong Liang.--- ** [[http://www.biomedcentral.com/1752-0509/6/S1/S15/abstract 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. ---**[[http://www.biomedcentral.com/1471-2105/13/70 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. ---**[[http://nar.oxfordjournals.org/content/early/2011/05/04/nar.gkr251 NOA: a novel network ontology analysis method]]**---//Nucleic Acids Research//, 39(13):e87, 2011.
~-Yong Wang, Katsuhisa Horimoto, Luonan Chen. ---**[[http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6001633&tag=1 An Integrated Pipeline for Gene Regulatory Network Inference]]**---//Proceedings of The 30th Chinese Control Conference (CCC)//, pp. 6593-6598, 2011. {{files download="Pipeline.pdf" text="PDF"}}
~- Yong Wang, Eric Franzosa, Xiang-Sun Zhang, and Yu Xia. ---**[[http://nar.oxfordjournals.org/content/38/18/5959 Protein evolution in yeast transcription factor subnetworks]]**--- //Nucleic Acids Research//, 38(18): 5959–5969, 2010. {{files download="NAR2010.pdf" text="PDF"}}
~- Yong Wang, Rui-Sheng Wang, Trupti Joshi, Dong Xu, Xiang-Sun Zhang, Luonan Chen, and Yu Xia. --- **[[http://www.igi-global.com/reference/details.asp?ID=34877&v=tableOfContents 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. {{files download="CMGRN2009.pdf" text="PDF"}}
~- Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, and Luonan Chen.--- **[[http://www.computer.org/portal/web/csdl/doi/10.1109/TCBB.2007.70250 Evaluating protein similarity from coarse structures]].**--- //IEEE/ACM Transactions on Computational Biology and Bioinformatics,// Vol. 6, No. 4, pp. 583-593, 2009. {{files download="TCBB2009.pdf" text="PDF"}}
~- Yong Wang, Xiang-Sun Zhang, and Yu Xia.--- ** [[http://nar.oxfordjournals.org/cgi/content/full/gkp625?ijkey=SRGbC88ZbnbWPme&keytype=ref Predicting eukaryotic transcriptional cooperativity by Bayesian network integration of genome-wide data]].**--- //Nucleic Acids Research//, Vol. 37, No. 18, pp. 5943-5958, 2009. {{files download="NAR2009.pdf" text="PDF"}}
~- Yong Wang, Xiang-Sun Zhang, and Luonan Chen.--- ** [[http://www.liebertonline.com/doi/abs/10.1089/omi.2009.0040 A network biology study on circadian rhythm by integrating various omics data]].**--- //OMICS: A Journal of Integrative Biology,// Vol. 13, No. 4, 2009. {{files download="OMICS2009.pdf" text="PDF"}}
~- Yong Wang and Yu Xia,--- ** [[http://www.aporc.org/LNOR/9/OSB2008F42.pdf 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.--- **[[http://www.biomedcentral.com/1471-2105/8/391/abstract Analysis on multi-domain cooperation for predicting protein-protein interactions]].**--- //BMC Bioinformatics//, 8:391, 2007. {{files download="BMCBioinfo2007.pdf" text="PDF"}}
~- Rui-Sheng Wang, Yong Wang, Xiang-Sun Zhang, Luonan Chen.--- **[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btm465v1 Inferring transcriptional regulatory networks from high-throughput data]].**--- //Bioinformatics//, Vol. 23, pp. 3056-3064, 2007. {{files download="Bioinformatics2007.pdf" text="PDF"}}
~- Yong Wang, Trupti Joshi, Xiang-Sun. Zhang, Dong Xu and Luonan Chen.--- **[[http://www.springerlink.com/content/?k=Inference+of+Gene+Regulatory+Networks+by+Linear+Programming Supervised Inference of Gene Regulatory Networks by Linear Programming]].**--- Lecture Notes in Bioinformatics, Vol. 4115, pp. 551-561, 2006. {{files download="LNBI2006.pdf" text="PDF"}}
~- Yong Wang, Trupti Joshi, Xiang-Sun Zhang, Dong Xu, and Luonan Chen.--- **[[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/19/2413 Inferring gene regulatory networks from multiple microarray datasets]].**--- //Bioinformatics//, 22(19):2413-2420, 2006. {{files download="Bioinformatics2006.pdf" text="PDF"}}
~- Xiang-Sun Zhang, Yong Wang, Zhong-Wei Zhan, Ling-Yun Wu, and Luonan Chen. --- **[[http://www.worldscinet.com/jbcb/03/0302/S0219720005001107.html Exploring protein's optimal HP configurations by self-organizing mapping]].**--- //Journal of Bioinformatics and Computational Biology//, Vol. 3, No. 2, pp. 385-400, 2005. {{files download="JBCB2005.pdf" text="PDF"}}
~- Full list of paper can be found [[http://scholar.google.com/citations?hl=en&user=M0fnh30AAAAJ Google Scholar]] or [[http://zhangroup.aporc.org/YongWang/files.xml?action=download&file=Yong+Wang+Vitae.pdf Here]]. Papers in bioinformatics and systems biology can be found in [[http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=DetailsSearch&term=Yong+Wang+Academy+of+Mathematics+and+Systems+Science PubMed]]
=== Softwares ===
~- [[http://doc.aporc.org/wiki/GRNInfer GRNInfer: Gene Regulatory Network Inference by Integrating Multiple Datasets ]]
~- [[http://doc.aporc.org/wiki/GNTInfer GNTInfer Gene Regulatory Network and Drug Target Inference]]
~- [[http://doc.aporc.org/wiki/MDCInfer MDCInfer: Protein-Protein Interaction Prediction by Linear Programming]]
~- [[http://doc.aporc.org/wiki/MNAligner MNAligner: Network Alignment by Quadratic Programming]]
~- [[http://doc.aporc.org/wiki/Samo SAMO: Structure Alignment by Multi-objective Optimization model]]
~- [[http://app.aporc.org/NOA/ NOA: Network Ontology Analysis tool]]
~- [[http://doc.aporc.org/wiki/NetPredATC NetPredATC: Network Network Predicting Drug's ATC Code]]
=== Links ===
~- [[http://www.researcherid.com/rid/J-9193-2012 My Research ID]]
~- [[http://scholar.google.com/citations?hl=en&user=M0fnh30AAAAJ My Citation in Google]]
~- [[http://scholar.google.com Google Scholar]]
~- [[http://apps.newisiknowledge.com/UA_GeneralSearch.do ISI Web of Knowledge]]
~- [[http://www.ncbi.nlm.nih.gov/pubmed/ PubMed]]
~- [[http://web.stanford.edu/group/wonglab/ Wonglab]]
~- [[http://intelligent.eic.osaka-sandai.ac.jp/ Chen Lab]]
~- [[http://xialab.bu.edu Yu Xia Lab]]
~- [[http://multimedia.mcb.harvard.edu/innerHi.swf Inner Life of the Cell]]
~- [[http://nook.cs.ucdavis.edu/~koehl/BioEbook/ Bio eBook]]
~- [[http://www.cbrc.jp/eng/organization/team_network.eng.html Prof. Horimoto's Team]]
~- [[http://people.gucas.ac.cn/~yongwang My Homepage in GUCAS]]
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