Wiki source for ShihuaZhang
[[http://zhangroup.aporc.org/ZhangShihua Chinese Page]]
""<img src="images/users/shzhang.jpg" alt="shihua.jpg" style="float: left; margin: 1.0%; padding: 0.5%;">""
====== Shihua Zhang ======
Assistant Professor of Academy of Mathematics and Systems Science, CAS
''Address:'' No.55, Zhongguancun East road, Beijing 100190, China
''Tel:'' 86-10-62616670
''Email:'' zsh@amss.ac.cn
::c::----
Shihua Zhang was born on May, 1980 in Shandong Province, China. Now he is Assistant Professor of the Institute of Applied Mathematics, Academy of Mathematics and Systems Science, at CAS. His interests are within Bioinformatics and Systems Biology, particularly in Biological network-related issues. He has published over 30 technical papers in the refereed journals and conference proceedings such as in Proteomics, Bioinformatics, PLoS Comput. Bio., Plos ONE, Computational Biology and Chemistry, BMC Structural Biology, Physical Review E, European Physical Journal B, Physica A.
See me on [[http://scholar.google.com/citations?hl=en&user=81AqAAYAAAAJ Google Scholar]] or [[http://www.researcherid.com/ProfileView.action?queryString=KG0UuZjN5WlbNDYeE9y49KKU1f%2FTG%2B4MHO2msi8BW3A%3D&SrcApp=CR&returnCode=ROUTER.Unauthorized& ISI]]
==={{color fg="white" bg="gray" text="Positions"}}===
~- 6/2008 - present, Assistant Professor.
~~& [[http://www.amss.ac.cn Academy of Mathematics and Systems Science]], Chinese Academy of Science (Beijing, China).
~-7/2008 - 12/2010, Postdoctoral Fellow.
~~&[[http://www.cmb.usc.edu/ Program in Molecular and Computational Biology]], Department of Biological Sciences, University of Southern California (Los Angeles, USA).
==={{color fg="white" bg="gray" text="Educational Background"}}===
~- 9/1999 - 7/2003, Bachelor of Science in Applied Mathematics,
~~& School of Mathematics and Statistics, Yunnan University (Kunming, Yunnan, China)
~- 9/2003 - 6/2008, PhD of Operational Research and Control (PhD-direct student),
~~& [[http://www.amss.ac.cn Academy of Mathematics and Systems Science]], Chinese Academy of Science (Beijing, China)
==={{color fg="white" bg="gray" text="Research Interests"}}===
~-Bioinformatics/Systems Biology
~~&Modeling and algorithms for molecular networks
~~&Integrative analysis of molecular networks with other biological data
~~&Algorithms for protein structures comparison and assemblies determination
~~&Modeling and algorithms for integration of multiple 'omic' data
~~&Computational methods for epigenomics
~-Complex networks/Network science
~~&Community structure in complex networks
~~&Structure and dynamics of networks
==={{color fg="white" bg="gray" text="Selected Publications"}}===
~- Discovery of multi-dimensional modules by integrative analysis of cancer genomic data.
~~& __Shihua Zhang__, Chun-Chi Liu, Wenyuan Li, Hui Shen, Peter Laird, Xianghong Jasmine Zhou.
~~& In submission, 2011.
~- Discovering multi-dimensional regulatory modules by a sparse multi-block partial least square regression method.
~~& Wenyuan Li*, __Shihua Zhang__*, Chun-Chi Liu, Xianghong Jasmine Zhou (*Co-first authors).
~~& Bioinformatics, in revision, 2012.
~- Common community Structure in Time-varying Networks.
~~& __Shihua Zhang__, Junfei Zhao, Xiang-Sun Zhang.
~~& [[http://pre.aps.org/abstract/PRE/v85/i5/e056110 Physical Review E]], 85, 056110, 2012. e-print:[[http://arxiv.org/abs/1111.1365v2 arXiv:1111.1365v2]].
~- A novel computational framework for simultaneous integration of multiple functional genomic data to identify microRNA-gene regulatory modules.
~~& __Shihua Zhang__, Qingjiao Li, Juan Liu, Xianghong Jasmine Zhou
~~& Bioinformatics (ISMB2011), 2011, 27:i401-i409. [[http://bioinformatics.oxfordjournals.org/content/27/13/i401.short?rss=1 PDF]]
~- Exploring the spatial and temporal organization of a cell’s proteome
~~& Martin Beck, Maya Topf, Zachary Frazier, Harianto Tjong, Min Xu, __Shihua Zhang__ and Frank Alber.
~~& Journal of Structural Biology, 2011, 173(3):483-496. [[http://www.ncbi.nlm.nih.gov/pubmed/21094684 PDF]]
~- A fast mathematical programming procedure for simultaneous fitting of assembly components into cryo-EM density maps.
~~& __Shihua Zhang__, Daven Vasishtan, Min Xu, Maya Topf, Frank Alber.
~~& Bioinformatics (ISMB2010), 2010, 26(12):i261-i268. [[http://f1000biology.com/article/id/3524956/evaluation Faculty of 1000 Biology]]
~- Determining modular organization of protein interaction networks by maximizing modularity density.
~~& __Shihua Zhang__, Xue-Mei Ning, Chris Ding, Xiang-Sun Zhang.
~~& BMC Systems Biology, 2010, 4:S10.
~- Detecting disease associated modules and prioritizing active genes based on high throughput data.
~~& Yu-Qing Qiu*, __Shihua Zhang__*, Xiang-Sun Zhang, Luonan Chen (*Co-first authors).
~~& [[http://www.biomedcentral.com/1471-2105/11/26 BMC Bioinformatics]], 11:26, 2010. doi:10.1186/1471-2105-11-26. [[http://www.biomedcentral.com/info/about/mostviewed/ Highly accessed]]
~- Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.
~~& Ji-Guang Wang, __Shihua Zhang__, Yong Wang, Xiang-Sun Zhang, Luonan Chen.
~~& [[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000521 PLoS Computational Biology]], 5(9): e1000521. doi:10.1371/journal.pcbi.1000521.
~- Identifying differentially expressed pathways based on a mixed integer linear programming model.
~~& Qiu Yuqing, __Shihua Zhang__, Xiang-Sun Zhang, Luonan Chen.
~~& IET Systems Biology, 3(6), 475-486, 2009.
~- Quantitative function for community detection.
~~& Zhenping Li*, __Shihua Zhang__*, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen (*Co-first authors).
~~&[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PLEEE8000077000003036109000001&idtype=cvips&gifs=yes Physical Review E]], 77, 036109, 2008.
~~&It has been selected by [[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=VIRT02000015000006000091000001&idtype=cvips&gifs=Yes Virtual Journal of Biological Physics Research]], 15(6), 2008.
~- Biomolecular network querying: a promising approach in systems biology.
~~&__Shihua Zhang__, Xiang-Sun Zhang and Luonan Chen.
~~&[[http://www.biomedcentral.com/bmcsystbiol/ BMC Systems Biology]], 2008, 2:5. doi:10.1186/1752-0509-2-5. (Complementary). [[http://www.biomedcentral.com/info/about/mostviewed/ Highly accessed]]
~- Discovering functions and revealing mechanisms at molecular level from biological networks.
~~&__Shihua Zhang__, Guanxu Jin, Xiang-Sun Zhang and Luonan Chen.
~~&[[http://www3.interscience.wiley.com/cgi-bin/abstract/115804878/ABSTRACT Proteomics]], 7(16), 2856-69, 2007.
~- Alignment of molecular networks by integer quadratic programming.
~~& Zhenping Li*, __Shihua Zhang__*, Yong Wang, Xiang-Sun Zhang and Luonan Chen (*Co-first authors).
~~& [[http://bioinformatics.oxfordjournals.org/ Bioinformatics]], [[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/1631 23(13):1631-1639, 2007; doi:10.1093/bioinformatics/btm156]].
~- A hybrid graph-theoretic method for mining overlapping functional modules in large sparse protein interaction networks.
~~&__Shihua Zhang__, Hong-Wei Liu, Xue-Mei Ning and Xiang-Sun Zhang.
~~& [[http://www.inderscience.com/browse/index.php?journalID=189 International Journal of Data Mining and Bioinformatics]], 3(1), 68-84, 2009.
~- Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast.
~~& Guangxu Jin, __Shihua Zhang__, Xiang-Sun Zhang, Luonan Chen
~~& [[http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0001207 PLoS ONE]] 2(11): e1207, 2007. doi:10.1371/journal.pone.0001207.
~-[[http://link.aps.org/abstract/PRE/v76/e046103 Uncovering fuzzy community structure in complex networks]]
~~&__Shihua Zhang__, Rui-Sheng Wang, Xiang-Sun Zhang
~~&[[http://pre.aps.org/ Physical Review E]], 76, 046103, 2007.
~~&It has been selected by [[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=VIRT02000014000008000128000001&idtype=cvips&gifs=Yes Virtual Journal of Biological Physics Research]], 14(8), 2007.
~- Graph kernels, hierarchical clustering, network community structure: experiment and comparative analysis.
~~& __Shihua Zhang__, Xue-Mei Ning and Xiang-Sun Zhang.
~~&[[http://www.edpsciences.org/articles/epjb/abs/2007/09/b06444/b06444.html European Physical Journal B]], 57, 67-74, 2007.
~- Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures
~~&Rui-Sheng Wang, __Shihua Zhang__, Yong Wang, Xiang-Sun Zhang, Luonan Chen
~~&[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V10-4TC34VB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=10&md5=b29f71dd1b7f09ca3abc6d2f20f3ab12 Neurocomputing]], 72, 134-141, 2008.
~-[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TVG-4KKFYKY-3&_user=5361375&_coverDate=01%2F15%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000066948&_version=1&_urlVersion=0&_userid=5361375&md5=d293363358012e4536deb99ca67bbd3a Identification of overlapping community structure in complex networks using fuzzy c-means clustering]]
~~& __Shihua Zhang__, Rui-Sheng Wang, and Xiang-Sun Zhang
~~& [[http://www.elsevier.com/wps/find/journaldescription.cws_home/505702/description#description Physica A: Statistical Mechanics and its Applictions]], 2007, 374, 483–490
~- Detecting community structure in complex networks based on a measure of information discrepancy.
~~& Junhua Zhang, __Shihua Zhang__, Xiang-Sun Zhang
~~& [[http://www.elsevier.com/wps/find/journaldescription.cws_home/505702/description#description Physica A: Statistical Mechanics and its Applictions]], 2008, 387(7), 1675-1682. [[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TVG-4R1KVP1-3&_user=1999482&_coverDate=11%2F01%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050602&_version=1&_urlVersion=0&_userid=1999482&md5=729e027bf020f4a34520979ca4c47860 doi:10.1016/j.physa.2007.10.061]].
~-[[http://www.springerlink.com/content/gp6861366h541474/?p=1bdd55bce8a644eaaccdb7ece73033b4&pi=0 Identifying modules in complex networks by a graph-theoretical method and its application in protein interaction networks]]
~~& Rui-Sheng Wang, __Shihua Zhang__, Xiang-Sun Zhang, Luonan Chen
~~& [[http://www.springer.com/east/home?SGWID=5-102-69-173621840-0&changeHeader=true&SHORTCUT=www.springer.com/series/1244 Lecture Notes in Artificial Intelligence]], 4682, 1090-1101, 2007.
~- Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.
~~& Luonan Chen, Ling-Yun Wu, Yong Wang, __Shihua Zhang__ and Xiang-Sun Zhang.
~~&[[http://www.biomedcentral.com/1472-6807/6/18 BMC Structural Biology]], 2006, 6:18. [[http://www.biomedcentral.com/info/about/mostviewed/ Highly accessed]]
~- Identification of functional modules in a PPI network by clique percolation clustering.
~~& __Shihua Zhang__, Xue-Mei Ning and Xiang-Sun Zhang.
~~& [[http://www.elsevier.com/wps/find/journaldescription.cws_home/627320/description#description Computational biology and chemistry]], 30(6), 445-451, 2006.
~- Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods.
~~&__Shihua Zhang__, Xue-Mei Ning, Hong-Wei Liu, and Xiang-Sun Zhang.
~~&[[http://www.springer.com/west/home/life+sci/bioinformatics?SGWID=4-10031-69-173623629-0 Lecture Notes in Bioinformatics]], 4115, 514-524, 2006.
----
==={{color fg="white" bg="gray" text="Honors and Awards"}}===
~- [[http://www.cdgdc.edu.cn/xwyyjsjyxx/zlpj/pgpsdtxx/267995.shtml National Excellent PhD thesis Award]], 2010.
~- [[http://www.pe.cas.cn/jypx/qgyxbsxwlw/200909/t20090921_2513751.html Excellent PhD thesis Award of Chinese Academy of Science]], 2009.
~- [[http://www.sciencenet.cn/htmlnews/2008/5/207177.html Top Grade Presidential Award of Chinese Academy of Science]], 2008.
~- BHPB Scholarship of Graduate University of Chinese Academy of Science, 2007.
~- Baojie Excellent PhD student Scholarship of Chinese Academy of Science, 2007.
~- Baogang Scholarship, 2003.
==={{color fg="white" bg="gray" text="Research Projects"}}===
~-Research on Some Important Problems in Bioinformatics (2005-2008)
~~& Important Direction Research Grant, Chinese Academy of Sciences (CAS), Joint Investigator.
~- Research on Models and Algorithms of Haplotype Inference Problem in Bioinformatics (2006-2008).
~~& National Natural Science Foundation of China (NSFC), Grant No. 60503004, Joint Inverstigator
~-Research on theory and algorithms of community detection in complex networks (2008-2010)
~~& National Natural Science Foundation of China (NSFC), Grant No. 10701080, Joint Investigator
==={{color fg="white" bg="gray" text="Index and Journals"}}===
~-[[http://apps.isiknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=2DOANfgOkP5@2KbHPKF&preferencesSaved= ISI Web of Knowledge]]
~-[[http://www.engineeringvillage2.org.cn/controller/servlet/Controller?CID=quickSearch&database=1 EI Engineering Village 2]]
~-[[Journal Journal and Conference Information]]
~-[[http://www.ieee.org/portal/pages/about/whatis/code.html;jsessionid=FN2W3vGDLyFn02PN3GTWfKph2vtlMG3LqlhDnB2GdHvLDlVYJXXr!931003289 IEEE Code of Ethics]]
==={{color fg="white" bg="gray" text="Useful links"}}===
~-[[http://zhangroup.aporc.org/ShihuaZhang/Bioinformatics_Lab]]
~- [[http://www.binf.umn.edu/whatsbinf.html Bioinformatics]]
~- [[http://stommel.tamu.edu/~baum/toolboxes.html Matlab toolbox]]
~- [[http://www.ee.columbia.edu/~marios/matlab/matlab_tricks.html Matlab tips and tricks]]
~- [[http://www.ctex.org CTEX.ORG]]
~- [[http://mathworld.wolfram.com/ Mathworld]]
~- [[http://www.cs.cmu.edu/~mleone/how-to.html]]
~- [[http://www.oakland.edu/enp/ Erdös Number]]
~- [[http://cyvision.if.sc.usp.br/~francisco/networks/softwares.htm Complex networks]]
~-[[http://mathworld.wolfram.com/ Mathematics resource]]
==={{color fg="white" bg="gray" text="Aphorism"}}===
~-"The whole of science is nothing more than a refinement of everyday thinking." —— Albert Einstein (1879-1955)
~-"In science, the important thing is to modify and change one’s ideas as science advances." —— Herbert Spencer (1820–1903)
~-"The good life is one inspired by love and guided by knowledge." —— Betrand Russell
~-"The difficulty lies, not in the new ideas, but in escaping the old ones, which ramify, for those brought up as most of us have been, into every corner of our minds.." ——John Maynard Keynes (1883 - 1946)
~-"Life is like riding a bicycle. To keep your balance, you must keep moving." —— Albert Einstein (1879-1955)
~-"It's not your aptitude but your attitude that determines your altitude in life." —— Jesse Jackson
~-"People can be divided into three classes, the few who make things happen, the many who watch things happen, and the overwhelming majority who have no idea what has happened."
""<img src="images/users/shzhang.jpg" alt="shihua.jpg" style="float: left; margin: 1.0%; padding: 0.5%;">""
====== Shihua Zhang ======
Assistant Professor of Academy of Mathematics and Systems Science, CAS
''Address:'' No.55, Zhongguancun East road, Beijing 100190, China
''Tel:'' 86-10-62616670
''Email:'' zsh@amss.ac.cn
::c::----
Shihua Zhang was born on May, 1980 in Shandong Province, China. Now he is Assistant Professor of the Institute of Applied Mathematics, Academy of Mathematics and Systems Science, at CAS. His interests are within Bioinformatics and Systems Biology, particularly in Biological network-related issues. He has published over 30 technical papers in the refereed journals and conference proceedings such as in Proteomics, Bioinformatics, PLoS Comput. Bio., Plos ONE, Computational Biology and Chemistry, BMC Structural Biology, Physical Review E, European Physical Journal B, Physica A.
See me on [[http://scholar.google.com/citations?hl=en&user=81AqAAYAAAAJ Google Scholar]] or [[http://www.researcherid.com/ProfileView.action?queryString=KG0UuZjN5WlbNDYeE9y49KKU1f%2FTG%2B4MHO2msi8BW3A%3D&SrcApp=CR&returnCode=ROUTER.Unauthorized& ISI]]
==={{color fg="white" bg="gray" text="Positions"}}===
~- 6/2008 - present, Assistant Professor.
~~& [[http://www.amss.ac.cn Academy of Mathematics and Systems Science]], Chinese Academy of Science (Beijing, China).
~-7/2008 - 12/2010, Postdoctoral Fellow.
~~&[[http://www.cmb.usc.edu/ Program in Molecular and Computational Biology]], Department of Biological Sciences, University of Southern California (Los Angeles, USA).
==={{color fg="white" bg="gray" text="Educational Background"}}===
~- 9/1999 - 7/2003, Bachelor of Science in Applied Mathematics,
~~& School of Mathematics and Statistics, Yunnan University (Kunming, Yunnan, China)
~- 9/2003 - 6/2008, PhD of Operational Research and Control (PhD-direct student),
~~& [[http://www.amss.ac.cn Academy of Mathematics and Systems Science]], Chinese Academy of Science (Beijing, China)
==={{color fg="white" bg="gray" text="Research Interests"}}===
~-Bioinformatics/Systems Biology
~~&Modeling and algorithms for molecular networks
~~&Integrative analysis of molecular networks with other biological data
~~&Algorithms for protein structures comparison and assemblies determination
~~&Modeling and algorithms for integration of multiple 'omic' data
~~&Computational methods for epigenomics
~-Complex networks/Network science
~~&Community structure in complex networks
~~&Structure and dynamics of networks
==={{color fg="white" bg="gray" text="Selected Publications"}}===
~- Discovery of multi-dimensional modules by integrative analysis of cancer genomic data.
~~& __Shihua Zhang__, Chun-Chi Liu, Wenyuan Li, Hui Shen, Peter Laird, Xianghong Jasmine Zhou.
~~& In submission, 2011.
~- Discovering multi-dimensional regulatory modules by a sparse multi-block partial least square regression method.
~~& Wenyuan Li*, __Shihua Zhang__*, Chun-Chi Liu, Xianghong Jasmine Zhou (*Co-first authors).
~~& Bioinformatics, in revision, 2012.
~- Common community Structure in Time-varying Networks.
~~& __Shihua Zhang__, Junfei Zhao, Xiang-Sun Zhang.
~~& [[http://pre.aps.org/abstract/PRE/v85/i5/e056110 Physical Review E]], 85, 056110, 2012. e-print:[[http://arxiv.org/abs/1111.1365v2 arXiv:1111.1365v2]].
~- A novel computational framework for simultaneous integration of multiple functional genomic data to identify microRNA-gene regulatory modules.
~~& __Shihua Zhang__, Qingjiao Li, Juan Liu, Xianghong Jasmine Zhou
~~& Bioinformatics (ISMB2011), 2011, 27:i401-i409. [[http://bioinformatics.oxfordjournals.org/content/27/13/i401.short?rss=1 PDF]]
~- Exploring the spatial and temporal organization of a cell’s proteome
~~& Martin Beck, Maya Topf, Zachary Frazier, Harianto Tjong, Min Xu, __Shihua Zhang__ and Frank Alber.
~~& Journal of Structural Biology, 2011, 173(3):483-496. [[http://www.ncbi.nlm.nih.gov/pubmed/21094684 PDF]]
~- A fast mathematical programming procedure for simultaneous fitting of assembly components into cryo-EM density maps.
~~& __Shihua Zhang__, Daven Vasishtan, Min Xu, Maya Topf, Frank Alber.
~~& Bioinformatics (ISMB2010), 2010, 26(12):i261-i268. [[http://f1000biology.com/article/id/3524956/evaluation Faculty of 1000 Biology]]
~- Determining modular organization of protein interaction networks by maximizing modularity density.
~~& __Shihua Zhang__, Xue-Mei Ning, Chris Ding, Xiang-Sun Zhang.
~~& BMC Systems Biology, 2010, 4:S10.
~- Detecting disease associated modules and prioritizing active genes based on high throughput data.
~~& Yu-Qing Qiu*, __Shihua Zhang__*, Xiang-Sun Zhang, Luonan Chen (*Co-first authors).
~~& [[http://www.biomedcentral.com/1471-2105/11/26 BMC Bioinformatics]], 11:26, 2010. doi:10.1186/1471-2105-11-26. [[http://www.biomedcentral.com/info/about/mostviewed/ Highly accessed]]
~- Disease-aging network reveals significant roles of aging genes in connecting genetic diseases.
~~& Ji-Guang Wang, __Shihua Zhang__, Yong Wang, Xiang-Sun Zhang, Luonan Chen.
~~& [[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000521 PLoS Computational Biology]], 5(9): e1000521. doi:10.1371/journal.pcbi.1000521.
~- Identifying differentially expressed pathways based on a mixed integer linear programming model.
~~& Qiu Yuqing, __Shihua Zhang__, Xiang-Sun Zhang, Luonan Chen.
~~& IET Systems Biology, 3(6), 475-486, 2009.
~- Quantitative function for community detection.
~~& Zhenping Li*, __Shihua Zhang__*, Rui-Sheng Wang, Xiang-Sun Zhang and Luonan Chen (*Co-first authors).
~~&[[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PLEEE8000077000003036109000001&idtype=cvips&gifs=yes Physical Review E]], 77, 036109, 2008.
~~&It has been selected by [[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=VIRT02000015000006000091000001&idtype=cvips&gifs=Yes Virtual Journal of Biological Physics Research]], 15(6), 2008.
~- Biomolecular network querying: a promising approach in systems biology.
~~&__Shihua Zhang__, Xiang-Sun Zhang and Luonan Chen.
~~&[[http://www.biomedcentral.com/bmcsystbiol/ BMC Systems Biology]], 2008, 2:5. doi:10.1186/1752-0509-2-5. (Complementary). [[http://www.biomedcentral.com/info/about/mostviewed/ Highly accessed]]
~- Discovering functions and revealing mechanisms at molecular level from biological networks.
~~&__Shihua Zhang__, Guanxu Jin, Xiang-Sun Zhang and Luonan Chen.
~~&[[http://www3.interscience.wiley.com/cgi-bin/abstract/115804878/ABSTRACT Proteomics]], 7(16), 2856-69, 2007.
~- Alignment of molecular networks by integer quadratic programming.
~~& Zhenping Li*, __Shihua Zhang__*, Yong Wang, Xiang-Sun Zhang and Luonan Chen (*Co-first authors).
~~& [[http://bioinformatics.oxfordjournals.org/ Bioinformatics]], [[http://bioinformatics.oxfordjournals.org/cgi/content/abstract/23/13/1631 23(13):1631-1639, 2007; doi:10.1093/bioinformatics/btm156]].
~- A hybrid graph-theoretic method for mining overlapping functional modules in large sparse protein interaction networks.
~~&__Shihua Zhang__, Hong-Wei Liu, Xue-Mei Ning and Xiang-Sun Zhang.
~~& [[http://www.inderscience.com/browse/index.php?journalID=189 International Journal of Data Mining and Bioinformatics]], 3(1), 68-84, 2009.
~- Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast.
~~& Guangxu Jin, __Shihua Zhang__, Xiang-Sun Zhang, Luonan Chen
~~& [[http://www.plosone.org/article/fetchArticle.action?articleURI=info:doi/10.1371/journal.pone.0001207 PLoS ONE]] 2(11): e1207, 2007. doi:10.1371/journal.pone.0001207.
~-[[http://link.aps.org/abstract/PRE/v76/e046103 Uncovering fuzzy community structure in complex networks]]
~~&__Shihua Zhang__, Rui-Sheng Wang, Xiang-Sun Zhang
~~&[[http://pre.aps.org/ Physical Review E]], 76, 046103, 2007.
~~&It has been selected by [[http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=VIRT02000014000008000128000001&idtype=cvips&gifs=Yes Virtual Journal of Biological Physics Research]], 14(8), 2007.
~- Graph kernels, hierarchical clustering, network community structure: experiment and comparative analysis.
~~& __Shihua Zhang__, Xue-Mei Ning and Xiang-Sun Zhang.
~~&[[http://www.edpsciences.org/articles/epjb/abs/2007/09/b06444/b06444.html European Physical Journal B]], 57, 67-74, 2007.
~- Clustering complex networks and biological networks by Nonnegative Matrix Factorization with various similarity measures
~~&Rui-Sheng Wang, __Shihua Zhang__, Yong Wang, Xiang-Sun Zhang, Luonan Chen
~~&[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6V10-4TC34VB-1&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_version=1&_urlVersion=0&_userid=10&md5=b29f71dd1b7f09ca3abc6d2f20f3ab12 Neurocomputing]], 72, 134-141, 2008.
~-[[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TVG-4KKFYKY-3&_user=5361375&_coverDate=01%2F15%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000066948&_version=1&_urlVersion=0&_userid=5361375&md5=d293363358012e4536deb99ca67bbd3a Identification of overlapping community structure in complex networks using fuzzy c-means clustering]]
~~& __Shihua Zhang__, Rui-Sheng Wang, and Xiang-Sun Zhang
~~& [[http://www.elsevier.com/wps/find/journaldescription.cws_home/505702/description#description Physica A: Statistical Mechanics and its Applictions]], 2007, 374, 483–490
~- Detecting community structure in complex networks based on a measure of information discrepancy.
~~& Junhua Zhang, __Shihua Zhang__, Xiang-Sun Zhang
~~& [[http://www.elsevier.com/wps/find/journaldescription.cws_home/505702/description#description Physica A: Statistical Mechanics and its Applictions]], 2008, 387(7), 1675-1682. [[http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6TVG-4R1KVP1-3&_user=1999482&_coverDate=11%2F01%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050602&_version=1&_urlVersion=0&_userid=1999482&md5=729e027bf020f4a34520979ca4c47860 doi:10.1016/j.physa.2007.10.061]].
~-[[http://www.springerlink.com/content/gp6861366h541474/?p=1bdd55bce8a644eaaccdb7ece73033b4&pi=0 Identifying modules in complex networks by a graph-theoretical method and its application in protein interaction networks]]
~~& Rui-Sheng Wang, __Shihua Zhang__, Xiang-Sun Zhang, Luonan Chen
~~& [[http://www.springer.com/east/home?SGWID=5-102-69-173621840-0&changeHeader=true&SHORTCUT=www.springer.com/series/1244 Lecture Notes in Artificial Intelligence]], 4682, 1090-1101, 2007.
~- Revealing divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison.
~~& Luonan Chen, Ling-Yun Wu, Yong Wang, __Shihua Zhang__ and Xiang-Sun Zhang.
~~&[[http://www.biomedcentral.com/1472-6807/6/18 BMC Structural Biology]], 2006, 6:18. [[http://www.biomedcentral.com/info/about/mostviewed/ Highly accessed]]
~- Identification of functional modules in a PPI network by clique percolation clustering.
~~& __Shihua Zhang__, Xue-Mei Ning and Xiang-Sun Zhang.
~~& [[http://www.elsevier.com/wps/find/journaldescription.cws_home/627320/description#description Computational biology and chemistry]], 30(6), 445-451, 2006.
~- Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods.
~~&__Shihua Zhang__, Xue-Mei Ning, Hong-Wei Liu, and Xiang-Sun Zhang.
~~&[[http://www.springer.com/west/home/life+sci/bioinformatics?SGWID=4-10031-69-173623629-0 Lecture Notes in Bioinformatics]], 4115, 514-524, 2006.
----
==={{color fg="white" bg="gray" text="Honors and Awards"}}===
~- [[http://www.cdgdc.edu.cn/xwyyjsjyxx/zlpj/pgpsdtxx/267995.shtml National Excellent PhD thesis Award]], 2010.
~- [[http://www.pe.cas.cn/jypx/qgyxbsxwlw/200909/t20090921_2513751.html Excellent PhD thesis Award of Chinese Academy of Science]], 2009.
~- [[http://www.sciencenet.cn/htmlnews/2008/5/207177.html Top Grade Presidential Award of Chinese Academy of Science]], 2008.
~- BHPB Scholarship of Graduate University of Chinese Academy of Science, 2007.
~- Baojie Excellent PhD student Scholarship of Chinese Academy of Science, 2007.
~- Baogang Scholarship, 2003.
==={{color fg="white" bg="gray" text="Research Projects"}}===
~-Research on Some Important Problems in Bioinformatics (2005-2008)
~~& Important Direction Research Grant, Chinese Academy of Sciences (CAS), Joint Investigator.
~- Research on Models and Algorithms of Haplotype Inference Problem in Bioinformatics (2006-2008).
~~& National Natural Science Foundation of China (NSFC), Grant No. 60503004, Joint Inverstigator
~-Research on theory and algorithms of community detection in complex networks (2008-2010)
~~& National Natural Science Foundation of China (NSFC), Grant No. 10701080, Joint Investigator
==={{color fg="white" bg="gray" text="Index and Journals"}}===
~-[[http://apps.isiknowledge.com/UA_GeneralSearch_input.do?product=UA&search_mode=GeneralSearch&SID=2DOANfgOkP5@2KbHPKF&preferencesSaved= ISI Web of Knowledge]]
~-[[http://www.engineeringvillage2.org.cn/controller/servlet/Controller?CID=quickSearch&database=1 EI Engineering Village 2]]
~-[[Journal Journal and Conference Information]]
~-[[http://www.ieee.org/portal/pages/about/whatis/code.html;jsessionid=FN2W3vGDLyFn02PN3GTWfKph2vtlMG3LqlhDnB2GdHvLDlVYJXXr!931003289 IEEE Code of Ethics]]
==={{color fg="white" bg="gray" text="Useful links"}}===
~-[[http://zhangroup.aporc.org/ShihuaZhang/Bioinformatics_Lab]]
~- [[http://www.binf.umn.edu/whatsbinf.html Bioinformatics]]
~- [[http://stommel.tamu.edu/~baum/toolboxes.html Matlab toolbox]]
~- [[http://www.ee.columbia.edu/~marios/matlab/matlab_tricks.html Matlab tips and tricks]]
~- [[http://www.ctex.org CTEX.ORG]]
~- [[http://mathworld.wolfram.com/ Mathworld]]
~- [[http://www.cs.cmu.edu/~mleone/how-to.html]]
~- [[http://www.oakland.edu/enp/ Erdös Number]]
~- [[http://cyvision.if.sc.usp.br/~francisco/networks/softwares.htm Complex networks]]
~-[[http://mathworld.wolfram.com/ Mathematics resource]]
==={{color fg="white" bg="gray" text="Aphorism"}}===
~-"The whole of science is nothing more than a refinement of everyday thinking." —— Albert Einstein (1879-1955)
~-"In science, the important thing is to modify and change one’s ideas as science advances." —— Herbert Spencer (1820–1903)
~-"The good life is one inspired by love and guided by knowledge." —— Betrand Russell
~-"The difficulty lies, not in the new ideas, but in escaping the old ones, which ramify, for those brought up as most of us have been, into every corner of our minds.." ——John Maynard Keynes (1883 - 1946)
~-"Life is like riding a bicycle. To keep your balance, you must keep moving." —— Albert Einstein (1879-1955)
~-"It's not your aptitude but your attitude that determines your altitude in life." —— Jesse Jackson
~-"People can be divided into three classes, the few who make things happen, the many who watch things happen, and the overwhelming majority who have no idea what has happened."
