Research:
The interests of our lab are within (i) bioinformatics and computational biology relating to genomics, epigenetics, and network biology, and (ii) data science relating to machine learning, optimization and statistical models and algorithms. As to (i), we focus on developing computational methods for analyzing large-scale biological data sets and discovering novel biological patterns. We also apply computational methods to genomic and epigenomic data to answer specific questions about gene regulation. As to (ii), we focus on developing powerful low-rank models and algorithms for resolving big data. Particularly, we have strong interests in developing joint low-rank models for multi-view or multi-modal data. We also curious about the underlying relationship between deep learning and low-rank models.
More specifically, our research interests include:
Optimization, statistics and machine learning for data science
Our group has a general interest in developing optimization, statistics and machine learning models and algorithms for those computational problems that arise from the biological data (e.g., single-cell transcriptomic data, 3D chromatin structure) and generic data science (e.g., multi-view data, image data, complex networks). We are particularly interested in computational and statistical methods for data representation and pattern discovery in diverse big data.
Cancer genomics
The first step for clinical diagnostics, prognostics, and targeted therapeutics of cancer is to comprehensively understand its molecular mechanisms. Large-scale cancer genomics projects are providing a large volume of data about genomic, epigenomic, and gene expression aberrations in multiple cancer types. We aim to combine data from different sources with computational techniques to discover the underlying combinatorial patterns and driver pathways underlying cancer as well as other diseases. We also aim to develop methods to integrate different data sources to classify tumor and predict the clinical outcome of patients based on the genotype and molecular features.
Computational epigenetics
Chromatin modifications have been comprehensively illustrated to play important roles in gene regulation and cell diversity in recent years. Given the rapid accumulation of genome-wide chromatin modification maps across multiple cell types, there is an urgent need for computational methods to analyze multiple maps to reveal combinatorial modification patterns and define functional DNA elements. We aim to develop computational methods to address these issues and answer specific biological questions.
Network biology and network science
Network science emerged as powerful tools for studying biological systems and complex diseases which summarizes biological systems as nodes and edges among them. The tasks of uncovering the organization of networks and utilizing them for the understanding of biology and disease complexity prompt rich and diverse interests. We aim to develop methods to understand the topological organization of networks and reveal molecular characteristics by combing network structure and biological features.

hihua Zhang, Ph.D. 中文

Principal Investigator

Professor

Academy of Mathematics and Systems Science, Chinese Academy of Sciences

55 Zhongguancun East Road, Beijing 100190, China

Phone: 86-10-82541360

Email: zsh@amss.ac.cn

Office: Siyuan Building S628
Education:

    Ph.D., Academy of Mathematics and Systems Science, CAS, 6/2008
    B.S., Yunnan University, 7/2003

Academic Appointment, Affiliation, and Employment History:

    Professor, Academy of Mathematics and Systems Science, CAS, 4/2018 -
    Associate Professor, Academy of Mathematics and Systems Science, CAS, 3/2013 --- 3/2018
    Assistant Professor, Academy of Mathematics and Systems Science, CAS, 6/2008 --- 2/2013

Visiting Experience:

    Harvard University, 08/2014 -- 4/2015
    Tokyo University, 09/2013 -- 3/2014
    National University of Singapore (NUS), 10/2012 -- 2/2013
    University of California, Los Angeles (UCLA), 10/2011 -- 12/2011
    Postdoctoral Fellow, University of Southern California (USC), 7/2008 -- 1/2011

Honors and Awards:

    ZHONG Jiaqing OR Prize, 2015.
    NSFC Outstanding Youth Fund, 2014.
    Outstanding Young Scientist Program of CAS, 2014.
    Youth Science and Technology Award of China, 2013.
    Lu Jia-Xi Young Investigator Award, 2013.
    Youth Innovation Promotion Association Member (2011--2014).
    Chen Jingrun Future Star (2011--2013).
    National Excellent PhD thesis Award, 2010.
    Special Presidential Prize of CAS, 2008.

Grants:

    NSFC No. 11661141019, 2017-2019 (PI)
    NSFC No. 61621003, 2017-2021 (Co-PI)
    NSFC No. 61422309, 2015-2017 (PI)
    NSFC No. 61379092, 2014-2017 (PI)
    NSFC No. 11001256, 2011-2013 (PI)
    NSFC No. 11131009, 2012-2016 (Co-PI)
    CAS Frontier Science Research Key Project No. QYZDB-SSW-SYS008, 2016-2020 (PI)
    Outstanding Young Scientist Program of CAS, 2014-2016 (PI)
    Youth Innovation Promotion Association Foundation of CAS, 2011-2014 (PI)
    Special Presidential Prize Foundation from CAS, No.4310900, 2010-2012 (PI)

Service to the Profession:

    Editorships and Editorial Boards:
    Associate Editor, BMC Genomics, 10/2013-
    Associate Editor, Frontiers in Genetics, 12/2013-
    Editor, Scientific Reports, 4/2015-
    Editor, Current Bioinformatics, 1/2016-
    Editor, ISRN Applied Mathematics, 01/2011-01/2014
    Review Editor: Frontiers in Statistical Genetics and Methodology
    Guest Editor, IEEE/ACM TCBB, 2014/2016/2017/2018
    Guest Editor, JGG, 2017
    Program Committee:GIW 2016, BIBM 2017, ISBRA 2017, ISB 2018, APBC 2019 and so on

Organizer:

    Youth Scholar Forum on Interdisciplinary Research of Mathematics, Computer Science and Biological Science, Conference Chair (2013-2018).
    ISBRA, PC Co-Chair, 2018

Reviewer:

    American Journal of Human Genetics, Bioinformatics, Cancer Research, PLoS Computational Biology, BMC Genomics, BMC Bioinformatics, IEEE TSP, IEEE/ACM TCBB and so on.
    IEEE/ACM TCBB Top Reviewer (2013/2014)

Current Members:

    Yusen Ye, Visiting PhD student (Xidian Uni.), 6/2016 ---
    Fang Jing, Visiting PhD student (Northwestern Polytechnical Uni.), 6/2016 ---
    Lihua Zhang, PhD student, 9/2013 ---
    Can Wang, PhD student, 9/2013 ---
    Zhen Cao, PhD student, 9/2015 ---
    Chihao Zhang, PhD student, 9/2015 ---
    Kangning Dong, PhD student, 9/2016 ---
    Dachang Dang, Master student, 9/2016 ---
    Xiaofang Yan, Master student, 9/2016 ---
    Kuo Gai, Master student, 9/2017 ---
    Xingyan Liu, Master student, 9/2017 ---
    Penglong Zhai, Master student, 9/2017 ---
    Biao Zhang, Master student, 1/2018 ---

Former Members:

    Xiaoyu Liu, Visiting student (Shandong Uni.), 10/2017 --- 05/2018
    Wenwen Min, Visiting PhD student (Wuhan Uni.), 7/2015 --- 12/2017
    Jinyu Chen, PhD student, 9/2012 --- 07/2017
    Bei Wang, (co-advising) PhD student, 9/2012 --- 12/2017
    Shuai Zhang, Master student, 9/2014 --- 7/2017
    Xuefeng Li, Master student, 9/2014 --- 7/2017
    Zhenxing Guo, Master student, 9/2014 --- 7/2017
    Xiaofei Yang, Visiting PhD student (Xidian Uni.), 6/2013 --- 12/2016
    Wenkai Ji, Master student, 9/2013 --- 7/2016
    Hanxiao Jing, Visiting student (USTC), 07/2017 --- 08/2017
    Wan He, Visiting student (Imperial College London), 01/2017 --- 08/2017
    Dachang Dang, Visiting student, 9/2015 ---7/2016
    Kangning Dong, Visiting student, 2/2016 --- 7/2016
    Lu Lu, Visiting student (Naikai Uni.), 07/2015 --- 12/2015
    Zhen Cao, Visiting student, 7/2014 --- 8/2015
    Zhaoqi Liu, (co-advising) PhD student, 6/2011 --- 7/2015
    Yiyi Yin, Visiting student (Naikai Uni.), 10/2014 --- 4/2015
    Junfei Zhao, (co-advising) PhD student, 6/2011 --- 7/2014
    Chen Chen, (co-advising) PhD student, 6/2011 --- 7/2014
    Wenwen Min, Visiting student (Yunnan Uni.), 7/2012 --- 9/2013
    Wanjun Liu, Visiting student (USTC), 7/2013 --- 8/2013
    Qingqing Liu, Visiting student (USTC), 2/2012 --- 6/2012
    Qingjiao Li, Visiting student (Wuhan Uni.), 6/2011 --- 7/2011
    Guanghua Hu, Visiting Professor (Yunnan Uni.), 6/2011 --- 8/2011

张世华，博士 English

研究员

中国科学院数学与系统科学研究院/国家数学与交叉科学中心

地址：北京市海淀区中关村东路55号，邮编100190

电话：86-10-82541360

邮箱：zsh@amss.ac.cn

办公室：思源楼628室
学术任职：

    2018/04—至今，中国科学院数学与系统科学研究院，研究员
    2013/03—2018/03，中国科学院数学与系统科学研究院，副研究员
    2008/06—2013/02，中国科学院数学与系统科学研究院，助理研究员

学术兼职：

    2015/01—至今，中国科学院随机复杂结构与数据科学重点实验室副主任
    2015/10—至今，中国科学院大学岗位教授
    2012/06—2016/01，中国科学院青年创新促进会数理分会会长

学习经历：

    2008/06，中国科学院数学与系统科学研究院 博士
    2003/07，云南大学数学系 大学本科

访问经历:

    2014/08—2015/04，哈佛大学
    2013/09—2014/03，东京大学
    2012/10—2013/02，新加坡国立大学
    2011/10—2011/12，加州大学洛杉矶分校
    2008/07—2011/01，南加州大学

荣誉与奖励:

    2017，教育部自然科学二等奖（排名第三）
    2015，钟家庆运筹学奖
    2014，国家自然科学基金“优秀青年”基金
    2014，中国科学院“卓越青年科学家”项目
    2013，中国青年科技奖
    2013，中国科学院卢嘉锡青年人才奖
    2011—2015，中国科学院青年创新促进会会员
    2011—2013，“陈景润未来之星”特殊人才计划
    2010，全国优秀博士论文奖
    2008，中国科学院院长奖特别奖

项目：

    国家自然科学基金 No. 11661141019, 2017-2019 (PI)
    国家自然科学基金 No. 61621003, 2017-2021 (Co-PI)
    国家自然科学基金 No. 61422309, 2015-2017 (PI)
    国家自然科学基金 No. 61379092, 2014-2017 (PI)
    国家自然科学基金 No. 11001256, 2011-2013 (PI)
    国家自然科学基金 No. 11131009, 2012-2016 (Co-PI)
    中国科学院前沿重点项目 No. QYZDB-SSW-SYS008, 2016-2020 (PI)
    中国科学院卓越青年科学家项目, 2014-2016 (PI)
    中国科学院青年创新促进会会员, 2011-2014 (PI)
    中国科学院院长奖特别奖创新基金 No.4310900, 2010-2012 (PI)

学术服务：

    编委会任职:
    副编辑，BMC Genomics, 10/2013-
    副编辑，Frontiers in Genetics, 12/2013-
    编委，Scientific Reports, 4/2015-
    编委，Current Bioinformatics, 1/2016-
    编辑，ISRN Applied Mathematics, 01/2011-01/2014
    编委，Frontiers in Statistical Genetics and Methodology, 01/2012-
    客座编辑，IEEE/ACM TCBB, 2014/2016/2017/2018
    客座编辑，JGG, 2017
    程序委员会:
    GIW 2016, BIBM 2017, ISBRA 2017, ISB 2018, APBC 2019等

会议组织:

    数学、计算机与生命科学交叉研究青年学者论坛, 2013/2014/2015/2016/2017/2018
    ISBRA, PC Co-Chair, 2018
    生物大数据与数据挖掘研讨会, Co-Chair, 2016

审稿人:

    American Journal of Human Genetics, Bioinformatics, Cancer Research, PLoS Computational Biology, BMC Genomics, BMC Bioinformatics, IEEE TSP, IEEE/ACM TCBB等40多个国际杂志
    IEEE/ACM TCBB杰出审稿人奖 (2013/2014)