• 生物信息计算与应用
  
• 运筹优化与数据科学
• 深度学习理论与算法
• 详细内容请参考个人实验室主页：http://page.amss.ac.cn/shihua.zhang/

招收硕博连读研究生1-2名、博士生1名

070105-运筹学与控制论
071400-统计学

运筹优化、机器学习与生物信息计算 

生物医学统计、深度学习理论与算法

2003-09--2008-06   中国科学院数学与系统科学研究院   博士

-- 研究生

-- 博士

2018-04--至今 中国科学院数学与系统科学研究院 研究员 

2014-08--2015-04 美国哈佛大学 访问研究员 

2013-09--2014-03 日本东京大学 访问研究员 

2013-03--2018-03 中国科学院数学与系统科学研究院 副研究员 

2012-10--2013-03 新加坡国立大学 访问学者 

2011-10--2011-12 加州洛杉矶分校 访问学者 

2008-07--2011-02 南加州大学 博士后研究 

2008-07--2013-02 中国科学院数学与系统科学研究院 助理研究员 

深度学习理论
数据科学与矩阵优化
矩阵论
大数据科学
深度学习概论
生物信息学前沿专题选讲
生物信息学前沿选讲
生物信息学与计算系统生物学
生物信息学与系统生物学

   

（1） 中国生物信息学十大进展, 其他, 2021
（2） 中国生物信息学十大算法和工具, 其他, 2019
（3） 国家万人计划青年拔尖人才, , 国家级, 2018
（4） 钟家庆运筹学奖, , 其他, 2015
（5） 中国科学院卓越青年科学家项目, , 部委级, 2014
（6） 国家自然科学基金优秀青年基金, , 国家级, 2014
（7） 中国青年科技奖, , 部委级, 2013
（8） 中国科学院卢嘉锡青年人才奖, , 部委级, 2013
（9） 陈景润未来之星, , 研究所（学校）, 2011
（10） 全国百篇优秀博士论文奖, , 国家级, 2010
（11） 中国科学院院长奖特等奖, , 部委级, 2008

[1] 韩青华, 张世华, 张炙炀, 周维. 基于可解释性深度学习的心电图分类. CN: CN114762605A, 2022-07-19.

   

[1] Li, Shang, Gai, Kuo, Dong, Kangning, Zhang, Yiyang, Zhang, Shihua. High-density generation of spatial transcriptomics with STAGE. NUCLEIC ACIDS RESEARCH[J]. 2024, 第 5 作者  通讯作者  52(9): 4843-4856, http://dx.doi.org/10.1093/nar/gkae294.
[2] Gai, Kuo, Zhang, Shihua. Tessellating the Latent Space for Non-Adversarial Generative Auto-Encoders. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE[J]. 2024, 第 2 作者  通讯作者  46(2): 780-792, http://dx.doi.org/10.1109/TPAMI.2023.3325282.
[3] Zhang, Biao, Zhang, Shuqin, Zhang, Shihua. Whole brain alignment of spatial transcriptomics between humans and mice with BrainAlign. NATURE COMMUNICATIONS[J]. 2024, 第 3 作者  通讯作者  15(1): http://dx.doi.org/10.1038/s41467-024-50608-2.
[4] Xiao, Kaixuan, Wang, Yu, Dong, Kangning, Zhang, Shihua. SmartGate is a spatial metabolomics tool for resolving tissue structures. BRIEFINGS IN BIOINFORMATICS[J]. 2023, 第 4 作者  通讯作者  24(3): http://dx.doi.org/10.1093/bib/bbad141.
[5] Cui, Guanshen, Dong, Kangning, Zhou, JiaYi, Li, Shang, Wu, Ying, Han, Qinghua, Yao, Bofei, Shen, Qunlun, Zhao, YongLiang, Yang, Ying, Cai, Jun, Zhang, Shihua, Yang, YunGui. Spatiotemporal transcriptomic atlas reveals the dynamic characteristics and key regulators of planarian regeneration. Nature Communications[J]. 2023, 第 12 作者  通讯作者  14(1): http://dx.doi.org/10.1038/s41467-023-39016-0.
[6] 郭书旗, 张绍武, 李岩, 张世华. 整合受体调控基因表达信息构建细胞通信网络 增强出版. 生物化学与生物物理进展. 2023, 第 4 作者623-633, https://kns.cnki.net/kcms2/article/abstract?v=8xl4CyPd-wWr4NT7QilSayRHgCPtLD4X3T5zpr4eMLoT8b92MvPGwz5wisFrKNbByngrqaZZUfRsrOHAd9bfZ7IgGnlMbKpapGWSqTOf2WdUOuNIVGzqOw0ebWG_RkO8&uniplatform=NZKPT&language=gb.
[7] 郭书旗, 张绍武, 李岩, 张世华. 整合受体调控基因表达信息构建细胞通信网络. 生物化学与生物物理进展[J]. 2023, 第 4 作者50(3): 623-633, http://www.pibb.ac.cn/pibbcn/article/abstract/20220099?st=article_issue.
[8] Zhang, Chihao, Zhang, Shihua, Li, Jingyi Jessica. A Python Package itca for Information-Theoretic Classification Accuracy: A Criterion That Guides Data-Driven Combination of Ambiguous Outcome Labels in Multiclass Classification. JOURNAL OF COMPUTATIONAL BIOLOGY[J]. 2023, 第 2 作者  通讯作者  30(11): 1246-1249, http://dx.doi.org/10.1089/cmb.2023.0191.
[9] Zhang, Chihao, Yang, Yang, Zhou, Wei, Zhang, Shihua. Distributed Bayesian Matrix Decomposition for Big Data Mining and Clustering. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING[J]. 2022, 第 4 作者  通讯作者  34(8): 3701-3713, http://dx.doi.org/10.1109/TKDE.2020.3029582.
[10] Zhai, Penglong, Zhang, Shihua. Adversarial Information Bottleneck. IEEE TRANSACTIONS ON NEURAL NETWORKS AND LEARNING SYSTEMS[J]. 2022, 第 2 作者  通讯作者  10, http://dx.doi.org/10.1109/TNNLS.2022.3172986.
[11] Shan, Xu, Chen, Jinyu, Dong, Kangning, Zhou, Wei, Zhang, Shihua. Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data. JOURNAL OF COMPUTATIONAL BIOLOGY[J]. 2022, 第 5 作者  通讯作者  29(7): 14, http://dx.doi.org/10.1089/cmb.2021.0617.
[12] Dong, Kangning, Zhang, Shihua. Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder. NATURE COMMUNICATIONS[J]. 2022, 第 2 作者  通讯作者  13(1): https://doaj.org/article/a1c1def7666840e088a2b9ddd9f163a7.
[13] Kangning Dong, Shihua Zhang. Deciphering spatial domains from spatially resolved transcriptomics with an adaptive graph attention auto-encoder. Nature Communications. 2022, 13: 
[14] Zhang, Chihao, Zhang, Shihua. Bayesian Joint Matrix Decomposition for Data Integration with Heterogeneous Noise. IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE[J]. 2021, 第 2 作者  通讯作者  43(4): 1184-1196, http://dx.doi.org/10.1109/TPAMI.2019.2946370.
[15] Dong, Kangning, Zhang, Shihua. Network diffusion for scalable embedding of massive single-cell ATAC-seq data. SCIENCE BULLETIN[J]. 2021, 第 2 作者  通讯作者  66(22): 2271-2276, http://dx.doi.org/10.1016/j.scib.2021.05.014.
[16] Jing, Fang, Zhang, ShaoWu, Cao, Zhen, Zhang, Shihua. An Integrative Framework for Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2021, 第 4 作者  通讯作者  18(1): 355-364, http://dx.doi.org/10.1109/TCBB.2019.2901789.
[17] Luo, Xin, Liu, Yuting, Dang, Dachang, Hu, Ting, Hou, Yingping, Meng, Xiaoyu, Zhang, Fengyun, Li, Tingting, Wang, Can, Li, Min, Wu, Haixu, Shen, Qiushuo, Hu, Yan, Zeng, Xuerui, He, Xiechao, Yan, Lanzhen, Zhang, Shihua, Li, Cheng, Su, Bing. 3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis. CELL[J]. 2021, 第 17 作者  通讯作者  184(3): 723-+, http://dx.doi.org/10.1016/j.cell.2021.01.001.
[18] Zhang, Lihua, Zhang, Shihua. Imputing single-cell RNA-seq data by considering cell heterogeneity and prior expression of dropouts. JOURNAL OF MOLECULAR CELL BIOLOGY[J]. 2021, 第 2 作者  通讯作者  13(1): 29-40, http://dx.doi.org/10.1093/jmcb/mjaa052.
[19] Min, Wenwen, Liu, Juan, Zhang, Shihua. Group-Sparse SVD Models via L-1- and L-0-norm Penalties and their Applications in Biological Data. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING[J]. 2021, 第 3 作者  通讯作者  33(2): 536-550, http://dx.doi.org/10.1109/TKDE.2019.2932063.
[20] Zhang, Chihao, Zhang, Shihua. Bayesian Joint Matrix Decomposition for Data Integration with Heterogeneous Noise. IEEE TRANS PATTERN ANAL MACH INTELL[J]. 2021, 第 2 作者  通讯作者  43(4): 1184-1196, http://arxiv.org/abs/1712.03337.
[21] Jiang, Hao, Yi, Ming, Zhang, Shihua. A kernel non-negative matrix factorization framework for single cell clustering. APPLIED MATHEMATICAL MODELLING[J]. 2021, 第 3 作者90: 875-888, http://dx.doi.org/10.1016/j.apm.2020.08.065.
[22] Luo, Xin, Liu, Yuting, Dang, Dachang, Hu, Ting, Hou, Yingping, Meng, Xiaoyu, Zhang, Fengyun, Li, Tingting, Wang, Can, Li, Min, Wu, Haixu, Shen, Qiushuo, Hu, Yan, Zeng, Xuerui, He, Xiechao, Yan, Lanzhen, Zhang, Shihua, Li, Cheng, Su, Bing. 3D Genome of macaque fetal brain reveals evolutionary innovations during primate corticogenesis. CELL[J]. 2021, 第 11 作者184(3): 723-+, http://dx.doi.org/10.1016/j.cell.2021.01.001.
[23] Zhang, Chihao, Zhang, Shihua. Bayesian Joint Matrix Decomposition for Data Integration with Heterogeneous Noise. IEEE Trans Pattern Anal Mach Intell[J]. 2021, 第 11 作者43(4): 1184-1196, http://arxiv.org/abs/1712.03337.
[24] 翟鹏龙, 刘星言, 段然, 张世华. COVID-19疫情的实时区域传播分析、预测与预警. 应用数学学报[J]. 2020, 第 4 作者43(2): 295-309, http://lib.cqvip.com/Qikan/Article/Detail?id=7102205567.
[25] Zhang, Chihao, Yang, Yang, Zhou, Wei, Zhang, Shihua. Distributed Bayesian Matrix Decomposition for Big Data Mining and Clustering. IEEE TRANSACTIONS ON KNOWLEDGE AND DATA ENGINEERING[J]. 2020, 第 4 作者  通讯作者  34(8): 3701-3713, http://dx.doi.org/10.1109/TKDE.2020.3029582.
[26] Cao, Zhen, Zhang, Shihua. Probe Efficient Feature Representation of Gapped K-mer Frequency Vectors from Sequences Using Deep Neural Networks. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2020, 第 2 作者  通讯作者  17(2): 657-667, http://dx.doi.org/10.1109/TCBB.2018.2868071.
[27] Jing, Fang, Zhang, ShaoWu, Zhang, Shihua. Prediction of enhancer-promoter interactions using the cross-cell type information and domain adversarial neural network. BMC BIOINFORMATICS[J]. 2020, 第 3 作者  通讯作者  21(1): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7648314/.
[28] Zhang Shihua. Towards Understanding of Residual and Mixed-Scale Dense Neural Networks via Convolutional Sparse Coding.. National Science Review. 2020, 第 1 作者
[29] Zhang, Lihua, Zhang, Shihua. Comparison of Computational Methods for Imputing Single-Cell RNA-Sequencing Data. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2020, 第 2 作者  通讯作者  17(2): 376-389, http://dx.doi.org/10.1109/TCBB.2018.2848633.
[30] Zhang Shihua. Towards Understanding of Residual and Mixed-Scale Dense Neural Networks via Convolutional Sparse Coding.. National Science Review. 2020, 第 1 作者
[31] Ye, Yusen, Gao, Lin, Zhang, Shihua. Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C Maps. ADVANCED SCIENCE[J]. 2019, 第 3 作者  通讯作者  6(23): https://www.doi.org/10.1002/advs.201900986.
[32] Kueffner, Robert, Zach, Neta, Bronfeld, Maya, Norel, Raquel, Atassi, Nazem, Balagurusamy, Venkat, Di Camillo, Barbara, Chio, Adriano, Cudkowicz, Merit, Dillenberger, Donna, GarciaGarcia, Javier, Hardiman, Orla, Hoff, Bruce, Knight, Joshua, Leitner, Melanie L, Li, Guang, Mangravite, Lara, Norman, Thea, Wang, Liuxia, Alkallas, Rached, Anghel, Catalina, Avril, Jeanne, Bacardit, Jaume, Balser, Barbara, Balser, John, BarSinai, Yoav, BenDavid, Noa, BenZion, Eyal, Bliss, Robin, Cai, Jialu, Chernyshev, Anatoly, Chiang, JungHsien, Chicco, Davide, Corriveau, Bhavna Ahuja Nicole, Dai, Junqiang, Deshpande, Yash, Desplats, Eve, Durgin, Joseph S, Espiritu, Shadrielle Melijah G, Fan, Fan, Fevrier, Philippe, Fridley, Brooke L, Godzik, Adam, Golinska, Agnieszka, Gordon, Jonathan, Graw, Stefan, Guo, Yuelong, Herpelinck, Tim, Hopkins, Julia, Huang, Barbara, Jacobsen, Jeremy, Jahandideh, Samad, Jeon, Jouhyun, Ji, Wenkai, Jung, Kenneth, Karanevich, Alex, Koestler, Devin C, Kozak, Michael, Kurz, Christoph, Lalansingh, Christopher, Larrieu, Thomas, Lazzarini, Nicola, Lerner, Boaz, Lesinski, Wojciech, Liang, Xiaotao, Lin, Xihui, Lowe, Jarrett, Mackey, Lester, Meier, Richard, Min, Wenwen, Mnich, Krzysztof, Nahmias, Violette, NoelMacDonnell, Janelle, ODonnell, Adrienne, Paadre, Susan, Park, Ji, PolewkoKlim, Aneta, Raghavan, Rama, Rudnicki, Witold, Saghapour, Ehsan, Salomond, JeanBernard, Sankaran, Kris, Sendorek, Dorota, Sharan, Vatsal, Shiah, YuJia, Sirois, JeanKarl, Sumanaweera, Dinithi N, Usset, Joseph, Vang, Yeeleng S, Vens, Celine, Wadden, Dave, Wang, David, Wong, Wing Chung, Xie, Xiaohui, Xu, Zhiqing, Yang, HsihTe, Yu, Xiang, Zhang, Haichen, Zhang, Li, Zhang, Shihua, Zhu, Shanfeng, Xiao, Jinfeng, Fang, WenChieh, Peng, Jian, Yang, Chen, Chang, HuanJui, Stolovitzky, Gustavo, ALS Stratification Consortium. Stratification of amyotrophic lateral sclerosis patients: a crowdsourcing approach. SCIENTIFIC REPORTS[J]. 2019, 第 100 作者9(1): https://doaj.org/article/835c2e26aa0e48858dd332220be4aeea.
[33] Jing, Fang, Zhang, ShaoWu, Zhang, Shihua. Brief Survey of Biological Network Alignment and a Variant with Incorporation of Functional Annotations. CURRENT BIOINFORMATICS[J]. 2019, 第 3 作者  通讯作者  14(1): 4-10, http://ir.amss.ac.cn/handle/2S8OKBNM/32551.
[34] Zhang Shihua. Group-sparse SVD models and their applications in biological data.. IEEE Transactions on Knowledge and Data Engineering (TKDE). 2019, 第 1 作者  通讯作者  
[35] Cao, Zhen, Zhang, Shihua. Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction. BIOINFORMATICS[J]. 2019, 第 2 作者  通讯作者  35(11): 1837-1843, http://ir.amss.ac.cn/handle/2S8OKBNM/35247, http://www.irgrid.ac.cn/handle/1471x/6869289, http://ir.amss.ac.cn/handle/2S8OKBNM/35248, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000476567500005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=3a85505900f77cc629623c3f2907beab.
[36] Zhang, Lihua, Zhang, Shihua. Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization. NUCLEIC ACIDS RESEARCH[J]. 2019, 第 2 作者  通讯作者  47(13): 6606-6617, http://ir.amss.ac.cn/handle/2S8OKBNM/35774, http://www.irgrid.ac.cn/handle/1471x/6869307, http://ir.amss.ac.cn/handle/2S8OKBNM/35775, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000490556600010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=3a85505900f77cc629623c3f2907beab.
[37] Duan, Bin, Zhou, Chi, Zhu, Chengyu, Yu, Yifei, Li, Gaoyang, Zhang, Shihua, Zhang, Chao, Ye, Xiangyun, Ma, Hanhui, Qu, Shen, Zhang, Zhiyuan, Wang, Ping, Sun, Shuyang, Liu, Qi. Model-based understanding of single-cell CRISPR screening. NATURE COMMUNICATIONS[J]. 2019, 第 6 作者10(1): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000468274900002&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=3a85505900f77cc629623c3f2907beab.
[38] Zhang Shihua. A general joint matrix factorization framework for data integration and its systematic algorithmic exploration.. IEEE Transactions on Fuzzy Systems (TFS). 2019, 第 1 作者  通讯作者  
[39] Ye, Yusen, Gao, Lin, Zhang, Shihua. MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps. NUCLEIC ACIDS RESEARCH[J]. 2019, 第 3 作者  通讯作者  47(11): e65-e65, http://ir.amss.ac.cn/handle/2S8OKBNM/35298, http://www.irgrid.ac.cn/handle/1471x/6869292, http://ir.amss.ac.cn/handle/2S8OKBNM/35299, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000475702000005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=3a85505900f77cc629623c3f2907beab.
[40] Ye, Yusen, Gao, Lin, Zhang, Shihua. Circular Trajectory Reconstruction Uncovers Cell-Cycle Progression and Regulatory Dynamics from Single-Cell Hi-C Maps. ADVANCED SCIENCE[J]. 2019, 第 11 作者6(23): http://ir.amss.ac.cn/handle/2S8OKBNM/35748, http://www.irgrid.ac.cn/handle/1471x/6869306, http://ir.amss.ac.cn/handle/2S8OKBNM/35749, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000488171600001&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=3a85505900f77cc629623c3f2907beab.
[41] Zhang Shihua. Group-sparse SVD models and their applications in biological data.. IEEE Transactions on Knowledge and Data Engineering (TKDE). 2019, 第 11 作者
[42] Zhang, Lihua, Zhang, Shihua. Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization. NUCLEIC ACIDS RESEARCH[J]. 2019, 第 11 作者47(13): 6606-6617, http://ir.amss.ac.cn/handle/2S8OKBNM/35774, http://www.irgrid.ac.cn/handle/1471x/6869307, http://ir.amss.ac.cn/handle/2S8OKBNM/35775, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000490556600010&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=3a85505900f77cc629623c3f2907beab.
[43] Ye, Yusen, Gao, Lin, Zhang, Shihua. MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps. NUCLEIC ACIDS RESEARCH[J]. 2019, 第 11 作者47(11): e65-e65, http://ir.amss.ac.cn/handle/2S8OKBNM/35298, http://www.irgrid.ac.cn/handle/1471x/6869292, http://ir.amss.ac.cn/handle/2S8OKBNM/35299, http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000475702000005&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=3a85505900f77cc629623c3f2907beab.
[44] Zhang Shihua. A general joint matrix factorization framework for data integration and its systematic algorithmic exploration.. IEEE Transactions on Fuzzy Systems (TFS). 2019, 第 11 作者
[45] Wang, Can, Zhang, Shihua. Reveal cell type-specific regulatory elements and their characterized histone code classes via a hidden Markov model. BMC GENOMICS[J]. 2018, 第 2 作者  通讯作者  19(S10): https://doaj.org/article/991219b901c849fcbbcc65ddd9312cc4.
[46] Min Wenwen, Liu Juan, Zhang Shihua. Sparse Weighted Canonical Correlation Analysis. CHINESE JOURNAL OF ELECTRONICS[J]. 2018, 第 3 作者  通讯作者  27(3): 459-466, http://lib.cqvip.com/Qikan/Article/Detail?id=675333407.
[47] Cao, ZhiWei, Wang, XiuJie, Zhang, ShiHua. Omics tools for the needle out of haystack?. JOURNAL OF GENETICS AND GENOMICS[J]. 2018, 第 3 作者  通讯作者  45(7): 343-344, http://lib.cqvip.com/Qikan/Article/Detail?id=676145093.
[48] Wang Bei, Chen Jinyu, Zhang Shihua. bmtkatoolkitfordeterminingmodulesinbiologicalbipartitenetworks. QUANTITATIVEBIOLOGY[J]. 2018, 第 3 作者6(2): 186, http://ir.amss.ac.cn/handle/2S8OKBNM/44166, http://www.irgrid.ac.cn/handle/1471x/6869545, http://ir.amss.ac.cn/handle/2S8OKBNM/44167.
[49] Zhang, Junhua, Zhang, Shihua. The Discovery of Mutated Driver Pathways in Cancer: Models and Algorithms. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2018, 第 2 作者15(3): 988-998, https://www.webofscience.com/wos/woscc/full-record/WOS:000434295100028.
[50] Min, Wenwen, Liu, Juan, Zhang, Shihua. Edge-group sparse PCA for network-guided high dimensional data analysis. BIOINFORMATICS[J]. 2018, 第 3 作者  通讯作者  34(20): 3479-3487, http://ir.amss.ac.cn/handle/2S8OKBNM/31658.
[51] Li, Wei Vivian, Zhao, Anqi, Zhang, Shihua, Li, Jingyi Jessica. MSIQ: JOINT MODELING OF MULTIPLE RNA-SEQ SAMPLES FOR ACCURATE ISOFORM QUANTIFICATION. ANNALS OF APPLIED STATISTICS[J]. 2018, 第 3 作者12(1): 510-539, https://www.webofscience.com/wos/woscc/full-record/WOS:000429908100020.
[52] Zhiwei Cao, Xiu-Jie Wang, Shihua Zhang. Omics tools for the needle out of haystack?. 遗传学报：英文版[J]. 2018, 第 3 作者45(7): 343-344, http://lib.cqvip.com/Qikan/Article/Detail?id=676145093.
[53] MIN Wenwen, LIU Juan, ZHANG Shihua. Sparse Weighted Canonical Correlation Analysis. 电子学报：英文版[J]. 2018, 第 3 作者27(3): 459-466, http://lib.cqvip.com/Qikan/Article/Detail?id=675333407.
[54] Chen, Jinyu, Zhang, Shihua. Matrix Integrative Analysis (MIA) of Multiple Genomic Data for Modular Patterns. FRONTIERS IN GENETICS[J]. 2018, 第 2 作者  通讯作者  9: https://doaj.org/article/e05c04e7c45d48a884cce69acfd85b9d.
[55] Chen, Jinyu, Zhang, Shihua. Discovery of two-level modular organization from matched genomic data via joint matrix tri-factorization. NUCLEIC ACIDS RESEARCH[J]. 2018, 第 2 作者  通讯作者  46(12): 5967-5976, http://dx.doi.org/10.1093/nar/gky440.
[56] Min, Wenwen, Liu, Juan, Zhang, Shihua. Network-Regularized Sparse Logistic Regression Models for Clinical Risk Prediction and Biomarker Discovery. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2018, 第 3 作者  通讯作者  15(3): 944-953, http://dx.doi.org/10.1109/TCBB.2016.2640303.
[57] Zhang, Junhua, Zhang, Shihua. Discovery of cancer common and specific driver gene sets. NUCLEIC ACIDS RESEARCH[J]. 2017, 第 2 作者  通讯作者  45(10): e86-e86, 
[58] Ye, Yusen, Gao, Lin, Zhang, Shihua. Integrative Analysis of Transcription Factor Combinatorial Interactions Using a Bayesian Tensor Factorization Approach. FRONTIERS IN GENETICS[J]. 2017, 第 3 作者  通讯作者  8: https://doaj.org/article/946afb6a88234042b29582f0450c957c.
[59] Wang, Can, Zhang, Shihua. Large-scale determination and characterization of cell type-specific regulatory elements in the human genome. JOURNAL OF MOLECULAR CELL BIOLOGY[J]. 2017, 第 2 作者  通讯作者  9(6): 463-476, http://dx.doi.org/10.1093/jmcb/mjx058.
[60] Wang, Can, Zhang, Shihua. Large-scale determination and characterization of cell type-specific regulatory elements in the human genome. JOURNAL OF MOLECULAR CELL BIOLOGY[J]. 2017, 第 11 作者9(6): 463-476, https://www.webofscience.com/wos/woscc/full-record/WOS:000425284600004.
[61] 路建波, 张世华, 马旭, 卢本卓. 一种基于特征点匹配的生物大分子装配方法. 数值计算与计算机应用. 2017, 第 2 作者155-166, https://kns.cnki.net/KCMS/detail/detail.aspx?dbcode=CJFQ&dbname=CJFDLAST2018&filename=SZJS201702007&v=MjAzMzJGQ3ZrVXI3TU5qZkJmYkc0SDliTXJZOUZZNFI4ZVgxTHV4WVM3RGgxVDNxVHJXTTFGckNVUjdxZmJ1WnQ=.
[62] Yang, Xiaofei, Gao, Lin, Zhang, Shihua. Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns. BRIEFINGS IN BIOINFORMATICS[J]. 2017, 第 11 作者18(5): 761-773, https://www.webofscience.com/wos/woscc/full-record/WOS:000411516400005.
[63] Chen, Jinyu, Zhang, Shihua. Integrative cancer genomics: models, algorithms and analysis. FRONTIERS OF COMPUTER SCIENCE[J]. 2017, 第 2 作者  通讯作者  11(3): 392-406, http://ir.amss.ac.cn/handle/2S8OKBNM/43833, http://www.irgrid.ac.cn/handle/1471x/6869536, http://ir.amss.ac.cn/handle/2S8OKBNM/43834.
[64] Zhang Shihua. Discovery of cancer common and specific gene sets.. Nucleic Acids Research. 2017, 第 11 作者
[65] Seyednasrollah, Fatemeh, Koestler, Devin C, Wang, Tao, Piccolo, Stephen R, Vega, Roberto, Greiner, Russell, Fuchs, Christiane, Gofer, Eyal, Kumar, Luke, Wolfinger, Russell D, Winner, Kimberly Kanigel, Bare, Chris, Neto, Elias Chaibub, Yu, Thomas, Shen, Liji, Abdallah, Kald, Norman, Thea, Stolovitzky, Gustavo, Soule, Howard R, Sweeney, Christopher J, Ryan, Charles J, Scher, Howard, I, Sartor, Oliver, Elo, Laura L, Zhou, Fang Liz, Guinney, Justin, Costello, James C, Abdallah, Kald, Airola, Antti, Aittokallio, Tero, Anghel, Catalina, Ankerst, Donna P, Azima, Helia, Baertsch, Robert, Ballester, Pedro J, Bare, Chris, Bhandari, Vinayak, Bot, Brian M, Buchardt, AnnSophie, Buturovic, Ljubomir, Cao, Da, Chalise, Prabhakar, Chang, Billy H W, Cho, Junwoo, Chu, TzuMing, Coley, R Yates, Conjeti, Sailesh, Correia, Sara, Costello, James C, Dai, Ziwei, Dai, Junqiang, Dang, Cuong C, Dargatz, Philip, Delavarkhan, Sam, Deng, Detian, Dhanik, Ankur, Du, Yu, Elangovan, Aparna, Ellis, Shellie, Elo, Laura L, Espiritu, Shadrielle M, Fan, Fan, Farshi, Ashkan B, Freitas, Ana, Fridley, Brooke, Fuchs, Christiane, Gofer, Eyal, Golinska, Agnieszka K, Graw, Stefan, Greiner, Russ, Guinney, Justin, Guo, Jing, Gupta, Pankaj, Guyer, Anna, I, Han, Jiawei, Hansen, Niels R, Hirvonen, Outi, Huang, Barbara, Huang, Chao, Hwang, Jinseub, Ibrahim, Joseph G, Jayaswal, Vivek, Jeon, Jouhyun, Ji, Zhicheng, Juvvadi, Deekshith, Jyrkkio, Sirkku, KanigelWinner, Kimberly, Katouzian, Amin, Kazanov, Marat D, Khan, Suleiman A, Khayyer, Shahin, Kim, Dalho, Koestler, Devin, Kokowicz, Fernanda, Kondofersky, Ivan, Krstajic, Damjan, Kumar, Luke, Kurz, Christoph, Kyan, Matthew, Laajala, Teemu D, Laimighofer, Michael, Lee, Eunjee, Lesinski, Wojciech, Li, Miaozhu, Li, Ye, Lian, Qiuyu, Liang, Xiaotao, Lim, Minseong, Lin, Henry, Lin, Xihui, Lin, Xihui, Lu, Jing, Mahmoudian, Mehrad, Manshaei, Roozbeh, Meier, Richard, Miljkovic, Dejan, Mirtti, Tuomas, Mnich, Krzysztof, Navab, Nassir, Neto, Elias C, Newton, Yulia, Norman, Thea, Pahikkala, Tapio, Pal, Subhabrata, Park, Byeongju, Patel, Jaykumar, Pathak, Swetabh, Pattin, Alejandrin, Peddinti, Gopal, Peng, Jian, Petersen, Anne H, Philip, Robin, Piccolo, Stephen R, Poelsterl, Sebastian, PolewkoKlim, Aneta, Rao, Karthik, Ren, Xiang, Rocha, Miguel, Rudnicki, Witold R, Ryan, Charles J, Ryu, Hyunnam, Sartor, Oliver, Scherb, Hagen, Sehgal, Raghav, Seyednasrollah, Fatemeh, Shang, Jingbo, Shao, Bin, Shen, Liji, Sher, Howard, Shiga, Motoki, Sokolov, Artem, Soellner, Julia F, Song, Lei, Soule, Howard, Stolovitzky, Gustavo, Stuart, Josh, Sun, Ren, Sweeney, Christopher J, Tahmasebi, Nazanin, Tan, KarTong, Tomaziu, Lisbeth, Usset, Joseph, Vang, Yeeleng S, Vega, Roberto, vieira, Vitor, Wang, David, Wang, Difei, Wang, Junmei, Wang, Lichao, Wang, Sheng, Wang, Tao, Wang, Yue, Wolfinger, Russ, Wong, Chris, Wu, Zhenke, Xiao, Jinfeng, Xie, Xiaohui, Xin, Doris, Yang, Hojin, Yu, Nancy, Yu, Thomas, Yu, Xiang, Zahedi, Sulmaz, Zanin, Massimiliano, Zhang, Chihao, Zhang, Jingwen, Zhang, Shihua, Zhang, Yanchun, Zhou, Fang Liz, Zhu, Hongtu, Zhu, Shanfeng, Zhu, Yuxin, Prostate Canc DREAM Challenge. A DREAM Challenge to guild Prediction Models for Short-Term Discontinuation of Docetaxel in Metastatic Castration- Resistant Prostate Cancer. JCO CLINICAL CANCER INFORMATICS[J]. 2017, 第 187 作者1: 
[66] Zhang Shihua. Joint modeling of multiple RNA-seq samples for accurate isoform quantification.. Annals of Applied Statistics. 2017, 第 11 作者
[67] Yang, Xiaofei, Gao, Lin, Zhang, Shihua. Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns. BRIEFINGS IN BIOINFORMATICS[J]. 2017, 第 3 作者  通讯作者  18(5): 761-773, http://dx.doi.org/10.1093/bib/bbw063.
[68] Can Wang, Shihua Zhang. Large-scale determination and characterization of cell type-specific regulatory elements in the human genorne. 分子细胞生物学报：英文版[J]. 2017, 第 2 作者9(6): 463-476, http://lib.cqvip.com/Qikan/Article/Detail?id=674913376.
[69] Zhang Shihua. Discovery of cancer common and specific gene sets.. Nucleic Acids Research. 2017, 第 1 作者  通讯作者  
[70] Guinney, Justin, Wang, Tao, Laajala, Teemu D, Winner, Kimberly Kanigel, Bare, J Christopher, Neto, Elias Chaibub, Khan, Suleiman A, Peddinti, Gopal, Airola, Antti, Pahikkala, Tapio, Mirtti, Tuomas, Yu, Thomas, Bot, Brian M, Shen, Liji, Abdallah, Kald, Norman, Thea, Friend, Stephen, Stolovitzky, Gustavo, Soule, Howard, Sweeney, Christopher J, Ryan, Charles J, Scher, Howard I, Sartor, Oliver, Xie, Yang, Aittokallio, Tero, Zhou, Fang Liz, Costello, James C, Abdallah, Kald, Aittokallio, Tero, Airola, Antti, Anghel, Catalina, Azima, Helia, Baertsch, Robert, Ballester, Pedro J, Bare, Chris, Bhandari, Vinayak, Bot, Brian M, Dang, Cuong C, Dunba, Maria BekkerNielsen, Buchardt, AnnSophie, Buturovic, Ljubomir, Cao, Da, Chalise, Prabhakar, Cho, Junwoo, Chu, TzuMing, Coley, R Yates, Conjeti, Sailesh, Correia, Sara, Costello, James C, Dai, Ziwei, Dai, Junqiang, Dargatz, Philip, Delavarkhan, Sam, Deng, Detian, Dhanik, Ankur, Du, Yu, Elangovan, Aparna, Ellis, Shellie, Elo, Laura L, Espiritu, Shadrielle M, Fan, Fan, Farshi, Ashkan B, Freitas, Ana, Fridley, Brooke, Friend, Stephen, Fuchs, Christiane, Gofer, Eyal, Peddinti, Gopalacharyulu, Graw, Stefan, Greiner, Russ, Guan, Yuanfang, Guinney, Justin, Guo, Jing, Gupta, Pankaj, Guyer, Anna I, Han, Jiawei, Hansen, Niels R, Chang, Billy H W, Hirvonen, Outi, Huang, Barbara, Huang, Chao, Hwang, Jinseub, Ibrahim, Joseph G, Jayaswal, Vivek, Jeon, Jouhyun, Ji, Zhicheng, Juvvadi, Deekshith, Jyrkkio, Sirkku, KanigelWinner, Kimberly, Katouzian, Amin, Kazanov, Marat D, Khan, Suleiman A, Khayyer, Shahin, Kim, Dalho, Golinska, Agnieszka K, Koestler, Devin, Kokowicz, Fernanda, Kondofersky, Ivan, Krautenbacher, Norbert, Krstajic, Damjan, Kumar, Luke, Kurz, Christoph, Kyan, Matthew, Laajala, Teemu D, Laimighofer, Michael, Lee, Eunjee, Lesinski, Wojciech, Li, Miaozhu, Li, Ye, Lian, Qiuyu, Liang, Xiaotao, Lim, Minseong, Lin, Henry, Lin, Xihui, Lu, Jing, Mahmoudian, Mehrad, Manshaei, Roozbeh, Meier, Richard, Miljkovic, Dejan, Mirtti, Tuomas, Mnich, Krzysztof, Navab, Nassir, Neto, Elias C, Newton, Yulia, Norman, Thea, Pahikkala, Tapio, Pal, Subhabrata, Park, Byeongju, Patel, Jaykumar, Pathak, Swetabh, Pattin, Alejandrina, Ankerst, Donna P, Peng, Jian, Petersen, Anne H, Philip, Robin, Piccolo, Stephen R, Poelsterl, Sebastian, PolewkoKlim, Aneta, Rao, Karthik, Ren, Xiang, Rocha, Miguel, Rudnicki, Witold R, Ryan, Charles J, Ryu, Hyunnam, Sartor, Oliver, Scherb, Hagen, Sehgal, Raghav, Seyednasrollah, Fatemeh, Shang, Jingbo, Shao, Bin, Shen, Liji, Sher, Howard, Shiga, Motoki, Sokolov, Artem, Soellner, Julia F, Song, Lei, Soule, Howard, Stolovitzky, Gustavo, Stuart, Josh, Sun, Ren, Sweeney, Christopher J, Tahmasebi, Nazanin, Tan, KarTong, Tomaziu, Lisbeth, Usset, Joseph, Vang, Yeeleng S, Vega, Roberto, Vieira, Vitor, Wang, David, Wang, Difei, Wang, Junmei, Wang, Lichao, Wang, Sheng, Wang, Tao, Wang, Yue, Wolfinger, Russ, Wong, Chris, Wu, Zhenke, Xiao, Jinfeng, Xie, Xiaohui, Xie, Yang, Xin, Doris, Yang, Hojin, Yu, Nancy, Yu, Thomas, Yu, Xiang, Zahedi, Sulmaz, Zanin, Massimiliano, Zhang, Chihao, Zhang, Jingwen, Zhang, Shihua, Zhang, Yanchun, Zhou, Fang Liz, Zhu, Hongtu, Zhu, Shanfeng, Zhu, Yuxin, Prostate Canc Challenge DREAM Comm. Prediction of overall survival for patients with metastatic castration-resistant prostate cancer: development of a prognostic model through a crowdsourced challenge with open clinical trial data. LANCET ONCOLOGY[J]. 2017, 第 191 作者18(1): 132-142, http://dx.doi.org/10.1016/S1470-2045(16)30560-5.
[71] 路建波, 高华方, 张世华, 卢本卓, 马旭. 缺失数据下蛋白质多结构叠加的迭代方法. 中国生物化学与分子生物学报[J]. 2017, 第 3 作者33(6): 630, http://ir.amss.ac.cn/handle/2S8OKBNM/47555, http://www.irgrid.ac.cn/handle/1471x/6869637, http://ir.amss.ac.cn/handle/2S8OKBNM/47556.
[72] Zhang Shihua. Joint modeling of multiple RNA-seq samples for accurate isoform quantification.. Annals of Applied Statistics. 2017, 第 1 作者  通讯作者  
[73] Chen, Jinyu, Zhang, Shihua. Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data. BIOINFORMATICS[J]. 2016, 第 11 作者32(11): 1724-1732, https://www.webofscience.com/wos/woscc/full-record/WOS:000377428700016.
[74] Min, Wenwen, Liu, Juan, Luo, Fei, Zhang, Shihua. A Two-Stage Method to Identify Joint Modules From Matched MicroRNA and mRNA Expression Data. IEEE TRANSACTIONS ON NANOBIOSCIENCE[J]. 2016, 第 4 作者  通讯作者  15(4): 362-370, https://www.webofscience.com/wos/woscc/full-record/WOS:000381445900008.
[75] Ning, Xuemei, Liu, Zhaoqi, Zhang, Shihua. Local community extraction in directed networks. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS[J]. 2016, 第 3 作者  通讯作者  452: 258-265, http://dx.doi.org/10.1016/j.physa.2016.01.101.
[76] Li, Zhenping, Wang, RuiSheng, Zhang, Shihua, Zhang, XiangSun. Quantitative function and algorithm for community detection in bipartite networks. INFORMATION SCIENCES[J]. 2016, 第 3 作者  通讯作者  367: 874-889, http://dx.doi.org/10.1016/j.ins.2016.07.024.
[77] Yuan, Qingjun, Gao, Junning, Wu, Dongliang, Zhang, Shihua, Mamitsuka, Hiroshi, Zhu, Shanfeng. DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank. BIOINFORMATICS[J]. 2016, 第 4 作者32(12): 18-27, https://www.webofscience.com/wos/woscc/full-record/WOS:000379734300003.
[78] Chen, Jinyu, Zhang, Shihua. Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data. BIOINFORMATICS[J]. 2016, 第 2 作者  通讯作者  32(11): 1724-1732, https://www.webofscience.com/wos/woscc/full-record/WOS:000377428700016.
[79] Lu, Jianbo, Xu, Guoliang, Zhang, Shihua, Lu, Benzhuo. An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data. ALGORITHMS FOR MOLECULAR BIOLOGY[J]. 2016, 第 3 作者  通讯作者  11(1): https://www.webofscience.com/wos/woscc/full-record/WOS:000378992100001.
[80] Yang, Xiaofei, Shao, Xiaojian, Gao, Lin, Zhang, Shihua. Comparative DNA methylation analysis to decipher common and cell type-specific patterns among multiple cell types. BRIEFINGS IN FUNCTIONAL GENOMICS[J]. 2016, 第 4 作者  通讯作者  15(6): 399-407, https://www.webofscience.com/wos/woscc/full-record/WOS:000392717700002.
[81] Ni, Xumin, Guo, Wei, Yuan, Kai, Yang, Xiong, Ma, Zhiming, Xu, Shuhua, Zhang, Shihua. A Probabilistic Method for Estimating the Sharing of Identity by Descent for Populations with Migration. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2016, 第 7 作者  通讯作者  13(2): 281-290, https://www.webofscience.com/wos/woscc/full-record/WOS:000374305300009.
[82] Chongzhi Zang, Tao Wang, Ke Deng, Bo Li, Shengen Hu, Qian Qin, Tengfei Xiao, Shihua Zhang, Clifford A Meyer, Housheng Hansen He, Myles Brown, Jun S Liu, Yang Xie, X Shirley Liu. High-dimensional genomic data bias correction and data integration using MANCIE. NATURE COMMUNICATIONS[J]. 2016, 第 8 作者7(1): https://doaj.org/article/aa14d67d31a54ea9b4ff50393da16654.
[83] Cao, Zhen, Zhang, Shihua. An integrative and comparative study of pan-cancer transcriptomes reveals distinct cancer common and specific signatures. SCIENTIFIC REPORTS[J]. 2016, 第 2 作者  通讯作者  6: http://dx.doi.org/10.1038/srep33398.
[84] Yang, Xiaofei, Shao, Xiaojian, Gao, Lin, Zhang, Shihua. Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin. HUMAN MOLECULAR GENETICS[J]. 2015, 第 4 作者24(15): 4374-4384, https://www.webofscience.com/wos/woscc/full-record/WOS:000361314100017.
[85] Min Wenwen, Liu Juan, Luo Fei, Zhang Shihua, Huan J, Miyano S, Shehu A, Hu X, Ma B, Rajasekaran S, Gombar VK, Schapranow IM, Yoo IH, Zhou JY, Chen B, Pai V, Pierce B. A novel two-stage method for identifying microRNA-gene regulatory modules in breast cancer. PROCEEDINGS 2015 IEEE INTERNATIONAL CONFERENCE ON BIOINFORMATICS AND BIOMEDICINE. 2015, 第 4 作者151-156, 
[86] Liu, Zhaoqi, Zhang, Shihua. Tumor characterization and stratification by integrated molecular profiles reveals essential pan-cancer features. BMC GENOMICS[J]. 2015, 第 2 作者  通讯作者  16(1): http://dx.doi.org/10.1186/s12864-015-1687-x.
[87] Yang, Xiaofei, Shao, Xiaojian, Gao, Lin, Zhang, Shihua. Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin. HUMAN MOLECULAR GENETICS[J]. 2015, 第 4 作者24(15): 4374-4384, https://www.webofscience.com/wos/woscc/full-record/WOS:000361314100017.
[88] Qiu, YuQing, Tian, Xue, Zhang, Shihua. Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS[J]. 2015, 第 3 作者12(5): 1112-1122, https://www.webofscience.com/wos/woscc/full-record/WOS:000362909500014.
[89] Zhang, Shihua, Chen, Luonan. Guest Editorial for Special Section on ISB/TBC 2014. IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 2015, 第 1 作者  通讯作者  12(5): 1074-1075, https://www.webofscience.com/wos/woscc/full-record/WOS:000362909500010.
[90] Tseng, YuTing, Li, Wenyuan, Chen, ChingHsien, Zhang, Shihua, Chen, Jeremy J W, Zhou, Xianghong Jasmine, Liu, ChunChi. IIIDB: a database for isoform-isoform interactions and isoform network modules. BMC GENOMICS[J]. 2015, 第 4 作者16(Suppl 2): S10-S10, http://dx.doi.org/10.1186/1471-2164-16-S2-S10.
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[92] Dai, Xiaofeng, Liu, Zhaoqi, Zhang, Shihua. Over-expression of EPS15 is a favorable prognostic factor in breast cancer. MOLECULAR BIOSYSTEMS[J]. 2015, 第 3 作者  通讯作者  11(11): 2978-2985, http://dx.doi.org/10.1039/c5mb00219b.
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[94] Zhang, Junhua, Wu, LingYun, Zhang, XiangSun, Zhang, Shihua. Discovery of co-occurring driver pathways in cancer. BMC BIOINFORMATICS[J]. 2014, 第 4 作者15(1): http://dx.doi.org/10.1186/1471-2105-15-271.
[95] Liu, Zhaoqi, Zhang, XiangSun, Zhang, Shihua. Breast tumor subgroups reveal diverse clinical prognostic power. SCIENTIFIC REPORTS[J]. 2014, 第 3 作者  通讯作者  4: http://dx.doi.org/10.1038/srep04002.
[96] Zhang, Shihua, Tian, Dechao, Ngoc Hieu Tran, Choi, Kwok Pui, Zhang, Louxin. Profiling the transcription factor regulatory networks of human cell types. NUCLEIC ACIDS RESEARCH[J]. 2014, 第 1 作者42(20): 12380-12387, https://www.webofscience.com/wos/woscc/full-record/WOS:000347693200011.
[97] Liu, Zhaoqi, Zhang, Shihua. Toward a systematic understanding of cancers: a survey of the pan-cancer study. FRONTIERS IN GENETICS. 2014, 第 2 作者  通讯作者  5: https://www.webofscience.com/wos/woscc/full-record/WOS:000347215100001.
[98] Li, Wenyuan, Kang, Shuli, Liu, ChunChi, Zhang, Shihua, Shi, Yi, Liu, Yan, Zhou, Xianghong Jasmine. High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance-based label propagation method. NUCLEIC ACIDS RESEARCH[J]. 2014, 第 4 作者42(6): http://dx.doi.org/10.1093/nar/gkt1362.
[99] Zhang Shihua. Discovery of cell-type specific regulatory elements in the human genome by differential chromatin modification analysis.. Nucleic Acids Research. 2013, 第 11 作者
[100] Zhang Shihua. Discovery of cell-type specific regulatory elements in the human genome by differential chromatin modification analysis.. Nucleic Acids Research. 2013, 第 1 作者  通讯作者  
[101] Li, Zhenping, Zhang, XiangSun, Wang, RuiSheng, Liu, Hongwei, Zhang, Shihua. Discovering Link Communities in Complex Networks by an Integer Programming Model and a Genetic Algorithm. PLOS ONE[J]. 2013, 第 5 作者  通讯作者  8(12): https://doaj.org/article/b93c748ba34a4473a4fc3e209bd9bccd.
[102] Zhang, ShiHua, Wang, XiuJie. Promote connections of young computational biologists in china. GENOMICS PROTEOMICS BIOINFORMATICS[J]. 2013, 第 1 作者11(4): 253, http://ir.amss.ac.cn/handle/2S8OKBNM/46418, http://www.irgrid.ac.cn/handle/1471x/6869605, http://ir.amss.ac.cn/handle/2S8OKBNM/46419.
[103] Chen, Chen, Zhang, Shihua, Zhang, XiangSun. Discovery of cell-type specific regulatory elements in the human genome using differential chromatin modification analysis. NUCLEIC ACIDS RESEARCH[J]. 2013, 第 2 作者  通讯作者  41(20): 9230-9242, https://www.webofscience.com/wos/woscc/full-record/WOS:000326746400012.
[104] Zhang, Junhua, Zhang, Shihua, Wang, Yong, Zhang, XiangSun. Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data. BMC SYSTEMS BIOLOGY[J]. 2013, 第 2 作者7(Suppl 2): S4-S4, http://dx.doi.org/10.1186/1752-0509-7-S2-S4.
[105] Zhao, Junfei, Zhang, Shihua, Wu, LingYun, Zhang, XiangSun. Efficient methods for identifying mutated driver pathways in cancer. BIOINFORMATICS[J]. 2012, 第 11 作者28(22): 2940-2947, https://www.webofscience.com/wos/woscc/full-record/WOS:000311303500011.
[106] Zhang, Shihua, Zhao, Junfei, Zhang, XiangSun. Common community structure in time-varying networks. PHYSICAL REVIEW E[J]. 2012, 第 11 作者85(5): http://dx.doi.org/10.1103/PhysRevE.85.056110.
[107] Zhang, Shihua, Liu, ChunChi, Li, Wenyuan, Shen, Hui, Laird, Peter W, Zhou, Xianghong Jasmine. Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. NUCLEIC ACIDS RESEARCH[J]. 2012, 第 1 作者40(19): 9379-9391, https://www.webofscience.com/wos/woscc/full-record/WOS:000310377200010.
[108] Zhao, Junfei, Zhang, Shihua, Wu, LingYun, Zhang, XiangSun. Efficient methods for identifying mutated driver pathways in cancer. BIOINFORMATICS[J]. 2012, 第 2 作者  通讯作者  28(22): 2940-2947, https://www.webofscience.com/wos/woscc/full-record/WOS:000311303500011.
[109] Xie, Jiang, Zhang, Wu, Zhang, Shihua, Wen, Tieqiao. A PARALLEL METHOD FOR QUERYING TARGET SUBNETWORK IN A BIOMOLECULAR NETWORK. INTERNATIONAL JOURNAL OF NUMERICAL ANALYSIS AND MODELING[J]. 2012, 第 3 作者9(2): 326-337, http://www.corc.org.cn/handle/1471x/2298202.
[110] Zhang, Shihua, Zhao, Junfei, Zhang, XiangSun. Common community structure in time-varying networks. PHYSICAL REVIEW E[J]. 2012, 第 1 作者  通讯作者  85(5): http://dx.doi.org/10.1103/PhysRevE.85.056110.
[111] Zhang, Shihua, Liu, ChunChi, Li, Wenyuan, Shen, Hui, Laird, Peter W, Zhou, Xianghong Jasmine. Discovery of multi-dimensional modules by integrative analysis of cancer genomic data. NUCLEIC ACIDS RESEARCH[J]. 2012, 第 1 作者40(19): 9379-9391, https://www.webofscience.com/wos/woscc/full-record/WOS:000310377200010.
[112] Li, Wenyuan, Zhang, Shihua, Liu, ChunChi, Zhou, Xianghong Jasmine. Identifying multi-layer gene regulatory modules from multi-dimensional genomic data. BIOINFORMATICS[J]. 2012, 第 2 作者28(19): 2458-2466, https://www.webofscience.com/wos/woscc/full-record/WOS:000309687500008.
[113] Zhang Shihua. A novel computational framework for simultaneous integration of multiple functional genomic data to identify microRNA-gene regulatory modules.. Bioinformatics. 2011, 第 1 作者
[114] Zhang, Shihua, Li, Qingjiao, Liu, Juan, Zhou, Xianghong Jasmine. A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. BIOINFORMATICS[J]. 2011, 第 1 作者  通讯作者  27(13): I401-I409, https://www.webofscience.com/wos/woscc/full-record/WOS:000291752600049.
[115] Zhang Shihua. A novel computational framework for simultaneous integration of multiple functional genomic data to identify microRNA-gene regulatory modules.. Bioinformatics. 2011, 第 1 作者
[116] Zhang, Shihua, Ning, XueMei, Ding, Chris, Zhang, XiangSun. Determining modular organization of protein interaction networks by maximizing modularity density. BMC SYSTEMS BIOLOGY[J]. 2010, 4(Suppl 2): S10-S10, http://dx.doi.org/10.1186/1752-0509-4-S2-S10.
[117] Zhang, Shihua, Vasishtan, Daven, Xu, Min, Topf, Maya, Alber, Frank. A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps. BIOINFORMATICS[J]. 2010, 第 1 作者26(12): i261-i268, https://www.webofscience.com/wos/woscc/full-record/WOS:000278689000032.
[118] Zhang, Shihua, Ning, XueMei, Ding, Chris, Zhang, XiangSun. Determining modular organization of protein interaction networks by maximizing modularity density. BMC SYSTEMS BIOLOGY[J]. 2010, 第 1 作者  通讯作者  4(Suppl 2): S10-S10, http://dx.doi.org/10.1186/1752-0509-4-S2-S10.
[119] Zhang, Shihua, Vasishtan, Daven, Xu, Min, Topf, Maya, Alber, Frank. A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps. BIOINFORMATICS[J]. 2010, 第 1 作者26(12): i261-i268, https://www.webofscience.com/wos/woscc/full-record/WOS:000278689000032.
[120] Qiu, YuQing, Zhang, Shihua, Zhang, XiangSun, Chen, Luonan. Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC BIOINFORMATICS[J]. 2010, 第 2 作者11(1): http://dx.doi.org/10.1186/1471-2105-11-26.
[121] Ning Xuemei, Zhang Shihua, Chen L, Zhang XS, Wu LY, Wang Y. A Robust Clustering Technique for Grouping Biological Data: an Illustrative Study in Gene Expression Data. OPTIMIZATION AND SYSTEMS BIOLOGY. 2009, 第 2 作者11: 267-+, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000281131900036.
[122] Zhang, Shihua, Liu, HongWei, Ning, XueMei, Zhang, XiangSun. A hybrid graph-theoretic method for mining overlapping functional modules in large sparse protein interaction networks. INTERNATIONAL JOURNAL OF DATA MINING AND BIOINFORMATICS[J]. 2009, 第 1 作者  通讯作者  3(1): 68-84, http://dx.doi.org/10.1504/IJDMB.2009.023885.
[123] Li, Zhenping, Zhang, Shihua, Zhang, XiangSun, Chen, Luonan. Exploring the constrained maximum edge-weight connected graph problem. ACTA MATHEMATICAE APPLICATAE SINICA-ENGLISH SERIES[J]. 2009, 第 2 作者25(4): 697-708, http://lib.cqvip.com/Qikan/Article/Detail?id=31511295.
[124] Zhang Shihua, Ning Xuemei, Ding Chris, Chen L, Zhang XS, Wu LY, Wang Y. Maximizing Modularity Density for Exploring Modular Organization of Protein Interaction Networks. OPTIMIZATION AND SYSTEMS BIOLOGY. 2009, 第 1 作者  通讯作者  11: 361-370, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000281131900047.
[125] Wang, Jiguang, Zhang, Shihua, Wang, Yong, Chen, Luonan, Zhang, XiangSun. Disease-Aging Network Reveals Significant Roles of Aging Genes in Connecting Genetic Diseases. PLOS COMPUTATIONAL BIOLOGY[J]. 2009, 第 2 作者5(9): https://doaj.org/article/f7efb0c5812346619ced3f2c4419ed8f.
[126] Li, Zhenping, Zhang, Shihua, Zhang, XiangSun, Chen, Luonan. Exploring the constrained maximum edge-weight connected graph problem. ACTA MATHEMATICAE APPLICATAE SINICA-ENGLISH SERIES[J]. 2009, 第 2 作者25(4): 697-708, http://lib.cqvip.com/Qikan/Article/Detail?id=31511295.
[127] Zhang, Shihua, Zhang, XiangSun, Chen, Luonan. Biomolecular network querying: a promising approach in systems biology. BMC SYSTEMS BIOLOGY[J]. 2008, 第 1 作者2(1): http://www.corc.org.cn/handle/1471x/2348709.
[128] Li, Zhenping, Zhang, Shihua, Wang, RuiSheng, Zhang, XiangSun, Chen, Luonan. Quantitative function for community detection. PHYSICAL REVIEW E[J]. 2008, 第 2 作者77(3): http://www.corc.org.cn/handle/1471x/2348799.
[129] Qiu YuQing, Zhang Shihua, Zhang XiangSun, Zhang XS, Chen L, Wu LY, Wang Y. Uncovering differentially expressed pathways with protein interaction and gene expression data. OPTIMIZATION AND SYSTEMS BIOLOGY, PROCEEDINGS. 2008, 第 2 作者9: 74-82, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000264181700010.
[130] Wang, RuiSheng, Zhang, Shihua, Wang, Yong, Zhang, XiangSun, Chen, Luonan. Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures. NEUROCOMPUTING[J]. 2008, 第 2 作者72(1-3): 134-141, http://www.corc.org.cn/handle/1471x/2349389.
[131] Wang, RuiSheng, Zhang, Shihua, Zhang, XiangSun, Chen, Luonan, Huang, DS, Heutte, L, Loog, M. Identifying modules in complex networks by a graph-theoretical method and its application in protein interaction networks. ADVANCEDINTELLIGENTCOMPUTINGTHEORIESANDAPPLICATIONSPROCEEDINGS. 2007, 第 2 作者4682: 1090-1101, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000250577100113.
[132] Zhang, Shihua, Wang, RuiSheng, Zhang, XiangSun. Uncovering fuzzy community structure in complex networks. PHYSICAL REVIEW E[J]. 2007, 第 1 作者  通讯作者  76(4): http://dx.doi.org/10.1103/PhysRevE.76.046103.
[133] Jin Guangxu, Zhang Shihua, Zhang XiangSun, Chen Luonan, Zhang XS, Chen LN, Wu LY, Wang Y. New insights into network motif clusters from the views of cellular Localizations and signal pathways. OPTIMIZATION AND SYSTEMS BIOLOGY. 2007, 第 2 作者7: 100-+, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000250141900013.
[134] Zhang, XiangSun, Wang, RuiSheng, Wu, LingYun, Zhang, ShiHua, Cben, Luonan, Kim, SI, Suh, TS. Inferring Protein-Protein Interactions by Combinatorial Models. WORLD CONGRESS ON MEDICAL PHYSICS AND BIOMEDICAL ENGINEERING 2006, VOL 14, PTS 1-6. 2007, 第 4 作者14: 183-+, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000260855900044.
[135] Jin, Guangxu, Zhang, Shihua, Zhang, XiangSun, Chen, Luonan. Hubs with Network Motifs Organize Modularity Dynamically in the Protein-Protein Interaction Network of Yeast. PLOS ONE[J]. 2007, 第 2 作者2(11): http://www.corc.org.cn/handle/1471x/2389076.
[136] Wang RuiSheng, Zhang Shihua, Zhang XiangSun, Chen Luonan, Huang DS, Heutte L, Loog M. Identifying modules in complex networks by a graph-theoretical method and its application in protein interaction networks. ADVANCED INTELLIGENT COMPUTING THEORIES AND APPLICATIONS, PROCEEDINGS. 2007, 第 2 作者4682: 1090-1101, 
[137] Zhang XiangSun, Wang RuiSheng, Wu LingYun, Zhang ShiHua, Cben Luonan, Kim SI, Suh TS. Inferring Protein-Protein Interactions by Combinatorial Models. WORLD CONGRESS ON MEDICAL PHYSICS AND BIOMEDICAL ENGINEERING 2006, VOL 14, PTS 1-6. 2007, 第 4 作者14: 183-+, 
[138] 张世华, 章祥荪. 以C_α-C_α距离为基础的构象空间的可视化研究. 生物信息学. 2006, 第 1 作者http://kns.cnki.net/KCMS/detail/detail.aspx?QueryID=0&CurRec=2548&recid=&FileName=XXSW200604002&DbName=CJFD2006&DbCode=CJFQ&yx=&pr=&URLID=&bsm=QK0103;.
[139] Li Zhenping, Wang Yong, Zhang Shihua, Zhang XiangSun, Chen Luonan, IEEE. Alignment of protein interaction networks by integer quadratic programming. 2006 28TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-15. 2006, 第 3 作者187-190, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000247284700046.
[140] Li Zhenping, Wang Yong, Zhang Shihua, Zhang XiangSun, Chen Luonan, IEEE. Alignment of protein interaction networks by integer quadratic programming. 2006 28TH ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY, VOLS 1-15. 2006, 第 3 作者187-190, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000247284700046.
[141] Zhang, Shihua, Ning, Xuemei, Zhang, XiangSun. Identification of functional modules in a PPI network by clique percolation clustering. COMPUTATIONAL BIOLOGY AND CHEMISTRY[J]. 2006, 第 1 作者  通讯作者  30(6): 445-451, http://dx.doi.org/10.1016/j.compbiolchem.2006.10.001.
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（ 1 ） 基于数据整合识别微小RNA 调控元件的优化模型和算法研究, 负责人, 国家任务, 2011-01--2013-12
（ 2 ） 中国科学院青年创新促进会, 负责人, 国家任务, 2011-01--2014-12
（ 3 ） 复杂网络中的优化问题及其在系统生物学中的应用, 参与, 国家任务, 2012-01--2016-12
（ 4 ） 陈景润未来之星, 负责人, 研究所自选, 2011-01--2013-12
（ 5 ） 生物信息学, 负责人, 国家任务, 2015-01--2017-12
（ 6 ） 卓越青年科学家项目, 负责人, 国家任务, 2014-07--2017-06
（ 7 ） 基于数据整合的计算癌症基因组学研究, 负责人, 国家任务, 2014-01--2017-12
（ 8 ） 网络化知识的基础理论与应用, 参与, 国家任务, 2017-01--2022-12
（ 9 ） 癌症基因组大数据深度分析中的优化建模和算法研究, 负责人, 国家任务, 2017-01--2019-12
（ 10 ） 国家万人计划青年拔尖人才, 负责人, 国家任务, 2018-01--2020-12
（ 11 ） 生物大数据的深度挖掘理论, 负责人, 中国科学院计划, 2016-07--2021-06
（ 12 ） 生物大数据的整合建模, 负责人, 中国科学院计划, 2017-07--2019-06
（ 13 ） 多维度、多尺度、多模态生物实验数据及其智能算法理论, 负责人, 国家任务, 2020-06--2025-05
（ 14 ） 基于贝叶斯推断的复杂JS数据分析, 负责人, 国家任务, 2019-08--2022-07

已指导学生

章帅  硕士研究生  070105-运筹学与控制论  

李学峰  硕士研究生  070105-运筹学与控制论  

闫晓芳  硕士研究生  070105-运筹学与控制论  

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张炙炀  硕士研究生  071400-统计学  

张彪  硕士研究生  070105-运筹学与控制论  

曹振  博士研究生  070105-运筹学与控制论  

王蓓  博士研究生  070105-运筹学与控制论  

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张丽华  博士研究生  070105-运筹学与控制论  

董康宁  博士研究生  070105-运筹学与控制论  

张驰浩  博士研究生  070105-运筹学与控制论  

现指导学生

张文豪  硕士研究生  070105-运筹学与控制论  

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阮天雨  博士研究生  070105-运筹学与控制论  

贾玉涵  硕士研究生  0710J3-生物信息学