| Yusen Ye, Lin Gao#, Shihua Zhang#. MSTD: an efficient method for detecting multi-scale topological domains from symmetric and asymmetric 3D genomic maps. (in submission). [Pubmed] |
| Zhenxing Guo, Shihua Zhang#. Sparse deep nonnegative matrix factorization. (in submission). [Pubmed] |
| Lihua Zhang, Shihua Zhang#. A unified joint matrix factorization framework for data integration. (in submission). [Pubmed] |
| Lihua Zhang, Shihua Zhang#. Learning common and specific patterns from data of multiple interrelated biological scenarios with matrix factorization. (in submission). [Pubmed] |
| Wenwen Min, Juan Liu#, Shihua Zhang#. L0-norm sparse graph-regularized SVD for biclustering. (in submission). [Pubmed] |
| Zhen Cao, Shihua Zhang#. Novel tricks of convolutional neural network architectures improve DNA–protein binding prediction. (in submission). [Pubmed] |
| Fang Jing, Shao-Wu Zhang#, Zhen Cao, Shihua Zhang#. An integrative framework for combing sequence and epigenomic data to predict transcription factor binding sites using deep learning. (in submission). [Pubmed] |
| Shihua Zhang#, Guanghua Hu, Wenwen Min. A neurodynamic framework for local community extraction in networks. (in submission). [Pubmed] |
| Chihao Zhang, Shihua Zhang#. Bayesian joint matrix decomposition for data integration with heterogeneous noise. IEEE Transactions on Pattern Analysis and Machine Intelligence (TPAMI) (2018), in revision. [arXiv] |
| Zhen Cao, Shihua Zhang#. Probe efficient feature representation of gapped k-mer frequency vectors from sequences using deep neural networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) (2018), in revision. [arXiv] |
| Jinyu Chen, Shihua Zhang#. Discovery of two-level modular organization from matched genomic data via joint matrix tri-factorization. Nucleic Acids Research (2018), gky440. [Pubmed] |
| Wenwen Min, Juan Liu#, Shihua Zhang#. Edge-group sparse PCA for network-guided high dimensional data analysis. Bioinformatics (2018), bty362. [Pubmed] |
| Wei Li, Anqi Zhao, Shihua Zhang#, Jingyi Li#. Joint modeling of multiple RNA-seq samples for accurate isoform quantification. The Annals of Applied Statistics (2018), DOI: 10.1214/17-AOAS1100. [arXiv] |
| Jinyu Chen, Shihua Zhang#. Matrix integrative analysis (MIA) of multiple genomic data for modular patterns. Frontiers in Genetics (2018), in press. [Pubmed] |
| Bei Wang, Jinyu Chen, Shihua Zhang#. BMTK: a toolkit for determining modules in biological bipartite networks. Quantitative Biology (2018), in press. [Pubmed] |
| Lihua Zhang, Shihua Zhang#. Comparison and evaluation of computational methods for imputing single-cell RNA-sequencing data. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB) (2018), in press. [Pubmed] |
| Junhua Zhang, Shihua Zhang#. Discovery of cancer common and specific gene sets. Nucleic Acids Research (2017), 45 (10): e86. [Paper] |
| Can Wang, Shihua Zhang#. Large-scale determination and characterization of cell type-specific regulatory elements in the human genome. Journal of Molecular Cell Biology (2017), 9(6), 463–476. [Pubmed] |
| Yusen Ye, Lin Gao#, Shihua Zhang#. Integrative analysis of transcription factor combinatorial interactions using a Bayesian tensor factorization approach. Frontiers in Genetics (2017), doi: 10.3389/fgene.2017.00140. [Pubmed] |
| Wenwen Min, Juan Liu# and Shihua Zhang#. Sparse weighted canonical correlation analysis. Chinese Journal of Electronics (2017), doi:10.1049/cje.2017.08.004. [Pubmed] |
| Fang Jiang, Shaowu Zhang# and Shihua Zhang#. A brief survey of methods for biological network alignment and a variant with incorporation of functional annotations. Current Bioinformatics (2017), DOI: 10.2174/1574893612666171020103747. [Pubmed] |
| Jinyu Chen, Shihua Zhang#. Integrative cancer genomics: models, algorithms and analysis. Frontiers of Computer Science, (2017), 11(3): 392-406. [Pubmed] |
| Jinyu Chen, Shihua Zhang#. Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data. Bioinformatics,(2016), 32(11):1724-1732. [Pubmed] |
| Junhua Zhang, Shihua Zhang#. The discovery of mutated driver pathways in cancer: models and algorithms. IEEE/ACM Transactions on Computational Biology and Bioinformatics (2016), doi:10.1109/TCBB.2016.2640963. [Pubmed] |
| Wenwen Min, Juan Liu# and Shihua Zhang#. Network-regularized sparse logistic regression models for clinical risk prediction and biomarker discovery. IEEE/ACM Transactions on Computational Biology and Bioinformatics (2016), doi:10.1109/TCBB.2016.2640303. [Pubmed] |
| Qingjun Yuan, Junning Gao, Dongliang Wu, Shihua Zhang, Hiroshi Mamitsuka, Shanfeng Zhu. DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank. Bioinformatics (ISMB2016) (2016), 32(12): i18-i27. [Pubmed] |
| Xiaofei Yang, Lin Gao#, Shihua Zhang#. Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns. Briefings in Bioinformatics (2016), doi: 10.1093/bib/bbw063. [Pubmed] |
| Xiaofei Yang, Xiaojian Shao, Lin Gao#, Shihua Zhang#. Comparative DNA methylation analysis to decipher common and cell type-specific patterns among multiple cell types. Briefing in Functional Genomics (2016), 15: 399-407. [Pubmed] |
| Xumin Ni, Wei Guo, Kai Yuan, Xiong Yang, Zhiming Ma, Shuhua Xu, Shihua Zhang#. A probabilistic method for estimating the sharing of identity by descent for populations with migration. IEEE/ACM Transactions on Computational Biology and Bioinformatics (2016), DOI: 10.1109/TCBB.2015.2480074. [Pubmed] |
| Wenwen Min, Juan Liu#, Fei Luo, Shihua Zhang#. A two-stage method to identify joint modules from matched microRNA and mRNA expression data. IEEE Transactions on Nanobioscience (2016), 15(4), 362-370. [Pubmed] |
| Shihua Zhang#. Computational methods for subtyping of tumors and their applications for deciphering tumor heterogeneity. Methods in Molecular Biology (2016), in press. [Pubmed] |
| Xuemei Ning, Zhaoqi Liu, Shihua Zhang#. Local community extraction in directed networks. Physica A (2016), 452:258-265. [Pubmed] |
| Zhenping Li, Rui-Sheng Wang, Shihua Zhang#, Xiang-Sun Zhang#. Quantitative function and algorithm for community detection in bipartite networks. Information Sciences (2016), 367/368, 874–889. [Pubmed] |
| Steven M. Hill, ... (including Zhaoqi Liu, Wenwen Min, Shihua Zhang) ...., et al. Inferring causal molecular networks: empirical assessment through a community-based effort. Nature Methods (2016), 13(4):310-318. [Pubmed] |
| Xiaofei Yang, Xiaojian Shao, Lin Gao#, Shihua Zhang#. Systematic DNA methylation analysis of multiple cell lines reveals common and specific patterns within and across tissues of origin. Human Molecular Genetics (2015), 24(15):4374-4384. [Pubmed][Supplementary data] |
| Xiaofeng Dai&, Zhaoqi Liu&, Shihua Zhang#. Over-expression of EPS15 is a favourable prognostic factor in breast cancer. Molecular BioSystems (2015), 11:2978-2985. [Pubmed] |
| Zhaoqi Liu, Shihua Zhang#. Tumor characterization and stratification by integrated molecular profiles reveals essential pan-cancer features. BMC Genomics (2015), 16, 503.[Article] |
| Yu-Qing Qiu, Xue Tian, Shihua Zhang#. Infer biodiversity of metagenomic samples and reveal homologous genomes based on the structure of taxonomy tree. IEEE/ACM TCBB (2015), 12(5), 1112-1122. [Pubmed] |
| Yu-Ting Tseng, Wenyuan Li, Shihua Zhang, Xianghong Jasmine Zhou and Chun-Chi Liu. IIIDB: A database for Isoform-Isoform Interactions and isoform network modules. BMC Genomics 2015 (APBC2015), 16(Suppl 2):S10. [Pubmed] |
| Eduati F, ... (including Zhang S, Zhao J) ...., et al. Prediction of human population responses to toxic compounds by a collaborative competition. Nat Biotechnol. (2015), 33(9):933-940.
|
| Shihua Zhang, Dechao Tian, Ngoc Hieu Tran, Kwok Pui Choi, Louxin Zhang. Profiling the transcription factor regulatory networks of human cell types. Nucleic Acids Research. (2014), 42(20):12380-12387. [Pubmed] |
Junhua Zhang#, Ling-Yun Wu, Xiang-Sun Zhang, Shihua Zhang#. Discovery of co-occurring driver pathways in cancer. BMC Bioinformatics (2014), 15:271.  [Pubmed] |
| James C Costello et al. (Shihua Zhang is listed as one co-author). The challenge of drug sensitivity prediction: an assessment of methods through collaborative competition. Nature Biotechnology (2014), doi: 10.1038/nbt.2877. [Pubmed] |
| Mukesh Bansal et al. (Shihua Zhang is listed as one co-author). A community computational challenge to predict the activity of pairs of compounds. Nature Biotechnology (2014), in press. [Article] |
| Zhaoqi Liu, Shihua Zhang#. Towards a systematic understanding of cancers: a survey of the pan-cancer study. Frontiers in Genetics (2014), 5:194. [Pubmed] |
| Shihua Zhang#, Xianghong Jasmine Zhou#. Matrix factorization methods for integrative cancer genomics. Methods in Molecular Biology (2014), 1176:229-42. [Pubmed] |
| Junfei Zhao, Xiang-Sun Zhang, Shihua Zhang#. Predicting cooperative drug effects by the quantitative cellular profiling of response to individual drugs. CPT: Pharmacometrics and Systems Pharmacology (2014), 3: e102. [Pubmed] |
| Zhaoqi Liu, Xiang-Sun Zhang, Shihua Zhang#. Breast tumour subgroups reveal diverse clinical predictive power. Scientific Report (2014), 4: 4002. [Pubmed] |
| Wenyuan Li, Shuli Kang, Chun-Chi Liu, Shihua Zhang, Yi Shi, Yan Liu, Xianghong Jasmine Zhou#. High-resolution functional annotation of human transcriptome: predicting isoform functions by a novel multiple instance based label propagation method. Nucleic Acids Research (2013), 42 (6):e39. doi: 10.1093/nar/gkt1362. [Pubmed] |
| Zhenping Li, Xiang-Sun Zhang, Rui-Sheng Wang, Hongwei Liu, Shihua Zhang#. Discovering link communities in complex networks by an integer programming model and a genetic algorithm. PLOS One (2013), 8(12):e83739. doi: 10.1371/journal.pone.0083739. [Pubmed] |
| Chen Chen&, Shihua Zhang&#, Xiang-Sun Zhang. Discovery of cell-type specific regulatory elements in the human genome by differential chromatin modification analysis. Nucleic Acids Research (2013), 41(20): 9230-9242. doi: 10.1093/nar/gkt712. [Article] |
| Junhua Zhang, Shihua Zhang#, Yong Wang, Xiang-Sun Zhang. Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data. BMC Systems Biology (2013), 7(Suppl 2):S4. [Pubmed] |
| Shihua Zhang#, Xiu-Jie Wang#. Promote Connections of Young Computational Biologists in China. Genomics, Proteomics & Bioinformatics (2013), 11, 253–256. (Meeting report) [Pubmed] |
| Shihua Zhang#. Integrating multiple types of data to identify microRNA-gene co-modules. Methods in Molecular Biology (2013), 1049, 215-229. [Pubmed] |
| Junfei Zhao&, Shihua Zhang&#, Ling-Yun Wu, Xiang-Sun Zhang. Efficient methods for identifying mutated driver pathways in cancer, Bioinformatics (2012) 28(22): 2940-2947. [Pubmed] |
| Shihua Zhang, Chun-Chi Liu, Wenyuan Li, Hui Shen, Peter Laird, Xianghong Jasmine Zhou. Discovery of multi-dimensional modules by integrative analysis of cancer genomic data, Nucleic Acids Research (2012), 40(19): 9379-9391. [Pubmed] |
| Wenyuan Li&, Shihua Zhang&, Chun-Chi Liu, Xianghong Jasmine Zhou. Identifying multi-layer gene regulatory modules from multi-dimensional genomic data. Bioinformatics (2012), 28(19): 2458-2466. [Pubmed] |
| Shihua Zhang#, Junfei Zhao, Xiang-Sun Zhang. Co-community structure in time-varying networks, Physical Review E (2012), 85, 056110. e-print:arXiv:1111.1365v2. [Pubmed] |
| Jiang Xie, Wu Zhang, Shihua Zhang, Tieqiao Wen. A parallel method for querying target subnetwork in a biomolecular network. International Journal of Numerical Analysis & Modeling (2012), 9(2): 326-337. [Article] |
| Ji-Guang Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen. Disease-aging network reveals significant roles of aging genes in connecting genetic diseases. PLoS Computational Biology, 5(9): e1000521, 2009. [Pubmed] |
| Zhenping Li&, Shihua Zhang&, Xiang-Sun Zhang, Luonan Chen . Exploring the Constrained Maximum Edge-Weight Connected Graph Problem. Acta Mathematicae Applicatae Sinica (E) 25(4), 697-708, 2009. [Article] |
| Qiu Yuqing, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen. Identifying differentially expressed pathways based on a mixed integer linear programming model. IET Systems Biology, 3(6), 475-486, 2009. [Pubmed] |
| Zhenping Li&, Shihua Zhang&, Ruisheng Wang, Xiang-Sun Zhang, Luonan Chen. Quantitative function for community detection. Physical Review E, 77, 036109, 2008. It has been selected by Virtual Journal of Biological Physics Research, 15(6), 2008. [Pubmed] |
| Shihua Zhang, Xiang-Sun Zhang, Luonan Chen. Biomolecular network querying: a promising approach in systems biology. BMC Systems Biology, 2008, 2:5. [Pubmed] |
| Shihua Zhang, Guanxu Jin, Xiang-Sun Zhang, Luonan Chen. Discovering functions and revealing mechanisms at molecular level from biological networks. Proteomics, 7(16), 2856-69, 2007. [Pubmed] |
| Zhenping Li&, Shihua Zhang&, Yong Wang, Xiang-Sun Zhang, Luonan Chen. Alignment of molecular networks by integer quadratic programming. Bioinformatics, 23(13), 1631-1639, 2007. [Pubmed] |
| Shihua Zhang, Hong-Wei Liu Xue-Mei Ning, Xiang-Sun Zhang. A hybrid graph-theoretic method for mining functional modules in large sparse protein interaction networks. International Journal of Data Mining in Bioinformatics, 3(1), 68-84, 2009. [Pubmed] |
| Guangxu Jin, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen. Hubs with network motifs organize modularity dynamically in the protein-protein interaction network of yeast. PLoS ONE 2(11): e1207, 2007. [Pubmed] |
| Shihua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang . Uncovering fuzzy community structure in complex networks. Physical Review E, 76, 046103, 2007. It has been selected by Virtual Journal of Biological Physics Research, 14(8), 2007. [Pubmed] |
| Shihua Zhang, Xue-Mei Ning, Xiang-Sun Zhang. Graph kernels, hierarchical clustering, network community structure: experiment and comparative analysis. Eur. Phys. J. B, 57, 67-74, 2007. [Article] |
| Shihua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang. Identification of overlapping community structure in complex networks using fuzzy c-means clustering. Physica A: Statistical Mechanics and its Applications, 374(1), 483-490, 2007. [Article] |
| Rui-Sheng Wang, Shihua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen. Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures. Neurocomputing 72 (2008) 134-141. [Article] |
| Junhua Zhang, Shihua Zhang, Xiang-Sun Zhang. Detecting community structure in complex networks based on a measure of information discrepancy. Physica A: Statistical Mechanics and its Applications, 387(7), 1675-1682, 2008. [Article] |
| Luonan Chen, Ling-Yun Wu, Yong Wang, Shihua Zhang, Xiang-Sun Zhang. Revealing Divergent evolution, identifying circular permutations and detecting active-sites by protein structure comparison. BMC Structural Biology, 2006, 6:18. [Pubmed] |
| Shihua Zhang, Xue-Mei Ning, Xiang-Sun Zhang. Identification of functional modules in PPI network by clique percolation clustering. Computational Biology and Chemistry, 30(6), 445-451, 2006. [Pubmed] |
| Shihua Zhang, Xue-Mei Ning, Hong-Wei Liu and Xiang-Sun Zhang. Prediction of protein complexes based on protein interaction data and functional annotation data using kernel methods. Lecture Note in Bioinformatics, 4115, 514-524, 2006. [Article] |
| Luonan Chen, Ling-Yun Wu, Ruiqi Wang, Yong Wang,Shihua Zhang, Xiang-Sun Zhang. Comparison of protein structures by multi-objective optimization. Genome Informatics, 16, 2, 114-124, 2005. [Pubmed] |
[Pubmed]