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2020 – today
- 2024
- [j70]Pan Lai, Yiran Tao, Jun Qin, Yuanai Xie, Shihua Zhang, Shanjiang Tang, Qirui Huang, Shengquan Liao:
Joint optimization of application placement and resource allocation for enhanced performance in heterogeneous multi-server systems. Comput. Networks 253: 110692 (2024) - [j69]Zheming Li, Yidan Chen, Bo Yang, Chenwei Li, Shihua Zhang, Wei Li, Hengwei Zhang:
Enhancing the transferability of adversarial attacks with diversified input strategies. J. Intell. Fuzzy Syst. 46(4): 10359-10373 (2024) - [j68]Kuo Gai
, Shihua Zhang
Tessellating the Latent Space for Non-Adversarial Generative Auto-Encoders. IEEE Trans. Pattern Anal. Mach. Intell. 46(2): 780-792 (2024) - [j67]Shihua Zhang
ConvMatch: Rethinking Network Design for Two-View Correspondence Learning. IEEE Trans. Pattern Anal. Mach. Intell. 46(5): 2920-2935 (2024) - [j66]Chihao Zhang
Matrix normal PCA for interpretable dimension reduction and graphical noise modeling. Pattern Recognit. 154: 110591 (2024) - [j65]Penglong Zhai
Adversarial Information Bottleneck. IEEE Trans. Neural Networks Learn. Syst. 35(1): 221-230 (2024) - [c17]Yuxin Deng, Kaining Zhang, Shihua Zhang, Yansheng Li, Jiayi Ma:
ResMatch: Residual Attention Learning for Feature Matching. AAAI 2024: 1501-1509 - [c16]Shihua Zhang, Zizhuo Li, Yuan Gao, Jiayi Ma:
DeMatch: Deep Decomposition of Motion Field for Two-View Correspondence Learning. CVPR 2024: 20278-20287 - [i24]Sicong Wang, Kuo Gai, Shihua Zhang:
Progressive Feedforward Collapse of ResNet Training. CoRR abs/2405.00985 (2024) - [i23]Kuo Gai, Shihua Zhang:
Analytical Solution of a Three-layer Network with a Matrix Exponential Activation Function. CoRR abs/2407.02540 (2024) - [i22]Kuo Gai, Sicong Wang, Shihua Zhang:
OTAD: An Optimal Transport-Induced Robust Model for Agnostic Adversarial Attack. CoRR abs/2408.00329 (2024) - 2023
- [j64]Kaixuan Xiao, Yu Wang, Kangning Dong, Shihua Zhang:
SmartGate is a spatial metabolomics tool for resolving tissue structures. Briefings Bioinform. 24(3) (2023) - [j63]Xingyu Jiang, Shihua Zhang, Xiaoping Zhang, Jiayi Ma
Improving sparse graph attention for feature matching by informative keypoints exploration. Comput. Vis. Image Underst. 235: 103803 (2023) - [j62]Chihao Zhang
A Python Package itca for Information-Theoretic Classification Accuracy: A Criterion That Guides Data-Driven Combination of Ambiguous Outcome Labels in Multiclass Classification. J. Comput. Biol. 30(11): 1246-1249 (2023) - [j61]Xiang Zhou, Kangning Dong, Shihua Zhang:
Integrating spatial transcriptomics data across different conditions, technologies and developmental stages. Nat. Comput. Sci. 3(10): 894-906 (2023) - [j60]Penglong Zhai
Learnable Graph-Regularization for Matrix Decomposition. ACM Trans. Knowl. Discov. Data 17(3): 32:1-32:20 (2023) - [c15]Shihua Zhang, Jiayi Ma:
ConvMatch: Rethinking Network Design for Two-View Correspondence Learning. AAAI 2023: 3472-3479 - [c14]Zizhuo Li, Shihua Zhang, Jiayi Ma:
U-Match: Two-view Correspondence Learning with Hierarchy-aware Local Context Aggregation. IJCAI 2023: 1169-1176 - [i21]Rui Zhang
Monte Carlo Neural Operator for Learning PDEs via Probabilistic Representation. CoRR abs/2302.05104 (2023) - 2022
- [j59]Zhen Cao, Yanting Huang, Ran Duan, Peng Jin, Zhaohui S. Qin
Disease category-specific annotation of variants using an ensemble learning framework. Briefings Bioinform. 23(1) (2022) - [j58]Tong Zhang, Yixuan Lin, Weimin He, FengXin Yuan, Yu Zeng, Shihua Zhang:
GCN-GENE: A novel method for prediction of coronary heart disease-related genes. Comput. Biol. Medicine 150: 105918 (2022) - [j57]Yu Hao, Xiaohua Wan, Rui Yan, Zhiyong Liu, Jintao Li, Shihua Zhang, Xuefeng Cui
VP-Detector: A 3D multi-scale dense convolutional neural network for macromolecule localization and classification in cryo-electron tomograms. Comput. Methods Programs Biomed. 221: 106871 (2022) - [j56]Xu Shan, Jinyu Chen, Kangning Dong, Wei Zhou, Shihua Zhang
Deciphering the Spatial Modular Patterns of Tissues by Integrating Spatial and Single-Cell Transcriptomic Data. J. Comput. Biol. 29(7): 650-663 (2022) - [j55]Chihao Zhang
Information-theoretic Classification Accuracy: A Criterion that Guides Data-driven Combination of Ambiguous Outcome Labels in Multi-class Classification. J. Mach. Learn. Res. 23: 341:1-341:65 (2022) - [j54]Yongbiao Xue, Yiming Bao, Zhang Zhang, Wenming Zhao, Jing-Fa Xiao, Shunmin He, Guoqing Zhang, Yixue Li, Guoping Zhao, Runsheng Chen, Jingyao Zeng, Yadong Zhang, Yunfei Shang, Jialin Mai, Shuo Shi, Mingming Lu, Congfan Bu, Zhewen Zhang, Zhenglin Du, Yinying Wang, Hongen Kang, Tianyi Xu, Lili Hao, Peilin Jia, Shuai Jiang, Qiheng Qian, Tongtong Zhu, Wenting Zong, Tong Jin, Yuansheng Zhang, Dong Zou, Qiang Du, Changrui Feng, Lina Ma, Sisi Zhang, Anke Wang, Lili Dong, Yanqing Wang, Wan Liu, Xing Yan, Yunchao Ling, Zhihua Zhou, Wang Kang, Tao Zhang, Shuai Ma, Haoteng Yan, Zunpeng Liu, Zejun Ji, Yusheng Cai, Si Wang, Moshi Song, Jie Ren, Qi Zhou, Jing Qu, Weiqi Zhang, Guanghui Liu, Xu Chen, Tingting Chen, Yanling Sun, Caixia Yu, Bixia Tang, Junwei Zhu, Shuang Zhai, Yubin Sun, Qiancheng Chen, Xiaoyu Yang, Xin Zhang, Zhengqi Sang, Yonggang Wang, Yilin Zhao, Huanxin Chen, Li Lan, Yingke Ma, Yaokai Jia, Xinchang Zheng, Meili Chen, Ming Chen, Guangyi Niu, Rong Pan, Wei Jing, Jian Sang, Chang Liu, Yujia Xiong, Mochen Zhang, Guoliang Wang, Lizhi Yi, Wei Zhao, Song Wu, Zhuang Xiong, Rujiao Li, Zheng Gong, Lin Liu, Zhao Li, Qianpeng Li, Sicheng Luo, Jiajia Wang, Yirong Shi, Honghong Zhou, Peng Zhang, Tingrui Song, Yanyan Li, Fei Yang, Mengwei Li, Zhaohua Li, Dongmei Tian, Xiaonan Liu, Cuiping Li, Xufei Teng, Shuhui Song, Yang Zhang, Ruru Chen, Rongqin Zhang, Feng Xu, Yifan Wang, Chenfen Zhou, Haizhou Wang, Andrew E. Teschendorff, Yungang He, Zhen Yang, Lun Li, Na Li, Ying Cui, Guangya Duan, Gangao Wu, Tianhao Huang, Enhui Jin, Hailong Kang, Zhonghuang Wang, Hua Chen, Mingkun Li, Wanshan Ning, Yu Xue, Yanhu Liu, Qijun Zhou, Xingyan Liu, Longlong Zhang, Bingyu Mao, Shihua Zhang, Yaping Zhang, Guodong Wang, Qianghui Zhu, Xin Li, Menghua Li, Yuanming Liu, Hong Luo, Xiaoyuan Wu, Haichun Jing, Yitong Pan, Leisheng Shi, Zhixiang Zuo, Jian Ren, Xinxin Zhang, Yun Xiao, Xia Li, Dan Liu, Chi Zhang, Zheng Zhao, Tao Jiang, Wanying Wu, Fangqing Zhao, Xianwen Meng, Di Peng, Hao Luo, Feng Gao, Shaofeng Lin, Chuijie Liu, Anyuan Guo, Hao Yuan, Tianhan Su, Yong E. Zhang, Yincong Zhou, Guoji Guo, Shanshan Fu, Xiaodan Tan, Weizhi Zhang, Mei Luo, Yubin Xie, Chenwei Wang, Xingyu Liao, Xin Gao, Jianxin Wang, Guiyan Xie, Chunhui Yuan, Feng Tian, Dechang Yang, Ge Gao, Dachao Tang, Wenyi Wu, Yujie Gou, Cheng Han, Qinghua Cui, Xiangshang Li, Chuan-Yun Li, Xiaotong Luo:
Database Resources of the National Genomics Data Center, China National Center for Bioinformation in 2022. Nucleic Acids Res. 50(D1): 27-38 (2022) - [j53]Bo Li
Predicting Cancer Lymph-Node Metastasis From LncRNA Expression Profiles Using Local Linear Reconstruction Guided Distance Metric Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 19(6): 3179-3189 (2022) - [j52]Fang Jing
Prediction of Transcription Factor Binding Sites With an Attention Augmented Convolutional Neural Network. IEEE ACM Trans. Comput. Biol. Bioinform. 19(6): 3614-3623 (2022) - [j51]Chihao Zhang
Distributed Bayesian Matrix Decomposition for Big Data Mining and Clustering. IEEE Trans. Knowl. Data Eng. 34(8): 3701-3713 (2022) - [j50]Wenwen Min
A Novel Sparse Graph-Regularized Singular Value Decomposition Model and Its Application to Genomic Data Analysis. IEEE Trans. Neural Networks Learn. Syst. 33(8): 3842-3856 (2022) - [c13]Rui Zhang
Rethinking Influence Functions of Neural Networks in the Over-Parameterized Regime. AAAI 2022: 9082-9090 - [c12]Weiming Wang, Weifeng Qian, Kai Tao, Zitao Wei, Shihua Zhang, Yan Xia, Yong Chen:
Investigation of Potential FEC Schemes for 800G-ZR Forward Error Correction. OFC 2022: 1-3 - 2021
- [j49]Kangning Dong, Shihua Zhang:
Joint reconstruction of cis-regulatory interaction networks across multiple tissues using single-cell chromatin accessibility data. Briefings Bioinform. 22(3) (2021) - [j48]Shihua Zhang, Xiaolong He, Rui Zhang, Wensheng Deng:
LncR2metasta: a manually curated database for experimentally supported lncRNAs during various cancer metastatic events. Briefings Bioinform. 22(3) (2021) - [j47]Kailing Yao, Yuhua Xu, Hong Li, Jin Chen, Shihua Zhang, Xingyue Yu:
Leveraging partially overlapping channels for intra- and inter-coalition communication in cooperative UAV swarms. Sci. China Inf. Sci. 64(4) (2021) - [j46]Haohui Wang, Chihao Zhang
Robust Bayesian matrix decomposition with mixture of Gaussian noise. Neurocomputing 449: 108-116 (2021) - [j45]Chihao Zhang
Bayesian Joint Matrix Decomposition for Data Integration with Heterogeneous Noise. IEEE Trans. Pattern Anal. Mach. Intell. 43(4): 1184-1196 (2021) - [j44]Wenwen Min
TSCCA: A tensor sparse CCA method for detecting microRNA-gene patterns from multiple cancers. PLoS Comput. Biol. 17(6) (2021) - [j43]Qunlun Shen
Approximate distance correlation for selecting highly interrelated genes across datasets. PLoS Comput. Biol. 17(11) (2021) - [j42]Fang Jing, Shao-Wu Zhang, Zhen Cao, Shihua Zhang
An Integrative Framework for Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning. IEEE ACM Trans. Comput. Biol. Bioinform. 18(1): 355-364 (2021) - [j41]Wenwen Min
Group-Sparse SVD Models via $L_1$L1- and $L_0$L0-norm Penalties and their Applications in Biological Data. IEEE Trans. Knowl. Data Eng. 33(2): 536-550 (2021) - [i20]Kuo Gai, Shihua Zhang:
A Mathematical Principle of Deep Learning: Learn the Geodesic Curve in the Wasserstein Space. CoRR abs/2102.09235 (2021) - [i19]Penglong Zhai, Shihua Zhang:
Adversarial Information Bottleneck. CoRR abs/2103.00381 (2021) - [i18]Chihao Zhang, Yiling Elaine Chen, Shihua Zhang, Jingyi Jessica Li:
Information-theoretic Classification Accuracy: A Criterion that Guides Data-driven Combination of Ambiguous Outcome Labels in Multi-class Classification. CoRR abs/2109.00582 (2021) - [i17]Rui Zhang, Shihua Zhang:
Rethinking Influence Functions of Neural Networks in the Over-parameterized Regime. CoRR abs/2112.08297 (2021) - 2020
- [j40]Zhenxing Guo, Shihua Zhang:
Sparse deep nonnegative matrix factorization. Big Data Min. Anal. 3(1): 13-28 (2020) - [j39]Fang Jing, Shao-Wu Zhang
Prediction of enhancer-promoter interactions using the cross-cell type information and domain adversarial neural network. BMC Bioinform. 21(1): 507 (2020) - [j38]Lihua Zhang, Shihua Zhang:
Comparison of Computational Methods for Imputing Single-Cell RNA-Sequencing Data. IEEE ACM Trans. Comput. Biol. Bioinform. 17(2): 376-389 (2020) - [j37]Zhen Cao, Shihua Zhang
Probe Efficient Feature Representation of Gapped K-mer Frequency Vectors from Sequences Using Deep Neural Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 17(2): 657-667 (2020) - [j36]Lihua Zhang, Shihua Zhang:
A General Joint Matrix Factorization Framework for Data Integration and Its Systematic Algorithmic Exploration. IEEE Trans. Fuzzy Syst. 28(9): 1971-1983 (2020) - [i16]Chihao Zhang, Yang Yang, Wei Zhang, Shihua Zhang:
Distributed Bayesian Matrix Decomposition for Big Data Mining and Clustering. CoRR abs/2002.03703 (2020) - [i15]Kuo Gai, Shihua Zhang:
Tessellated Wasserstein Auto-Encoders. CoRR abs/2005.09923 (2020) - [i14]Penglong Zhai, Shihua Zhang:
Learnable Graph-regularization for Matrix Decomposition. CoRR abs/2010.08513 (2020)
2010 – 2019
- 2019
- [j35]Zhen Cao, Shihua Zhang:
Simple tricks of convolutional neural network architectures improve DNA-protein binding prediction. Bioinform. 35(11): 1837-1843 (2019) - [i13]Chihao Zhang, Kuo Gai, Shihua Zhang:
Matrix Normal PCA for Interpretable Dimension Reduction and Graphical Noise Modeling. CoRR abs/1911.10796 (2019) - [i12]Zhiyang Zhang, Shihua Zhang:
Towards Understanding Residual and Dilated Dense Neural Networks via Convolutional Sparse Coding. CoRR abs/1912.02605 (2019) - 2018
- [j34]Wenwen Min
Edge-group sparse PCA for network-guided high dimensional data analysis. Bioinform. 34(20): 3479-3487 (2018) - [j33]Bei Wang, Jinyu Chen, Shihua Zhang:
BMTK: a toolkit for determining modules in biological bipartite networks. Quant. Biol. 6(2): 186-192 (2018) - [j32]Wenwen Min
Network-Regularized Sparse Logistic Regression Models for Clinical Risk Prediction and Biomarker Discovery. IEEE ACM Trans. Comput. Biol. Bioinform. 15(3): 944-953 (2018) - [j31]Junhua Zhang, Shihua Zhang
The Discovery of Mutated Driver Pathways in Cancer: Models and Algorithms. IEEE ACM Trans. Comput. Biol. Bioinform. 15(3): 988-998 (2018) - [c11]Fang Jing, Shao-Wu Zhang, Zhen Cao, Shihua Zhang:
Combining Sequence and Epigenomic Data to Predict Transcription Factor Binding Sites Using Deep Learning. ISBRA 2018: 241-252 - [c10]Yi Cai, Weiming Wang, Weifeng Qian, Jia Xing, Kai Tao, Junjie Yin, Shihua Zhang, Ming Lei, Erkun Sun, Ke Yang, Hungchang Chien, Qun Liao, Huan Chen:
FPGA Investigation on Error-Floor Performance of a Concatenated Staircase and Hamming Code for 400G-ZR Forward Error Correction. OFC 2018: 1-3 - [e1]Fa Zhang, Zhipeng Cai, Pavel Skums, Shihua Zhang:
Bioinformatics Research and Applications - 14th International Symposium, ISBRA 2018, Beijing, China, June 8-11, 2018, Proceedings. Lecture Notes in Computer Science 10847, Springer 2018, ISBN 978-3-319-94967-3 [contents] - [i11]Wenwen Min, Juan Liu, Shihua Zhang:
Group-sparse SVD Models and Their Applications in Biological Data. CoRR abs/1807.10956 (2018) - 2017
- [j30]Xiaofei Yang, Lin Gao, Shihua Zhang:
Comparative pan-cancer DNA methylation analysis reveals cancer common and specific patterns. Briefings Bioinform. 18(5): 761-773 (2017) - [j29]Shihua Zhang
TBC2health: a database of experimentally validated health-beneficial effects of tea bioactive compounds. Briefings Bioinform. 18(5): 830-836 (2017) - [j28]Jinyu Chen, Shihua Zhang:
Integrative cancer genomics: models, algorithms and analysis. Frontiers Comput. Sci. 11(3): 392-406 (2017) - [j27]Kailing Yao, Youming Sun, Zheng Zhang, Shihua Zhang, Shengnan Li, Yuhua Xu
When to offload in two-tier smallcell networks: a Stackelberg game approach with pre-offloading-decision. Wirel. Networks 23(8): 2499-2508 (2017) - [i10]Lihua Zhang, Shihua Zhang:
A Unified Joint Matrix Factorization Framework for Data Integration. CoRR abs/1707.08183 (2017) - [i9]Zhenxing Guo, Shihua Zhang:
Sparse Deep Nonnegative Matrix Factorization. CoRR abs/1707.09316 (2017) - [i8]Wenwen Min, Juan Liu, Shihua Zhang:
Sparse Weighted Canonical Correlation Analysis. CoRR abs/1710.04792 (2017) - [i7]Chihao Zhang, Shihua Zhang:
Bayesian Joint Matrix Decomposition for Data Integration with Heterogeneous Noise. CoRR abs/1712.03337 (2017) - 2016
- [j26]Jianbo Lu, Guoliang Xu, Shihua Zhang, Benzhuo Lu:
An effective sequence-alignment-free superpositioning of pairwise or multiple structures with missing data. Algorithms Mol. Biol. 11: 18 (2016) - [j25]Jinyu Chen, Shihua Zhang:
Integrative analysis for identifying joint modular patterns of gene-expression and drug-response data. Bioinform. 32(11): 1724-1732 (2016) - [j24]Qingjun Yuan, Junning Gao, Dongliang Wu, Shihua Zhang, Hiroshi Mamitsuka
DrugE-Rank: improving drug-target interaction prediction of new candidate drugs or targets by ensemble learning to rank. Bioinform. 32(12): 18-27 (2016) - [j23]Zhen-Ping Li, Rui-Sheng Wang, Shihua Zhang
Quantitative function and algorithm for community detection in bipartite networks. Inf. Sci. 367-368: 874-889 (2016) - [j22]Xumin Ni, Wei Guo, Kai Yuan
A Probabilistic Method for Estimating the Sharing of Identity by Descent for Populations with Migration. IEEE ACM Trans. Comput. Biol. Bioinform. 13(2): 281-290 (2016) - [i6]Wenwen Min
L0-norm Sparse Graph-regularized SVD for Biclustering. CoRR abs/1603.06035 (2016) - [i5]Wenwen Min, Juan Liu, Shihua Zhang:
Network-regularized Sparse Logistic Regression Models for Clinical Risk Prediction and Biomarker Discovery. CoRR abs/1609.06480 (2016) - 2015
- [j21]Yu-Ting Tseng, Wenyuan Li, Ching-Hsien Chen, Shi-Hua Zhang, Jeremy J. W. Chen
IIIDB: a database for isoform-isoform interactions and isoform network modules. BMC Genom. 16(S-2): S10 (2015) - [j20]Shi-Hua Zhang, Luonan Chen:
Guest Editorial for Special Section on ISB/TBC 2014. IEEE ACM Trans. Comput. Biol. Bioinform. 12(5): 1074-1075 (2015) - [j19]Yu-Qing Qiu, Xue Tian, Shi-Hua Zhang:
Infer Metagenomic Abundance and Reveal Homologous Genomes Based on the Structure of Taxonomy Tree. IEEE ACM Trans. Comput. Biol. Bioinform. 12(5): 1112-1122 (2015) - [c9]Wenwen Min
A novel two-stage method for identifying microRNA-gene regulatory modules in breast cancer. BIBM 2015: 151-156 - [i4]Zhen-Ping Li, Rui-Sheng Wang, Shi-Hua Zhang, Xiang-Sun Zhang:
Quantitative Function and Algorithm for Community Detection in Bipartite Networks. CoRR abs/1501.00432 (2015) - [i3]Xue-Mei Ning, Zhaoqi Liu, Shihua Zhang:
Local community extraction in directed networks. CoRR abs/1508.02177 (2015) - [i2]Shihua Zhang, Guanghua Hu, Wenwen Min
A neurodynamic framework for local community extraction in networks. CoRR abs/1511.09368 (2015) - 2014
- [j18]Junhua Zhang, Ling-Yun Wu, Xiang-Sun Zhang, Shihua Zhang:
Discovery of co-occurring driver pathways in cancer. BMC Bioinform. 15: 271 (2014) - 2013
- [j17]Rui Xu, Shihua Zhang:
Modelling and analysis of a delayed predator-prey model with disease in the predator. Appl. Math. Comput. 224: 372-386 (2013) - [j16]Shihua Zhang, Rui Xu:
Travelling waves and global attractivity of an SIRS disease model with spatial diffusion and temporary immunity. Appl. Math. Comput. 224: 635-651 (2013) - [j15]Junhua Zhang, Shi-Hua Zhang, Yong Wang, Xiang-Sun Zhang:
Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data. BMC Syst. Biol. 7(S-2): S4 (2013) - [j14]Shihua Zhang, Xiu-Jie Wang:
Promote Connections of Young Computational Biologists in China. Genom. Proteom. Bioinform. 11(4): 253-256 (2013) - 2012
- [j13]Wenyuan Li, Shi-Hua Zhang, Chun-Chi Liu, Xianghong Jasmine Zhou:
Identifying multi-layer gene regulatory modules from multi-dimensional genomic data. Bioinform. 28(19): 2458-2466 (2012) - [j12]Junfei Zhao, Shi-Hua Zhang, Ling-Yun Wu, Xiang-Sun Zhang:
Efficient methods for identifying mutated driver pathways in cancer. Bioinform. 28(22): 2940-2947 (2012) - [c8]Junhua Zhang, Shi-Hua Zhang, Yong Wang, Junfei Zhao, Xiang-Sun Zhang:
Identifying mutated core modules in glioblastoma by integrative network analysis. ISB 2012: 304-309 - 2011
- [j11]Shi-Hua Zhang, Qingjiao Li, Juan Liu, Xianghong Jasmine Zhou:
A novel computational framework for simultaneous integration of multiple types of genomic data to identify microRNA-gene regulatory modules. Bioinform. 27(13): 401-409 (2011) - [c7]Jiang Xie, Shi-Hua Zhang, Tieqiao Wen, Guangtai Ding, Shu Yu, Zhili Gu, Wu Zhang:
A Querying Method with Feedback Mechanism for Protein Interaction Network. HISB 2011: 351-358 - [i1]Shi-Hua Zhang, Junfei Zhao, Xiang-Sun Zhang:
Co-community Structure in Multiple Evolving Networks. CoRR abs/1111.1365 (2011) - 2010
- [j10]Shi-Hua Zhang, Daven Vasishtan, Min Xu, Maya Topf
A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps. Bioinform. 26(12): 261-268 (2010) - [j9]Yu-Qing Qiu, Shi-Hua Zhang, Xiang-Sun Zhang, Luonan Chen:
Detecting disease associated modules and prioritizing active genes based on high throughput data. BMC Bioinform. 11: 26 (2010) - [j8]Chao Wu, Fan Zhang, Xia Li, Shihua Zhang
Composite functional module inference: detecting cooperation between transcriptional regulation and protein interaction by mantel test. BMC Syst. Biol. 4: 82 (2010) - [j7]Shi-Hua Zhang, Xue-Mei Ning, Chris H. Q. Ding, Xiang-Sun Zhang:
Determining modular organization of protein interaction networks by maximizing modularity density. BMC Syst. Biol. 4(S-2): S10 (2010)
2000 – 2009
- 2009
- [j6]Shi-Hua Zhang, Hong-Wei Liu, Xue-Mei Ning, Xiang-Sun Zhang:
A hybrid graph-theoretic method for mining overlapping functional modules in large sparse protein interaction networks. Int. J. Data Min. Bioinform. 3(1): 68-84 (2009) - [j5]Jiguang Wang
Disease-Aging Network Reveals Significant Roles of Aging Genes in Connecting Genetic Diseases. PLoS Comput. Biol. 5(9) (2009) - [c6]Min Xu, Shi-Hua Zhang, Frank Alber:
3D Rotation Invariant Features for the Characterization of Molecular Density Maps. BIBM 2009: 74-78 - [c5]Jiang Xie, Weibing Feng, Shi-Hua Zhang, Songbei Li, Guoyong Mao, Luwen Zhang
A Method for Querying Conserved Subnetwork in a Large-Scale Biomolecular Network. HPCA (China) 2009: 473-478 - [p1]Shi-Hua Zhang, Rui-Sheng Wang, Xiang-Sun Zhang, Luonan Chen:
Fuzzy System Methods in Modeling Gene Expression and Analyzing Protein Networks. Fuzzy Systems in Bioinformatics and Computational Biology 2009: 165-189 - 2008
- [j4]Shihua Zhang, Xiang-Sun Zhang, Luonan Chen:
Biomolecular network querying: a promising approach in systems biology. BMC Syst. Biol. 2: 5 (2008) - [j3]Rui-Sheng Wang, Shi-Hua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Clustering complex networks and biological networks by nonnegative matrix factorization with various similarity measures. Neurocomputing 72(1-3): 134-141 (2008) - 2007
- [j2]Zhen-Ping Li, Shi-Hua Zhang, Yong Wang, Xiang-Sun Zhang, Luonan Chen:
Alignment of molecular networks by integer quadratic programming. Bioinform. 23(13): 1631-1639 (2007) - [c4]Rui-Sheng Wang, Shi-Hua Zhang, Xiang-Sun Zhang, Luonan Chen:
Identifying Modules in Complex Networks by a Graph-Theoretical Method and Its Application in Protein Interaction Networks. ICIC (2) 2007: 1090-1101 - 2006
- [j1]Shi-Hua Zhang, Xue-Mei Ning, Xiang-Sun Zhang:
Identification of functional modules in a PPI network by clique percolation clustering. Comput. Biol. Chem. 30(6): 445-451 (2006) - [c3]Zhen-Ping Li, Yong Wang, Shihua Zhang, Xiang-Sun Zhang, Luonan Chen:
Alignment of Protein Interaction Networks by Integer Quadratic Programming. EMBC 2006: 5527-5530 - [c2]Shi-Hua Zhang, Hong-Wei Liu, Xue-Mei Ning, Xiang-Sun Zhang:
A Graph-Theoretic Method for Mining Functional Modules in Large Sparse Protein Interaction Networks. ICDM Workshops 2006: 130-135 - [c1]Shi-Hua Zhang, Xue-Mei Ning, Hong-Wei Liu, Xiang-Sun Zhang:
Prediction of Protein Complexes Based on Protein Interaction Data and Functional Annotation Data Using Kernel Methods. ICIC (3) 2006: 514-524
Coauthor Index
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