学术信息网 西电导航 关于 使用说明 搜索 系统首页 登录 控制面板 收藏 马小科的留言板
学术论文

    在国际著名期刊IEEE TKDE、Pattern Recognition、Cell Stem Cell、Bioinformatics、PLoS Computational Biology等发表SCI检索的论文50多篇,其中第一作者/通信作者论文40余篇。

部分发表论文与专著

2019年 (*为通信作者)

[1] Xiaoke Ma*,Di Dong, Quan Wang. Community detection in multi-layer networks using joint nonnegative matrix factorization. IEEE Transactions on Knowledeg  and Data Engineering. 31(2):273-286. 2019  CCF A, IF=3.48

[2] Xiaoke Ma*, Penggang Sun, Zhong-Yuan Zhang. An integrative framework for protein interaction and methylation data to discover epigenetic modules. IEEE/ACM Trans. Comp. Bio. and Bioin. DOI:10.1109/TCBB.2018.281666, 2018  中科院II区,CCF B, IF=1.97

[3] Jianbang Zhao, Xiaoke Ma*.  Multiple partial regularized nonnegative matrix factorization for predicting ontological functions of lncRNAs. Frontiers in Genetics. 9:685. 2019.  中科院II区,IF=4.21

[4] Xiaoke Ma*,Dongyuan Li, Shiyin Tan, Zhihao Huang. Detecting evolving communities in dynamic networks using graph regularized evolutionary nonnegative matrix factorization. Physica A.  530:121279. 中科院III区,IF=2.50

[5] Xiaoke Ma*, Shiyin Tan, Dongyuan Li, Wenming Wu, Penggang Sun, Maoguo Gong. An integrative framework of heterogeneous genomic data for cancer dynamic modules based on matrix decomposition. BMC Genomics. Accepted. 中科院II区,IF=4.14

[6] Dongyuan Li, Xiaoke Ma*. Nonnegative matrix factorization for dynamic modules in cancer temporal networks. IEEE conference  on Bioinformatics  and Biomedicine (IEEE BIBM).  accepted, 2019.  CCF B

[7] Zuheng Xia, Jingjing Deng, Xianghua Xie, Xiaoke Ma*. Transfer learning for gene prioritization. IEEE conference  on Bioinformatics  and Biomedicine (IEEE BIBM).  accepted, 2019.  CCF B

[8] Xiaoke Ma*, Benhui Zhang, Zhiyu Ma, Changzhou Ma, Zuheng Xia. Co-regularized Nonnegative Matrix Factorization for Evolving Community Detection in Dynamic Networks. Information Sciences. In revision.

[9] Tengteng Yu, Chenxing Du, Zhen Yu, Lanting Liu, Zhao Lei, Zhongqing Li, Jie Xu, Xiaojing Wei, Shuhui Deng, Dehui Zou, Gang An, Yu-Tzu Tai, Guido Tricot, Xiaoke Ma*, Lugui Qiu*, Fenghuang Zhan*, Mu Hao*. PHF19 Promotes Drug Resistance via Increased EZH2 Phosphorylation in Multiple Myeloma. Journal of Hematology & Oncology. In revision.

[10] Xiaoke Ma*, Jingjing Deng. Joint nonnegative matrix factorization and network embedding for graph co-clustering. In submission.

[11] Dongyuan Li, Xiaoke Ma*. Dynamic community detection by fusing network embedding and nonnegative matrix factorization. In submission.

[12] Zhihao Huang, Xiaoxiong Zhong, Maoguo Gong, Xiaoke Ma*.  Community detection in attribute networks by dynamically joint node attributes and topological structure. In submission.

[13] Shiyin Tan, Xiaoke Ma*.  joint feature extraction and multi-label learning for temporal link prediction. In submission.

 

2018年

[1] Long Gao, Uzun Yasin, Peng Gao, Bing He, Xiaoke Ma, Jiahui Wang, Jindong Han, Kai Tan. Identifying noncoding risk variants using disease-relevant regulatory networks. Nature Communications. 8:702, 2018 中科院I区,IF=12.14

[2] Xiaoke Ma*, Wanxin Tang, et al. Extracting stage-specific and dynamic modules through analyzing multiple networks associated with cancer progression. IEEE/ACM Trans. Comp. Bio. and Bioin. 15(8):647--658, 2018  中科院II区,CCF B, IF=1.97

[3] Xiaoke Ma*, Penggang Sun, Guimin Qin. Identifying  condition-specific modules by clustering multiple networks. IEEE/ACM Trans. Comp. Bio. and Bioinfo. 15(5):1636-1648, 2018 中科院II区,CCF B, IF=1.97

[4] Xiaoke Ma*, Bingbo Wang, Liang Yu. Semi-supervised spectral algorithms for community detection in complex networks based on equivalence of clustering methods. Physica A. 490(2018)786--802. 中科院III区,IF=2.48

[5] Xiaoke Ma*, Penggang Sun, Yu Wang. Graph regularized nonnegative matrix factorization for temporal link prediction in dynamic networks. Physica A. 496(2018)121--136. 中科院III区,IF=2.48

[6] Xiaoke Ma*, Penggang Sun. Fusing heterogeneous genomic data to discover cancer progression related dynamic modules. IEEE conference  on Bioinformatics  and Biomedicine (IEEE BIBM). pp. 114-121, 2018.  CCF B

[7] Enli Zhang, Xiaoke Ma*.   Regularized multi-view subspace clustering for common modules across cancer stages. Molecules. 23, 1016. 中科院III区,IF=3.42

[8] 付立东,马小科*. 进化谱分算法检测动态网络社团结构. 西安电子科技大学学报. 45(2): 43-48. 2018 EI

 

2017年

[1] Xiaoke Ma*,Di Dong. Evolutionary Nonnegative Matrix Factorization Algorithms for Community Detection in Dynamic Networks. IEEE Trans. Know.  & Data. Eng. 29(5)1045-1058 CCF A, IF=3.48
[2] Fengyin Li, Bing He, Xiaoke Ma, Shuyang Yu, Rupali R. Bhave, Steven R. Lentz, Kai Tan, Monica L. Guzman, Chen Zhao,  Hai-Hui Xue. Prostaglandin E1 and Its Analog Misoprostol Inhibit Human CML Stem Cell Self-Renewal via EP4 Receptor Activation and Repression of AP-1. Cell Stem Cell. 21(2017)1--15  中科院I区,IF=23.96 封面论文  Cell出版社评价“最透明”与“最具同行评议”论文

[3] Xiaoke Ma*, Penggang Sun, Guimin Qin. Nonnegative matrix factorization algorithms for link prediction in temporal networks using graph communicability. Pattern Recognition. 71(2017)361-374 CCF B, IF=4.99
[4] Penggang Sun, Xiaoke Ma*. Dominating communities for hierarchical control of complex networks. Information Sciences. 414(2017)247--259 CCF B, IF=4.96
[5] Wanxin Tang,Dongmei Zhang, Xiaoke Ma*. RNA-Sequencing Reveals Genome-Wide Long Non-coding RNAs Profiling Associated with Early Development of Diabetic Nephropathy. Oncotarget. 8(62)105832--105847 中科院I区,IF=5.96
[6] Xiaoke Ma, Zaiyi Liu, Zhongyuan Zhang, Xiaotai Huang, Wanxin Tang*. Multiple network algorithm for epigenetic modules via the integration of genome-wide DNA methylation and gene expression data. BMC Bioinformatics. 1:18 中科院II区,IF=2.67
[7] Penggang Sun, Xiaoke Ma*. Understanding the controllability of complex networks from the microcosmic to the macrocosmic.  New Journal of Physics. 19: 013022 中科院II区,IF=3.69
[8] Penggang Sun, Xiaoke Ma*. Controllability and observability of cascading failure networks. Journal of Statistical Mechanics: Theory and Experiment. 2017:043404 中科院II区,IF=2.49
[9] Peizhuo Wang, Lin Gao, Xiaoke Ma*. Dynamic community detection based on network structural perturbation and topological similarity. Journal of Statistical Mechanics: Theory and Experiment. 2017:013401 中科院II区,IF=2.49

[10] Penggang Sun, Xiaoke Ma*. Understanding control of network spreading from network controllability. Journal of Statistical Mechanics: Theory and Experiment. 2017:093405 中科院II区,IF=2.49
[11] Xiaoke Ma*, Peizhuo Wang, Liang Yu, Xiaofei Yang. Discovering DNA methylation patterns for longnon-coding RNAs associated with cancer subtypes. Computional Biology and Chemistry. 69:164--170 中科院III区,IF=1.67 APBC2017推荐

[12] Penggang Sun, Xiaoke Ma*. Dominating complex networks by identifying minimum skeletons. Chaos, Solitons and Fractals. 104:182--191.  中科院IV区,IF=1.45

[13]  Xiaoke Ma*, Penggang Sun, Jianbang Zhao. Multi-objective optimization algorithm to discover condition-specific modules in multiple networks. Molecules.  22, 2228.  中科院III区,IF=3.40

 

 2016-2013年

[1] Xiaoke Ma, Long Gao, Georgios Karamanlidis, et al. Revealing Pathway Dynamics in Heart Diseases by Analyzing Multiple Differential Networks. PLoS Comput. Biol. 2015: e1003442  CCF B, IF=6.32

[2] Xiaoke Ma, Long Gao, Kai Tan. Modeling disease progression using dynamics of pathway connectivity. Bioinformatics. 2014, 30:2343--2350 中科院I区,CCF B, IF=7.32

[3] Xingli Guo, Lin Gao, Qi Liao, Hui Xiao, Xiaoke Ma, Xiaofei Yang, Haitao Luo, Guoguang Zhao, Dechao Bu, Fei Jiao, Qixiang Shao, RunSheng Chen* and Yi Zhao. Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks. Nuclear Acids Research. 2013, 41:e35. 中科院I区,CCF B, IF=10.14

[4] Feng Li, Lin Gao, Xiaoke Ma, Xiaofei Yang. Detection of driver pathways using mutated gene network in cancer. Molecular BioSystem. 2016,  中科院III区,IF=3.29

[5] Liang Yu, Bingbo Wang, Xiaoke Ma, Lin Gao. The extraction of drug-disease correlations based on module distance in incomplete human interactome. BMC Systems Biology, 2016, 10(Suppl 4):111 中科院II区,IF=2.33

[6] Liang Yu, Xiaoke Ma, Long Zhang, Jing Zhao, Lin Gao. Prediction of new drug indications based on clinical data and network modularity. Scientific Reports. 2016, 6:32530 中科院II区,IF=4.33

 

2012-2010年

[1] Xiaoke Ma*, Lin Gao. Predicting protein complexes in protein interaction networks using a core-attachment algorithm based on graph communicability. Information Sciences. 2012, 189:233--254. CCF B, IF=4.96

[2] Xiaoke Ma,Lin Gao*. Biological network analysis: insights into structure and functions. Briefings in Functional Genomics. 2012, 6:434--442. 中科院II区,IF=4.26

[3] Xiaoke Ma, Lin Gao*. Discovering protein complexes in protein interaction networks via exploring the weak ties effect. BMC Systems Biology. 2012, 6(Suppl 1):S6. 中科院II区,IF=2.33

[4] 付立东,高琳,马小科. 基于社团检测的复杂网络中心性方法. 中国科学:信息科学,42(5):550-560. 2012. 中科院II区,CCF B

[5] Xiaoke Ma*. Lin Gao. Detecting protein complexes in PPI networks: The roles of interactions. IEEE International Conference on Systems Biology. pp. 52-59  2011.

[6] Xiaoke Ma*,Lin Gao. Non-traditional spectral clustering algorithms for the detection of community structure in complex networks: a comparative analysis. Journal of Statistical Mechanics: Theory and Experiment. 2011:P05012 中科院II区,IF=2.49
[7] Xiaoke Ma*, Lin Gao, Xuerong Yong, Lidong Fu. Semi-supervised clustering algorithm for community structure detection in complex networks. Physica A. 2010, 389:187--197. 中科院III区,IF=2.48

[8] Xiaoke Ma*, Lin Gao, Xuerong Yong. Eigenspaces of networks reveal the overlapping and hierarchical community structure more precisely. Journal of Statistical Mechanics: Theory and Experiment. 2010:P08012 中科院II区,IF=2.49

[9] Lidong Fu, Lin Gao, Xiaoke Ma. A centrality measure based on the spectral optimization of modularity density. Sciences in China Series F. 2010, 53:1727--1737 CCF B,IF=1.37