生物信息学

1. 2019.1-2022.12  成分数据分析方法及其在宏基因组数据中的应用，基金委面上 （主持人）

2. 2016.7-2021.6蛋白质机器三维结构导向的新型药物研发关键技术研究，科技部重点研发计划，（学术骨干）

3. 2015.1-2019.12课题3：疾病相关生物分子网络的构建、动态演化及调控规律，科技部重大研究计划 （主持人：课题组长）

4. 2015.1-2018.12 基于网络的全基因组关联分析方法，基金委面上 （主持人）

5. 2012.1-2015.12 遗传相互作用网络的构建和分析，基金委面上 （主持人）

6. 2009.1-2011.12   基于探针杂交机制的生物芯片数据预处理统计方法研究, 基金委面上（主持人）

7. 2008.1-2010.12   蛋白质复杂网络构建与分析及其在肝癌疾病中的应用,  863项目 （主持人）

8. 2006.1-2008.12   转录因子结合位点(TSBS)研究， 基金委面上（主持人）

1.Huili Yuan, Shun He , Minghua Deng*. Compositional data network analysis via lasso penalized D-trace loss. Bioinformatics, https://doi.org/10.1093/bioinformatics/btz098, Published: 14 February 2019

2.Yujuan Gao, Sheng Wang, Minghua Deng* and Jinbo Xu*. RaptorX-Angle: real-value prediction of protein backbone dihedral angles through a hybrid method of clustering and deep learning. BMC Bioinformatics 2018, 19 (Suppl 4) :100. https://doi.org/10.1186 /s12859-018-2065-x. APBC 2018 Best Paper Award.

3.Huili Yuan; Ruibin Xi; Chong Chen; Minghua Deng*. Differential network analysis using a D-trace loss. Biometrika 2017, 4: 755–770.

4.Changjing Wu, Hongyu Zhao, Huaying Fang and Minghua Deng*. Graphical model selection with latent variables.Electronic Journal of Statistics 2017, 11, 3485–3521.

5.Zengmiao Wang, Huaying Fang, Nelson Leung-Sang Tang and Minghua Deng. VCNet: vector-based gene co-expression network construction and its application to RNA-seq data. Bioinformatics 33(14):2173–2181, 2017.

6.Huaying Fang, Chengcheng Huang, Hongyu Zhao and Minghua Deng. CCLasso: Correlation Inference for Compositional Data through Lasso. Bioinformatics. 2015 Oct 1;31(19):3172-80. doi: 10.1093/bioinformatics/btv349..

7.Lin Wang, Wei Zheng, Hongyu Zhao, Minghua Deng. Statistical Analysis Reveals Co-Expression Patterns of Many Pairs of Genes in Yeast Are Jointly Regulated by Interacting Loci. PLoS Genetics 9(3): e1003414,2013.

8.Lin Hou, Lin Wang, Minping Qian, Dong Li, Chao Tang, Yunping Zhu, Minghua Deng, Fangting Li. Modular analysis of the probabilistic genetic interaction network. Bioinformatics 27(6):853-859,2011.

9.Hao Zheng, Xingyi Hang, Ji Zhu, Minping Qian, Wubin Qu, Chenggang Zhang, Minghua Deng. REMAS: a new regression model to identify alternative splicing events from exon array data. BMC Bioinformatics 10 (Suppl 1):S18, 2009. APBC2009 Best Paper Award.

10.Minghua Deng, Shepra Mehta, Fengzhu Sun, Ting Chen. Inferring domain-domain interactions from protein-protein interactions. Genome Research 12(10):1540-1548,2002. See also The ACM-SIGACT 6th Annual International Conference on Computational Molecular Biology (RECOMB02), 95-103, April, 2002.