Research Overview:

The long-term interest of our lab is computational biology and bioinformatics, where we focus on creating systematic models of heterogeneous phenotypes, e.g., malignant tumor, biological development, for discovering inherent biological patterns and offering novel insights into clinical or practical implications. Particularly, network-based models have the potential to reveal crucial molecular events underlying different types of cell functions, and can be built by combining biological networks and molecular profiles. Additionally, sample-centric integration models can provide more opportunities to characterize cell subpopulations at high resolution through a comprehensive view from multiple genomics data.

Key words: bioinformatics; network biology; data integration

Recent research papers are listed in the following, and another load is on the way.

(1) Qianqian Shi, Chuanchao Zhang, Minrui Peng, Xiangtian Yu, Tao Zeng^*, Juan Liu^* and Luonan Chen^*. Pattern fusion analysis by adaptive alignment of multiple heterogeneous omics data. Bioinformatics, 2017, 33 (17): 2706-2714

(2) Qianqian Shi, Chuanchao Zhang, Weifeng Guo, Tao Zeng, Lina Lu, Zhonglin Jiang, Ziming Wang, Juan Liu and Luonan Chen^*. Local network component analysis for quantifying transcription factor activities. Methods, 2017, 124: 25-35

(3) Qianqian, Shi^#, Xiaoping Liu^#, Tao Zeng, William Wang^* and Luonan Chen^*. Detecting disease genes of non-small lung cancer based on consistently differential interactions. Cancer and Metastasis Reviews, 2015, 34(2): 195-208

(4) Weifeng Guo, Shaowu Zhang^*, Lili Liu, Fei Liu, Qianqian Shi, Lei Zhang, Ying Tang, Tao Zeng^*, Luonan Chen^*. Discovering personalized driver mutation profiles of single samples in cancer by network control strategy. Bioinformatics, 2018, doi.org/10.1093/bioinformatics/bty006

(5) Weifeng Guo, Shaowu Zhang^*, Qianqian Shi, Chengming Zhang, Tao Zeng^* and Luonan Chen^*. A novel algorithm for finding optimal driver nodes to target control complex networks and its applications for drug targets identification. BMC Genomics, 2018, 19(Suppl 1): 924

(6) Bing Hu, Qianqian Shi, Yu Guo, Xiyezi Diao, Heng Guo, Jinsong Zhang, Liang Yu, Hao Dai, Luonan Chen^*. The oscillatory boundary conditions of different frequency bands in Parkinson's disease. Journal of Theoretical Biology, 2018, doi: 10.1016/j.jtbi.2018.04.040

(7) Chuanchao Zhang, Juan Liu^*, Qianqian Shi, Tao Zeng^* and Luonan Chen^*. Identifying functional interpretable network biomarkers by comparative network stratification. BMC bioinformatics, 2017, 18(3): 48

Chuanchao Zhang, Juan Liu^*, Qianqian Shi, Tao Zeng^* and Luonan Chen^*. Differential function analysis: identifying structure and activation variations in dysregulated pathways. Science China Information Sciences (SCIS), 2017, 60(1): 012108