1) Qi Liu, Yi Yang, Yixue Li, Zili Zhang. Global and threshold-free transcriptional regulatory networks reconstruction through integrating ChIP-chip and expression data. Curr Protein Pept Sci. 2011,12(7):631-42.
2) Yi Yang, Zili Zhang, Yixue Li, Xinguang Zhu, Qi Liu*. Identifying cooperative transcriptional factors by combining ChIP-chip data and knock-out data. Cell Research, 2010, 20(11): 1276-1278. (corresponding author)
3) Qi Liu, Yejun Tan, Tao Huang, Guohui Ding, Zhidong Tu, Lei Liu, Yixue Li, Hongyue Dai, Lu Xie. TF-centered downstream gene set enrichment analysis: Inference of causal regulators by integrating TF-DNA interaction and protein post-translational modification information. BMC Bioinformatics, 2010, 11:s5. (1)
4) Qi Liu, Guohui Ding, Tao Huang, Yixue Li et al., Considering dependencies amongst genes help to adjust the significance rank of DEGs. Chinese Journal of Chemistry, 2010,28:1284-1290
5) Jiang Lihua，Li Yixue，Liu Qi*. Reconstruction of gene regulatory networks by integrating ChIP-chip, knockout and expression data. Progress in Biochemistry and Biophysics，2010, 37(9): 996-1005. (corresponding author)
6) Haoyu Cheng, Lihua Jiang, Maoying Wu and Qi Liu*. Inferring Transcriptional Interactions by the Optimal Integration of ChIP-chip and Knock-out Data. Bioinformatics and Biology Insights 2009:3 129-140 (corresponding author)
7) Qi, Liu, Jia, Xiong, Yong, Deng. A subjective methodology for risk quantification based on generalized fuzzy numbers，INTERNATIONAL JOURNAL OF GENERAL SYSTEMS，2008, 37(2):149-165. (5)
8) Li J, Liu Z, Pan Y, Liu Q, Fu X, Cooper NG, Li Y, Qiu M, Shi T. Regulatory Module Network of bHLH Transcription Factors in Mouse Brain. Genome Biol. 2007 Nov 19;8(11):R244 (12)
9) Sun J, Sun Y, Ding G, Liu Q, Wang C, He Y, Shi T, Li Y, Zhao Z. InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinformatics. 2007,8(1):414 (16)
10) Ziliang Qian, Lingyi Lu, Liu Qi, and Yixue Li，An efficient method for statistical significance calculation of transcription factor binding sites，Bioinformation. 2007; 2(5): 169-174.
11) Liu Qi, Deng Yong, Wang Chuan, Shi Tieliu, Li Yixue. Correlating Expression Data with Gene Function using Gene Ontology, Chinese Journal of Chemistry 2006, 24(9):1247-1254. (1)
12) Li J, Liu Q, Qiu M, Pan Y, Li Y, Shi T. Identification and analysis of the mouse basic/Helix-Loop-Helix transcription factor family. Biochem Biophys Res Commun. 2006, 350(3):648-656. (7)
13) Ding G, Kang J, Liu Q, Shi T, Pei G, Li Y. Insights into the coupling of duplication events and macroevolution from an age profile of animal transmembrane gene families. PLoS Comput Biol. 2006, 2(8):e102. (8)
14) Jingchun Sun, Qi Liu, et al., Refined phylogenetic profiles method for predicting protein–protein interactions. Bioinformatics, 2005, 21(16):3409-3415 (co-first author).
15) Guoping Zhao, ……Qi Liu,… Yixue Li, ……, . Chinese SARS Molecular Epidemiology Consortia. Molecular Evolution of the SARS Coronavirus During the Course of the SARS Epidemic in China. Science 2004, 303:1666-1669
16) Deng Y*, Liu Q*, Li YX. Scoring hidden Markov models to discriminate barrel membrane proteins, Computational biology and Chemistry, 2004, 28(3):189-194 (co-first author)
17) Liu Qi, Zhu Yisheng, Wang Baohua and Li Yixue, A HMM-based method to predict the transmembrane regions of b-barrel membrane proteins, Computational biology and Chemistry, 2003,27(1): 69-76.
18) Liu Qi, Zhu Yisheng, Wang Baohua and Li Yixue, Identification of -barrel membrane proteins based on amino acid composition properties and predicted secondary structure, Computational biology and Chemistry, 2003,27(3): 355-361
19) Liu Qi, Zhu Yisheng, Wang Baohua and Li Yixue, TSSOM:Transmembrane segments prediction by self-organizing map, The Chinese Journal of Electronics, 2003,12(1):111-115
20) Liu Qi, Chen Zhongqiang, Wang Baohua, Zhu Yisheng and Li Yixue, Research on several prediction methods of membrane protein structure and topology, High Technology Letters, 2001, 7(3):1-4
21) Liu Qi, Chen Zhongqiang, Wang Baohua, Zhu Yisheng and Li Yixue, An Improved Algorithm for Transmembrane Protein Prediction. In Proceedings of The Sixth International conference for Younger Computer Scientists (ICYCS), 2001, 485-488.
22) DengYong, Liu Qi. A new similarity measure of generalized fuzzy numbers and its application to pattern recognition. Pattern Recognition Letters. 2004, 25:875－883.
23) Chen Zhongqiang, Liu Qi, Zhu Yisheng, Li Yixue and Xu Yuhong. A hydrophobicity based neural network method for predicting transmembrane segments in protein sequences. In Proceedings of EMBC2001 23rd Annual International Conference of the IEEE-EMBS, 2001, 25-28。
研究成果
在組學數據的綜合分析，蛋白質相互作用的預測和轉錄調控網路的構建等方面，取得了一系列的研究成果。1）發展了一種改進的基於協同進化譜的蛋白質-蛋白質相互作用預測方法。首次提出不同基因組間基因的同源性分析的比對分值、基因組的數量和如何選取基因組對於提取物種的協同進化信息，進而預測蛋白質-蛋白質相互作用的準確度具有重要的影響, 據此發展了更為合理的基於精確係統發育譜方法的蛋白質-蛋白質相互作用預測方法和評估策略；2）首次提出整合轉錄調控關係相關的物理結合證據和功能相關證據，發展了綜合ChIP-chip數據，表達譜數據和轉錄因子敲除數據來構建調控網路的全局尋優方法，該方法不僅提高了轉錄調控關係預測的可靠性，而且為多組學數據的綜合分析提供了新的思路；3）通過多組學數據的綜合分析，發展了一種準確性更高的協同作用轉錄因子識別方法；4）首次將蛋白質修飾數據和轉錄組數據相結合，提出了轉錄調控的級聯模型，該模型能有效地識別那些造成基因表達譜變化的關鍵轉錄因子。在Science, Cell Research, Genome Biology, PLOS Computational Biology, Bioinformatics, Current Protein & Peptide Sciences, BMC Bioinformatics, BBRC, Computational Biology and Chemistry，Pattern Recognition Letters等國內外核心刊物上發表論文近三十篇，累計影響因子超過70點，SCI引用超過400次。
