學(xué)習(xí)經(jīng)歷：

1993,9－1997,7 湖南大學(xué)電氣工程系電磁測(cè)量技術(shù)及儀器專業(yè) 學(xué)士

1997,9－2000,1 湖南大學(xué)電氣工程系測(cè)試計(jì)量技術(shù)及儀器專業(yè) 碩士

2000,2－2003,5 上海交通大學(xué)生命科學(xué)技術(shù)學(xué)院生物醫(yī)學(xué)工程專業(yè) 博士

工作經(jīng)歷：

2003,7－2005,12 中科院上海生命科學(xué)研究院生物信息中心 助理研究員

2006,1－2006，8 上海交通大學(xué)生命科學(xué)技術(shù)學(xué)院 講師

2006，8-至今 上海交通大學(xué)生命科學(xué)技術(shù)學(xué)院 副教授

2011，6-至今 美國(guó)范德堡大學(xué)（Vanderbilt University）醫(yī)學(xué)院生物醫(yī)學(xué)信息系博士后

入選主要人才培養(yǎng)計(jì)劃及獲得的榮譽(yù)

2010 上海交通大學(xué) SMC-晨星青年學(xué)者獎(jiǎng)勵(lì)計(jì)劃（B類）

2009 上海交通大學(xué) 優(yōu)秀青年教師后備人才一等獎(jiǎng)

2008 上海交通大學(xué) 優(yōu)秀青年教師后備人才二等獎(jiǎng)

主持或參加的各類科研項(xiàng)目以及基金項(xiàng)目等情況

1. 國(guó)家自然科學(xué)基金面上項(xiàng)目，基于多目標(biāo)蟻群優(yōu)化的轉(zhuǎn)錄調(diào)控網(wǎng)絡(luò)全局重構(gòu)，2011年1月至2013年12月，項(xiàng)目負(fù)責(zé)人

2. 973項(xiàng)目，影響蛋白質(zhì)修飾的活性小分子化合物的發(fā)現(xiàn)和活性機(jī)制研究，2009年1月至2013年8月，合作單位負(fù)責(zé)人。

3. 國(guó)家自然科學(xué)基金青年基金項(xiàng)目，基于多種生物學(xué)數(shù)據(jù)整合的基因調(diào)控網(wǎng)絡(luò)重構(gòu)研究，2008年1月至2010年12月，項(xiàng)目負(fù)責(zé)人。

4. 863項(xiàng)目, 面向轉(zhuǎn)化醫(yī)學(xué)的生物醫(yī)學(xué)信息集成體系及計(jì)算平臺(tái)研究, 2008,1-2010,12，合作單位負(fù)責(zé)人

1)復(fù)雜疾病的系統(tǒng)生物學(xué)研究;

2)microRNA調(diào)控機(jī)制研究；

3)基于高通量測(cè)序的基因選擇性剪切機(jī)制研究

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 proteinu2013protein 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。

在組學(xué)數(shù)據(jù)的綜合分析，蛋白質(zhì)相互作用的預(yù)測(cè)和轉(zhuǎn)錄調(diào)控網(wǎng)絡(luò)的構(gòu)建等方面，取得了一系列的研究成果。1）發(fā)展了一種改進(jìn)的基于協(xié)同進(jìn)化譜的蛋白質(zhì)-蛋白質(zhì)相互作用預(yù)測(cè)方法。首次提出不同基因組間基因的同源性分析的比對(duì)分值、基因組的數(shù)量和如何選取基因組對(duì)于提取物種的協(xié)同進(jìn)化信息，進(jìn)而預(yù)測(cè)蛋白質(zhì)-蛋白質(zhì)相互作用的準(zhǔn)確度具有重要的影響, 據(jù)此發(fā)展了更為合理的基于精確系統(tǒng)發(fā)育譜方法的蛋白質(zhì)-蛋白質(zhì)相互作用預(yù)測(cè)方法和評(píng)估策略；2）首次提出整合轉(zhuǎn)錄調(diào)控關(guān)系相關(guān)的物理結(jié)合證據(jù)和功能相關(guān)證據(jù)，發(fā)展了綜合ChIP-chip數(shù)據(jù)，表達(dá)譜數(shù)據(jù)和轉(zhuǎn)錄因子敲除數(shù)據(jù)來(lái)構(gòu)建調(diào)控網(wǎng)絡(luò)的全局尋優(yōu)方法，該方法不僅提高了轉(zhuǎn)錄調(diào)控關(guān)系預(yù)測(cè)的可靠性，而且為多組學(xué)數(shù)據(jù)的綜合分析提供了新的思路；3）通過(guò)多組學(xué)數(shù)據(jù)的綜合分析，發(fā)展了一種準(zhǔn)確性更高的協(xié)同作用轉(zhuǎn)錄因子識(shí)別方法；4）首次將蛋白質(zhì)修飾數(shù)據(jù)和轉(zhuǎn)錄組數(shù)據(jù)相結(jié)合，提出了轉(zhuǎn)錄調(diào)控的級(jí)聯(lián)模型，該模型能有效地識(shí)別那些造成基因表達(dá)譜變化的關(guān)鍵轉(zhuǎn)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(guó)內(nèi)外核心刊物上發(fā)表論文近三十篇，累計(jì)影響因子超過(guò)70點(diǎn)，SCI引用超過(guò)400次。