复旦大学生物医学信息学实验室
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From data to discovery, and turning discovery into health!
 
2018
  1. Liu, Z*.,Lian, B*.,Dong, Q.,Sun, H., Wei, J.,Sheng, Y.,Li, Y.,Xie, L*.,Liu, L*.,Qin, L*.(2018) Whole-exome mutational and transcriptional landscapes of combined hepatocellular cholangiocarcinoma and intrahepatic cholangiocarcinoma reveal molecular diversity. Biochimica et Biophysica Acta  - Molecular Basis of Disease1864(6): 2360-2368.https://www.sciencedirect.com/science/article/pii/S0925443918300383#ac0005
 
2017
  1. Gang Liu, Wenhong Hou, Chuanpeng Dong, Aoshen Wu ,Huilin Xu, Weiwei Wei, Lei Liu (2017). Nodes staging score to quantify lymph nodes for examination in gastric cancer. Accepted.
  2. Liu, G*., Dong, C*.,Wang, X*.,Hou, G*.,Zheng, Y.,Xu, H., Zhan, X.,  Liu, L*. (2017)Regulatory activity based risk model identifies survival of stage II and III colorectal carcinoma. Oncotarget8(58): 98360-98370.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5716735/
  3. Liu, G*., Zhan, X*.,Dong, C*., Liu, L*. (2017)Genomics alterations of metastatic and primary tissues across 15 cancer types. Sci Rep. Oct 16;7(1):13262. https://www.nature.com/articles/s41598-017-13650-3
  4. Qiao, N*., Ren, H., Liu, L*.(2017)Genomic diversity and phylogeography of norovirus in China. BMC Medical Genomics10,51.https://bmcmedgenomics.biomedcentral.com/articles/10.1186/s12920-017-0287-9
  5. Dong, C*., Wang, X*., Xu, H*., Zhan, X., Ren, H., Liu, Z., Liu, G*., Liu, L*.(2017) Identification of a cytokine-cytokine receptor interaction gene signature for predicting clinical outcomes in patients with colorectal cancer. Int J Clin Exp Med, 10(6), 9009-9018.http://www.ijcem.com/files/ijcem0052269.pdf
  6. Hou, G*., Chen, L*., Liu, G*., Li, L., Yang, Y., Yan, H., Zhang, H., Tang, J., Yang, Y., Lin, X., Chen, X., Luo, G., Zhu, Y., Tang, S., Zhang, J., Liu, H., Gu, Q., Zhao, L., Li, Y., Liu, L*., Zhou, W*., Wang, H*.(2017)Aldehyde dehydrogenase-2 (ALDH2) opposes hepatocellular carcinoma progression by regulating AMP-activated protein kinase signaling in mice.Hepatology65(5):1628-1644.      https://www.ncbi.nlm.nih.gov/pubmed/28027570
  7. Hou, G*., Dong, C*., Dong, Z*., Liu, G*., Xu, H., Chen, L., Liu, L*., Wang,H*., Zhou, W*.(2017)Upregulate KIF4A Enhances Proliferation, Invasion of Hepatocellular Carcinoma and Indicates poor prognosis Across Human Cancer Types. Scientific Reports7, 4148.http://doi.org/10.1038/s41598-017-04176-9
  8. Huang, T*., Dong, C*., Zhou, G., Lu, S., Luan, Y., Gu, X., Liu, L*.,Ding, X*.(2017)A potential panel of four-long non-coding RNA signature in prostate cancer predicts biochemical recurrence and disease-free survival. International Urology and Nephrology,825-835.https://link.springer.com/article/10.1007/s11255-017-1536-8
  9. Zhan, X*., Dong, C*., Liu, Gang*., Li, Y*., Liu, L*.(2017) Panel of Seven Long Non-Coding RNA as a Candidate Prognostic Biomarker for Ovarian Cancer. OncoTargets and Therapy10,2805–2813.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5466362/
 
2016
  1. Liu G, Dong C, Liu L. Integrated Multiple "-omics" Data Reveal Subtypes of Hepatocellular Carcinoma. PLoS One 2016;11:e0165457.
  2. Hou G, Liu G, Yang Y, et al. Neuraminidase 1 (NEU1) promotes proliferation and migration as a diagnostic and prognostic biomarker of hepatocellular carcinoma. Oncotarget 2016;7:64957-64966.
  3. Chuanpeng Dong*, Gang Liu, Huilin Xu, Juan Duan, Lei Liu.:Identification of an eight-gene signature related to cancer stem cells for predicting clinical outcomes in colorectal cancer patients. Oncology Letters. Oct, 2016.
  4. Hou G, Chen L, Liu G, et al. Aldehyde Dehydrogenase-2 (ALDH2) Opposes HCC Progression By Regulating AMPK Signaling. Hepatology 2016.
  5. Gang Liu, Guojun Hou, Liang Li, Yixue Li, Weiping Zhou*, Lei Liu*, Potential diagnostic and prognostic marker dimethylglycine dehydrogenase  (DMGDH) suppresses hepatocellular carcinoma metastasis in vitro and in vivo, Oncotarget, 2016, 7(22): 32607-32616
  6. Yuan Sheng-Xian,Wang Jie,Yang Fu,Tao Qi-Fei,Zhang Jin,Wang Li-Li,Yang Yuan,Liu Hui,Wang Zhen-Guang,Xu Qing-Guo,Fan Jia,Liu Lei*,Sun Shu-Han,Zhou Wei-Ping,Long noncoding RNA DANCR increases stemness features of hepatocellular carcinoma by derepression of CTNNB1.,Hepatology,2016,63(2):499-511
  7. Gan J,Qiao N, Strahan R, et al. Manipulation of ubiquitin/SUMO pathways in human herpesviruses infection[J]. Reviews in Medical Virology, 2016.
  8. Niu Qiao, Xuan-Yi Wang, Lei Liu. Temporal Evolutionary Dynamics of Norovirus GII.4 Variants in China between 2004 and 2015[J]. Plos One, 2016.
  9. Yin Wang, Rudong Li, Yuhua Zhou, Zongxin Ling, Xiaokui Guo, Lu Xie, Lei Liu* ,Motif-based text mining of microbial metagenome redundancy profiling data for disease classification, BioMed Research International, Volume 2016 (2016), Article ID 6598307, 11 pages http://dx.doi.org/10.1155/2016/6598307
  10. Liang Yan, Su Qu, Gang Liu, Lei Liu, Yao Yu, Guohui Ding,Yanfeng Zhao, Yixue Li, Youhua Xie*, Junqi Zhang*, Di Qu*,Comparative Transcriptomic Analysis of Primary Duck Hepatocytes Provides Insight into Differential Susceptibility to DHBV Infection,PLoS ONE,2016,11(2):DOI:10.1371/journal.pone.0149702
  11. Qin Meilin,Liu Gang,Huo Xisong,Tao Xuemei,Sun Xiaomeng,Ge Zhouhong,Yang Juan,Fan Jia,Liu Lei*,Qin Wenxin,Hsa_circ_0001649: A circular RNA and potential novel biomarker for hepatocellular carcinoma.,Cancer Biomarkers,2016,16(1):161-169
 
2015
  1. Xiaomeng S, Kexu Z, et al. Trend Prediction of Biomedical Technology by Semantic Analysis[J]. HIS 2015, LNCS 9085, 2015: 225-230.
 
2014
  1. Sheng-Xian Yuan,Qi-Fei Tao,Jie Wang,Fu Yang,Lei Liu,Li-Li Wang,Jin Zhang,Yuan Yang,Hui Liu,Fang Wang,Shu-Han Sun*,Wei-Ping Zhou*,Antisense long non-coding RNA PCNA-AS1 promotes tumor growth by regulating proliferating cell nuclear antigen in hepatocellular carcinoma,Cancer Letters,2014,349(1):87-94
  2. Hui Wang, Weide Zhang, Qiang Zeng, Zuofeng Li, ,Kaiyan Feng, Lei Liu*, Extracting important information from Chinese Operation Notes with natural language processing methods, Journal of Biomedical Informatics, 2014. 48:130-136
 
2013
  1. Juanjuan Xiao, Ying Wang, Zuofeng Li; Xufeng Zhang, Kaiyan Feng, Lei Liu*, Assessing the Gender Differences of Adverse Effects in HIV Infection Treatment Based on FDA AERS Database, Current Bioinformatics, 2013.5(8):583-590(8).
  2. Bi-Qing Li, Hui Yu, Zheng Wang, Guohui Ding, Lei Liu*, MicroRNA mediated network and DNA Methylation in Colorectal Cancer, Protein Peptide Letter, 2013,3(20):1-12
 
2012
  1. Rudong Li and Lei Liu*. Characterizing criticality of proteins by systems dynamics: Escherichia coli central carbon metabolism as a working example. BMC Systems Biology, 2012,S11.
  2. Bi-Qing Li, Tao Huang, Lei Liu*, Yu-Dong Cai*, Kuo-Chen Chou. Identification of Colorectal Cancer Related Genes with mRMR and Shortest Path in Protein-Protein Interaction Network. PLoS One, 2012,7(4):e33393
 
2011
  1. Zuofeng Li, Xingnan Liu, Jingran Wen, Ye Xu, Xin Zhao, Xuan Li, Lei Liu,*, and Xiaoyan Zhang*  DRUMS: A Human Disease Related Unique Gene Mutation Search Engine. HUMAN MUTATION, 2011, 32:E2259-E2265
  2. Rudong Li, Yuanyuan Li, Ling-Yi Lu, Cong Ren, Yi-Xue Li, Lei Liu*. An improved kinetic model for the acetone-butanol-ethanol pathway of Clostridium acetobutylicum and model-based perturbation analysis. BMC Systems Biology, 2011, 5(Suppl.): S12.
  3. Lele Hu, Lulu Zheng, Zhiwen Wang, Bing Li, Lei Liu*. Using Pseudo Amino Acid Composition to Predict Protease Families by Incorporating a Series of Protein Biological Features. Protein & Peptide Letters, 2011, 18(6):552-558.
  4. Peng Jia, Liming Xuan, Lei Liu*, Chaochun Wei*. MetaBinG: Using GPUs to accelerate metagenomic sequence classification. PLoS One, 2011, 6(11):e25353.
  5. The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma, Tao Huang, Lei Liu, Qi Liu, Guohui Ding, Yejun Tan, Zhidong Tu, Yixue Li, *Hongyue Dai, *Lu Xie, International Journal of Computational Biology and Drug Design, Inderscience, 4(1), pp 5-17,  2011.
 
2007-2010
  1. Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinoma, Huang, Tao, Ding, Guohui, Li, Yixue, Liu, Lei, Tan, Eugene, Dai, Hongyue, Liu, Qi, Tu, Zhidong, Xie, Lu, 2010 ACM International Conference on Bioinformatics and Computational Biology, ACM-BCB 2010, pp 502-507, 2010/8/2
  2. ESCPP: An evaluation and alerting system for the compatibility between practice guidelines and practicing medicine using Arden syntax, Liu, Xingnan, Xu, Ye, Li, Zuofeng, Liu, Lei*, Zhang, Xiaoyan*, 1st International Conference on Information Science and Engineering, ICISE2009, pp 3649-3652, 2009/12/26
  3. Comparison of AdaBoost and logistic regression for detecting colorectal cancer patients with synchronous liver metastasis, Wen, Jingran, Zhang, Xiaoyan, Xu, Ye, Li, Zuofeng, Liu, Lei*, 2nd International Conference on Biomedical and Pharmaceutical Engineering, ICBPE 2009, 2009/12/2
  4. Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms, Tu, Kang, Yu, Hui, Hua, You-Jia, Li, Yuan-Yuan, Liu, Lei*, Xie, Lu*, Li, Yi-Xue*, Nucleic Acids Research, 37(18), pp 5969-5980,  2009/10
  5. Relationship between topology and functions in metabolic network evolution, Wang Zhuo, Chen Qi, Liu Lei*, 科学通报(英文版)(Chinese Science Bulletin), 54(5), pp 776-782,  2009/3
  6. Modeling the age distribution of gene duplications in vertebrate genome using mixture density, Wang, Zhen, Ding, Guohui, Yu, Zhonghao, Liu, Lei*, Li, Yixue*, Genomics, 93(2), pp 146-151,  2009/2
  7. Though with constraints imposed by endosymbiosis, preferential attachment is still a plausible mechanism responsible for the evolution of the chloroplast metabolic network, Wang, Z., Zhu, X. -G., Chang, X., Chen, Y. Z., Li, Y. X., Liu, L*., Journal of Evolutionary Biology, 22(1), pp 71-79,  2009/1
  8. Photosynthetic metabolism of C-3 plants shows highly cooperative regulation under changing environments: A systems biological analysis, Luo, Ruoyu, Wei, Haibin, Ye, Lin, Wang, Kankan, Chen, Fan, Luo, Lijun, Liu, Lei, Li, Yuanyuan, Crabbe, M. James C., Jin, Li, Li, Yixue*, Zhong, Yang*, Proceedings of the National Academy of Sciences of the United States of America, 106(3), pp 847-852,  2009/1/20
  9. CHSMiner: a GUI tool to identify chromosomal homologous segments, Wang, Zhen, Ding, Guohui, Yu, Zhonghao, Liu, Lei*, Li, Yixue*, Algorithms for Molecular Biology, 4(1),  p 2,  2009/1/15
  10. Metabolic Profiling Reveals Distinct Variations Linked to Nicotine Consumption in Humans - First Results from the KORA Study, Wang-Sattler, Rui, Yu, Yao, Mittelstrass, Kirstin, Lattka, Eva, Altmaier, Elisabeth, Gieger, Christian, Ladwig, Karl H., Dahmen, Norbert, Weinberger, Klaus M., Hao, Pei, Liu, Lei, Li, Yixue, Wichmann, H. -Erich, Adamski, Jerzy, Suhre, Karsten, Illig, Thomas*, PLoS One, 3(12),  p e3863,  2008/12/5
  11. Gene expression module-based chemical function similarity search, Li, Yun, Hao, Pei, Zheng, Siyuan, Tu, Kang, Fan, Haiwei, Zhu, Ruixin, Ding, Guohui, Dong, Changzheng, Wang, Chuan, Li, Xuan, Thiesen, H. -J., Chen, Y. Eugene, Jiang, Hualiang, Liu, Lei*, Li, Yixue*, Nucleic Acids Research, 36(20),  p e137,  2008/11
  12. MPSQ: a web tool for protein-state searching, Zheng, Siyuan, Sheng, Jia, Wang, Chuan, Wang, Xiaojing, Yu, Yao, Li, Yun, Michie, Alex, Dai, Jianliang, Zhong, Yang, Hao, Pei, Liu, Lei*, Li, Yixue*, Bioinformatics, 24(20), pp 2412-2413,  2008/10/15
  13. Tree of Life Based on Genome Context Networks, Ding, Guohui, Yu, Zhonghao, Zhao, Jing, Wang, Zhen, Li, Yun, Xing, Xiaobin, Wang, Chuan, Liu, Lei, Li, Yixue*, PLoS One, 3(10),  p e3357,  2008/10/9
  14. Modeling the effects of cell cycle M-phase transcriptional inhibition on circadian oscillation, Kang, Bin, Li, Yuan-Yuan, Chang, Xiao, Liu, Lei*, Li, Yi-Xue*, Plos Computational Biology, 4(3),  p e1000019,  2008/3
  15. Comparative genomics of human-like Schistosoma japonicum genes indicates a putative mechanism for host-parasite relationship, Yu, Fudong, Li, Yixue, Liu, Lei*, Li, Yuanyuan*, Genomics, 91(2), pp 152-157,  2008/2
  16. Characterization of an 18,166 EST dataset for cassava (Manihot esculenta Crantz) enriched for drought-responsive genes, Lokko, Y., Anderson, J. V., Rudd, S., Raji, A., Horvath, D., Mikel, M. A., Kim, R., Liu, L., Hernandez, A., Dixon, A. G. O., Ingelbrecht, I. L*., Plant Cell Reports, 26(9), pp 1605-1618,  2007/9
  17. A BAC-based physical map of the channel catfish genome, Xu, Peng, Wang, Shaolin, Liu, Lei, Thorsen, Jim, Kucuktas, Huseyin, Liu, Zhanjiang*, Genomics, 90(3), pp 380-388,  2007/9
  18. Evaluation of COMPASS as a comparative mapping tool for ESTs using horse radiation hybrid maps, Coleman, S. J., Gong, G., Gaile, D. P., Chowdhary, B. P., Bailey, E., Liu, L., MacLeod, J. N*., Animal Genetics, 38(3), pp 294-302,  2007/6
  19. Characterization of an EST database for the perennial weed leafy spurge: An important resource for weed biology research, Anderson, James V*., Horvath, David P., Chao, Wun S., Foley, Michael E., Hernandez, Alvaro G., Thimmapuram, Jyothl, Liu, Lie, Gong, George L., Band, Mark, Kim, Ryan, Mikel, Mark A., Weed Science, 55(3), pp 193-203, MAY-JUN 2007/6
  20. "Towards the ictalurid catfish transcriptome: generation and analysis of 31,215 catfish ESTs, Li, Ping, Peatman, Eric, Wang, Shaolin, Feng, Jinian, He, Chongbo, Baoprasertkul, Puttharat, Xu, Peng, Kucuktas, Huseyin, Nandi, Samiran, Somridhivej, Benjaporn, Serapion, Jerry, Simmons, Micah, Turan, Cemal, Liu, Lei, Muir, William, Dunham, Rex, Brady, Yolanda, Grizzle, John, Liu, Zhanjiang* BMC Genomics, 8:177,  2007/6/18
 
 
 
 
 

 

Biomedical Informatics Lab, Institute of Biomedical Science, Fudan University