Yixue Li

Adhemar Zerlotini, Eric R. G. R. Aguiar, Fudong Yu, Huayong Xu, Yixue Li, Neil D. Young, Robin B. Gasser, Anna V. Protasio, Matthew Berriman, David S. Roos, Jessica C. Kissinger, Guilherme Oliveira: SchistoDB: an updated genome resource for the three key schistosomes of humans. Nucleic Acids Research 41(Database-Issue): 728-731 (2013)

Piyush Diwan, Patricia Carey, Eric Franz, Yixue Li, Thomas Bitterman, David E. Hudak, Rajiv Ramnath: Applying software product line engineering in building web portals for supercomputing services. SAC 2013: 1765-1771

Ying He, Menghuan Zhang, Yuanhu Ju, Zhong-Hao Yu, Daqing Lv, Han Sun, Weilan Yuan, Fei He, Jianshe Zhang, Hong Li, Jing Li, Rui Wang-Sattler, Yixue Li, Guoqing Zhang, Lu Xie: dbDEPC 2.0: updated database of differentially expressed proteins in human cancers. Nucleic Acids Research 40(Database-Issue): 964-971 (2012)

Xin Zhao, Qi Liu, Qingqing Cai, Yanyun Li, Congjian Xu, Yixue Li, Zuofeng Li, Xiaoyan Zhang: Dr.VIS: a database of human disease-related viral integration sites. Nucleic Acids Research 40(Database-Issue): 1041-1046 (2012)

Qianghu Wang, Jie Sun, Meng Zhou, Haixiu Yang, Yan Li, Xiang Li, Sali Lv, Xia Li, Yixue Li: A novel network-based method for measuring the functional relationship between gene sets. Bioinformatics 27(11): 1521-1528 (2011)

Kailin Tang, Ruixin Zhu, Yixue Li, Zhi-Wei Cao: Discrimination of Approved Drugs from Experimental Drugs by Learning Methods. BMC Bioinformatics 12: 157 (2011)

Hui Yu, Bao-Hong Liu, Zhi-Qiang Ye, Chun Li, Yi-Xue Li, Yuan-Yuan Li: Link-based Quantitative Methods to Identify Differentially Coexpressed Genes and Gene Pairs. BMC Bioinformatics 12: 315 (2011)

Yan Ji, Yixiang Shi, Guohui Ding, Yixue Li: A new strategy for better genome assembly from very short reads. BMC Bioinformatics 12: 493 (2011)

Guangyong Zheng, Haibo Wang, Chaochun Wei, Yixue Li: iGepros: an integrated gene and protein annotation server for biological nature exploration. BMC Bioinformatics 12(S-14): S6 (2011)

Tao Huang, Lei Liu, Qi Liu, Guohui Ding, Yejun Tan, Zhidong Tu, Yixue Li, Hongyue Dai, Lu Xie: The role of Hepatitis C Virus in the dynamic protein interaction networks of hepatocellular cirrhosis and carcinoma. I. J. Computational Biology and Drug Design 4(1): 5-18 (2011)

Yun Li, Kang Tu, Siyuan Zheng, Jingfang Wang, Yixue Li, Pei Hao, Xuan Li: Association of Feature Gene Expression with Structural Fingerprints of Chemical Compounds. J. Bioinformatics and Computational Biology 9(4): 503-519 (2011)

Zhimin Huang, Liang Zhu, Yan Cao, Geng Wu, Xinyi Liu, Yingyi Chen, Qi Wang, Ting Shi, Yaxue Zhao, Yuefei Wang, Weihua Li, Yixue Li, Haifeng Chen, Guoqiang Chen, Jian Zhang: ASD: a comprehensive database of allosteric proteins and modulators. Nucleic Acids Research 39(Database-Issue): 663-669 (2011)

Hao Ye, Li Ye, Hong Kang, Duanfeng Zhang, Lin Tao, Kailin Tang, Xueping Liu, Ruixin Zhu, Qi Liu, Y. Z. Chen, Yixue Li, Zhi-Wei Cao: HIT: linking herbal active ingredients to targets. Nucleic Acids Research 39(Database-Issue): 1055-1059 (2011)

KaiYan Feng, JunHui Gao, KaiRui Feng, Lei Liu, Yixue Li: Active and Passive Nearest Neighbor Algorithm: A Newly-Developed Supervised Classifier. ICIC (2) 2011: 189-196

Bao-Hong Liu, Hui Yu, Kang Tu, Chun Li, Yi-Xue Li, Yuan-Yuan Li: DCGL: an R package for identifying differentially coexpressed genes and links from gene expression microarray data. Bioinformatics 26(20): 2637-2638 (2010)

Yun-Qin Chen, Hui Yu, Yi-Xue Li, Yuan-Yuan Li: Sorting out inherent features of head-to-head gene pairs by evolutionary conservation. BMC Bioinformatics 11(S-11): S16 (2010)

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 interactions and protein post-translational modifications information. BMC Bioinformatics 11(S-11): S5 (2010)

Yixiang Shi, Yi-Xue Li, Yuan-Yuan Li: Large number of phosphotransferase genes in the Clostridium beijerinckii NCIMB 8052 genome and the study on their evolution. BMC Bioinformatics 11(S-11): S9 (2010)

Hong Li, Ying He, Guohui Ding, Chuan Wang, Lu Xie, Yixue Li: dbDEPC: a database of Differentially Expressed Proteins in human Cancers. Nucleic Acids Research 38(Database-Issue): 658-664 (2010)

Tao Huang, Guohui Ding, Yixue Li, Lei Liu, Eugene Tan, Hongyue Dai, Qi Liu, Zhidong Tu, Lu Xie: Dysfunctional gene/protein networks in hepatitis C virus-induced hepatocellular cirrhosis and carcinoma. BCB 2010: 502-507

Zhen Wang, Guohui Ding, Zhong-Hao Yu, Lei Liu, Yixue Li: CHSMiner: a GUI tool to identify chromosomal homologous segments. Algorithms for Molecular Biology 4 (2009)

Hong Li, Guohui Ding, Lu Xie, Yixue Li: PAnnBuilder: an R package for assembling proteomic annotation data. Bioinformatics 25(8): 1094-1095 (2009)

Pei Hao, Siyuan Zheng, Jie Ping, Kang Tu, Christian Gieger, Rui Wang-Sattler, Yang Zhong, Yixue Li: Human gene expression sensitivity according to large scale meta-analysis. BMC Bioinformatics 10(S-1) (2009)

Yao Yu, Kang Tu, Siyuan Zheng, Yun Li, Guohui Ding, Jie Ping, Pei Hao, Yixue Li: GEOGLE: context mining tool for the correlation between gene expression and the phenotypic distinction. BMC Bioinformatics 10: 264 (2009)

Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang: A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. Journal of Computational Biology 16(8): 1183-1193 (2009)

Guohui Ding, Peter Lorenz, Michael Kreutzer, Yixue Li, Hans-Jürgen Thiesen: SysZNF: the C2H2 zinc finger gene database. Nucleic Acids Research 37(Database-Issue): 267-273 (2009)

Su-Jun Li, Mao Peng, Hong Li, Boshu Liu, Chuan Wang, Jia-Rui Wu, Yi-Xue Li, Rong Zeng: Sys-BodyFluid: a systematical database for human body fluid proteome research. Nucleic Acids Research 37(Database-Issue): 907-912 (2009)

Hong Xi, Jongsun Park, Guohui Ding, Yong-Hwan Lee, Yixue Li: SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry. Nucleic Acids Research 37(Database-Issue): 913-920 (2009)

Pedro Alves, Randy J. Arnold, David E. Clemmer, Yixue Li, James P. Reilly, Quanhu Sheng, Haixu Tang, Zhiyin Xun, Rong Zeng, Predrag Radivojac: Fast and accurate identification of semi-tryptic peptides in shotgun proteomics. Bioinformatics 24(1): 102-109 (2008)

Siyuan Zheng, Jia Sheng, Chuan Wang, Xiaojing Wang, Yao Yu, Yun Li, Alex Michie, Jianliang Dai, Yang Zhong, Pei Hao, Lei Liu, Yixue Li: MPSQ: a web tool for protein-state searching. Bioinformatics 24(20): 2412-2413 (2008)

Guangyong Zheng, Kang Tu, Qing Yang, Yun Xiong, Chaochun Wei, Lu Xie, Yangyong Zhu, Yixue Li: ITFP: an integrated platform of mammalian transcription factors. Bioinformatics 24(20): 2416-2417 (2008)

Qingwei Xu, Yixiang Shi, Qiang Lu, Guoqing Zhang, Qing-ming Luo, Yixue Li: GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations. BMC Bioinformatics 9(S-1) (2008)

Xiaojing Wang, Di Wu, Siyuan Zheng, Jing Sun, Lin Tao, Yixue Li, Zhi-Wei Cao: Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies. BMC Bioinformatics 9(S-12) (2008)

Guangyong Zheng, Ziliang Qian, Qing Yang, Chaochun Wei, Lu Xie, Yangyong Zhu, Yixue Li: The combination approach of SVM and ECOC for powerful identification and classification of transcription factor. BMC Bioinformatics 9 (2008)

Guohui Ding, Yan Sun, Hong Li, Zhen Wang, Haiwei Fan, Chuan Wang, Dan Yang, Yixue Li: EPGD: a comprehensive web resource for integrating and displaying eukaryotic paralog/paralogon information. Nucleic Acids Research 36(Database-Issue): 255-262 (2008)

Jian Cui, Peng Li, Guang Li, Feng Xu, Chen Zhao, Yuhua Li, Zhongnan Yang, Guang Wang, Qingbo Yu, Yi-Xue Li, Tieliu Shi: AtPID: Arabidopsis thaliana protein interactome database - an integrative platform for plant systems biology. Nucleic Acids Research 36(Database-Issue): 999-1008 (2008)

Bin Kang, Yuan-Yuan Li, Xiao Chang, Lei Liu, Yi-Xue Li: Modeling the Effects of Cell Cycle M-phase Transcriptional Inhibition on Circadian Oscillation. PLoS Computational Biology 4(3) (2008)

Yong Fuga Li, Randy J. Arnold, Yixue Li, Predrag Radivojac, Quanhu Sheng, Haixu Tang: A Bayesian Approach to Protein Inference Problem in Shotgun Proteomics. RECOMB 2008: 167-180

Ziliang Qian, Lingyi Lu, Xiao-Jun Liu, Yu-Dong Cai, Yixue Li: An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization. Bioinformatics 23(18): 2449-2454 (2007)

Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li, Zhongming Zhao: InPrePPI: an integrated evaluation method based on genomic context for predicting protein-protein interactions in prokaryotic genomes. BMC Bioinformatics 8 (2007)

Hui Yu, Feng Wang, Kang Tu, Lu Xie, Yuan-Yuan Li, Yi-Xue Li: Transcript-level annotation of Affymetrix probesets improves the interpretation of gene expression data. BMC Bioinformatics 8 (2007)

Jing Zhao, Guohui Ding, Lin Tao, Hong Yu, Zhong-Hao Yu, Jianhua Luo, Zhi-Wei Cao, Yi-Xue Li: Modular co-evolution of metabolic networks. BMC Bioinformatics 8 (2007)

Lingyi Lu, Ziliang Qian, Yu-Dong Cai, Yixue Li: ECS: An automatic enzyme classifier based on functional domain composition. Computational Biology and Chemistry 31(3): 226-232 (2007)

Xiaojing Wang, Wu Wei, Siyuan Zheng, Zhi-Wei Cao, Yixue Li: Ab-origin: An Improved Tool of Heavy Chain Rearrangement Analysis for Human Immunoglobulin. International Conference on Computational Science (2) 2007: 363-369

Yixue Li: Biological data integration and high-performance computing. China HPC 2007: 51-61

Yuan-Yuan Li, Lei Qin, Zong-Ming Guo, Lei Liu, Hao Xu, Pei Hao, Jiong Su, Yixiang Shi, Wei-Zhong He, Yi-Xue Li: In silico discovery of human natural antisense transcripts. BMC Bioinformatics 7: 18 (2006)

Xiaojing Yu, Chuan Wang, Yixue Li: Classification of protein quaternary structure by functional domain composition. BMC Bioinformatics 7: 187 (2006)

Peilin Jia, Tieliu Shi, Yu-Dong Cai, Yixue Li: Demonstration of two novel methods for predicting functional siRNA efficiency. BMC Bioinformatics 7: 271 (2006)

Jing Zhao, Hong Yu, Jianhua Luo, Zhi-Wei Cao, Yi-Xue Li: Hierarchical modularity of nested bow-ties in metabolic networks. BMC Bioinformatics 7: 386 (2006)

Sujun Li, Boshu Liu, Rong Zeng, Yu-Dong Cai, Yixue Li: Predicting O-glycosylation sites in mammalian proteins by using SVMs. Computational Biology and Chemistry 30(3): 203-208 (2006)

Guoqing Zhang, Zhi-Wei Cao, Qing-ming Luo, Yu-Dong Cai, Yixue Li: Operon prediction based on SVM. Computational Biology and Chemistry 30(3): 233-240 (2006)

Xing-Ming Zhao, Ji-Xiang Du, Hong-Qiang Wang, Yunping Zhu, Yixue Li: A new technique for selecting features from protein sequences. IJPRAI 20(2): 271-283 (2006)

Chun-Hou Zheng, Yan Chen, Xiu-Xia Li, Yi-Xue Li, Yunping Zhu: Tumor classification based on independent component analysis. IJPRAI 20(2): 297-310 (2006)

Zhuo Fang, Jiong Yang, Yixue Li, Qing-ming Luo, Lei Liu: Knowledge guided analysis of microarray data. : 401-411 (2006)

Qiang Lu, Pei Hao, Vasa Curcin, Wei-Zhong He, Yuan-Yuan Li, Qing-ming Luo, Yike Guo, Yi-Xue Li: KDE Bioscience: Platform for bioinformatics analysis workflows. : 440-450 (2006)

Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li: Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance. PLoS Computational Biology 2(7) (2006)

Guohui Ding, Jiuhong Kang, Qi Liu, Tieliu Shi, Gang Pei, Yixue Li: Insights into the Coupling of Duplication Events and Macroevolution from an Age Profile of Animal Transmembrane Gene Families. PLoS Computational Biology 2(8) (2006)

Yuan-Yuan Li, Hui Yu, Zong-Ming Guo, Ting-Qing Guo, Kang Tu, Yi-Xue Li: Correction: Systematic Analysis of Head-to-Head Gene Organization: Evolutionary Conservation and Potential Biological Relevance. PLoS Computational Biology 2(8) (2006)

Yixue Li, Yu Xu, Gengzhong Feng, Wenqiang Dai: On Loan-to-Value Ratios of Inventory Financing with Doubly Stochastic Poisson Default Processes. APSCC 2006: 663-666

Zhuo Wang, Xin-Guang Zhu, Yazhu Chen, Yi-Xue Li, Lei Liu: Comparison of Modularization Methods in Application to Different Biological Networks. VDMB 2006: 185-195

Pei Hao, Wei-Zhong He, Yin Huang, Liang-Xiao Ma, Ying Xu, Hong Xi, Chuan Wang, Boshu Liu, Jin-Miao Wang, Yi-Xue Li, Yang Zhong: MPSS: an integrated database system for surveying a set of proteins. Bioinformatics 21(9): 2142-2143 (2005)

Jingchun Sun, Jinlin Xu, Zhen Liu, Qi Liu, Aimin Zhao, Tieliu Shi, Yi-Xue Li: Refined phylogenetic profiles method for predicting protein-protein interactions. Bioinformatics 21(16): 3409-3415 (2005)

Guang-Zheng Zhang, De-Shuang Huang, Yunping Zhu, Yi-Xue Li: Improving protein secondary structure prediction by using the residue conformational classes. Pattern Recognition Letters 26(15): 2346-2352 (2005)

Yong Deng, Qi Liu, Yi-Xue Li: Scoring hidden Markov models to discriminate -barrel membrane proteins. Computational Biology and Chemistry 28(3): 189-194 (2004)

Qi Liu, Yi-Sheng Zhu, Baohua Wang, Yi-Xue Li: A HMM-based method to predict the transmembrane regions of \beta-barrel membrane proteins. Computational Biology and Chemistry 27(1): 69-76 (2003)

Qi Liu, Yi-Sheng Zhu, Baohua Wang, Yi-Xue Li: Identification of -barrel membrane proteins based on amino acid composition properties and predicted secondary structure. Computational Biology and Chemistry 27(3): 355-361 (2003)