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Yixue Li

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TOP 3
Yan Li; Shangwei Ning; Donglin Sun; Peng Wang; Qianghu Wang; Yun Xiao; Xu Chaohan; Xin Chen; Teng Huang; Xia Li; Yixue Li
Prioritising risk pathways of complex human diseases based on functional profiling.
F Zhao; Yixue Li; Wenli Liu; M Wu; Y Deng; F Guan; X Hou; X Huang; J Lei
Schistosoma japonicum: susceptibility of neonate mice born to infected and noninfected mothers following subsequent challenge.
Shuhao Yu; Yang Yu; Lulu Zheng; Chunyan Li; Xuan Li; Yixue Li; Chenchen Ma; Pei Hao
Causal co-expression method with module analysis to screen drugs with specific target.

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All Publications

2013: Yan Li; Shangwei Ning; Donglin Sun; Peng Wang; Qianghu Wang; Yun Xiao; Xu Chaohan; Xin Chen; Teng Huang; Xia Li; Yixue Li
Prioritising risk pathways of complex human diseases based on functional profiling.
European journal of human genetics : EJHG 2013;21(6):666-72.
2013: F Zhao; Yixue Li; Wenli Liu; M Wu; Y Deng; F Guan; X Hou; X Huang; J Lei
Schistosoma japonicum: susceptibility of neonate mice born to infected and noninfected mothers following subsequent challenge.
Parasite immunology 2013;35(5-6):157-63.
2013: Shuhao Yu; Yang Yu; Lulu Zheng; Chunyan Li; Xuan Li; Yixue Li; Chenchen Ma; Pei Hao
Causal co-expression method with module analysis to screen drugs with specific target.
Gene 2013;518(1):145-51.
2013: Shen Niu; Yu-Dong Cai; Weiren Cui; Kai-Yan Feng; Lei Gu; Zhisong He; Tao Huang; Haipeng Li; Yixue Li
Inter- and intra-chain disulfide bond prediction based on optimal feature selection.
Protein and peptide letters 2013;20(3):324-35.
2013: Yan Ji; Yixiang Shi; Chuan Wang; Jianliang Dai; Yixue Li
Meta genome-wide network from functional linkages of genes in human gut microbial ecosystems.
Protein and peptide letters 2013;20(3):371-8.
2013: Tao Xu; Zhonghao Yu; H-Erich Wichmann; Jerzy Adamski; Erik Bader; Xiao Dong; Christina Holzapfel; Thomas Illig; Marta Jaremek; Karl H Ladwig; Yixue Li; Katrin Perstorfer; Annette Peters; Cornelia Prehn; Wolfgang Rathmann; Werner Roemisch-Margl; Karsten Suhre; Fabian Theis; Henri Wallaschofski; Rui Wang-Sattler
Effects of smoking and smoking cessation on human serum metabolite profile: results from the KORA cohort study.
BMC medicine 2013;11():60.
2013: Qun Wu; Yixue Li; Suqin Peng; Yao Yu; Yan Xu
Genome Sequence of Bacillus licheniformis CGMCC3963, a Stress-Resistant Strain Isolated in a Chinese Traditional Solid-State Liquor-Making Process.
Genome announcements 2013;1(1):.
2013: Adhemar Zerlotini; Eric R G R Aguiar; Matthew Berriman; Robin B Gasser; Jessica Kissinger; Yixue Li; Anna V Protasio; David S Roos; Huayong Xu; Neil D Young; Fudong Yu; Guilherme Oliveira
SchistoDB: an updated genome resource for the three key schistosomes of humans.
Nucleic acids research 2013;41(Database issue):D728-31.
2013: Xiao Dong; Biqing Li; Chao Li; Yunting Xia; Tao Xu; Liyun Yuan; Tingyan Zhong; Guohui Ding; Yixue Li
Evaluating coverage of exons by HapMap SNPs.
Genomics 2013;101(1):20-3.
2012: Zhonghao Yu; Guangju Zhai; Heinz-Erich Wichmann; Tao Xu; Jerzy Adamski; Christian Gieger; Ying He; Joachim Heinrich; Thomas Illig; Eva Lattka; Yixue Li; Kirstin Mittelstraß; Annette Peters; Cornelia Prehn; Werner Römisch-Margl; Paula Singmann; Nicole Soranzo; Tim D Spector; Marie Standl; Karsten Suhre; Elisabeth Thiering; Rui Wang-Sattler
Human serum metabolic profiles are age dependent.
Aging cell 2012;11(6):960-7.
2012: Dieter W Heermann; Hansjoerg Jerabek; Lei Liu; Yixue Li
A model for the 3D chromatin architecture of pro and eukaryotes.
Methods (San Diego, Calif.) 2012;58(3):307-14.
2012: Ying He; Dongya Ge; Hans-Jürgen Thiesen; Rui Wang-Sattler; Lu Xie; Zhonghao Yu; Yixue Li
Cell type specificity of signaling: view from membrane receptors distribution and their downstream transduction networks.
Protein & cell 2012;3(9):701-13.
2012: Shen Niu; Zhen Wang; Guoqing Zhang; Dongya Ge; Yixue Li
Prediction of functional phosphorylation sites by incorporating evolutionary information.
Protein & cell 2012;3(9):675-90.
2012: Liyun Yuan; Y Eugene Chen; Zhe Chen; Guohui Ding; Yixue Li
A novel strategy for deciphering dynamic conservation of gene expression relationship.
Journal of molecular cell biology 2012;4(3):177-9.
2012: Guan-Wen Yan; Yue Chen; Yixue Li; Hai-Feng Chen
Revealing interaction mode between HIV-1 protease and mannitol analog inhibitor.
Chemical biology & drug design 2012;79(6):916-25.
2012: Yudong Cai; Lele Hu; Tao Huang; Xiaohe Shi; Lu Xie; Yixue Li
Prediction of lysine ubiquitination with mRMR feature selection and analysis.
Amino acids 2012;42(4):1387-95.
2012: Hao Ye; Zhiwei Cao; Kailin Tang; Linlin Yang; Yixue Li
Study of drug function based on similarity of pathway fingerprint.
Protein & cell 2012;3(2):132-9.
2012: Suping Deng; Yixue Li; Yixiang Shi; Liyun Yuan; Guohui Ding
Detecting the borders between coding and non-coding DNA regions in prokaryotes based on recursive segmentation and nucleotide doublets statistics.
BMC genomics 2012;13 Suppl 8():S19.
2012: Yajun Wang; Xiaogang Xu; Yao Yu; Pei Hao; Yixue Li; Bohu Pan; Zhifeng Shao; Xuan Li
Optimizing hybrid assembly of next-generation sequence data from Enterococcus faecium: a microbe with highly divergent genome.
BMC systems biology 2012;6 Suppl 3():S21.
2012: Lingyao Zeng; Jian Yu; Weilan Yuan; Qiongzhu Dong; Fei He; Tao Huang; Huliang Jia; Yixue Li; Lunxiu Qin; Lu Xie
Differential combinatorial regulatory network analysis related to venous metastasis of hepatocellular carcinoma.
BMC genomics 2012;13 Suppl 8():S14.
2012: Shuhao Yu; Lulu Zheng; Chunyan Li; Xuan Li; Yun Li; Yixue Li; Chenchen Ma; Pei Hao
A cross-species analysis method to analyze animal models' similarity to human's disease state.
BMC systems biology 2012;6 Suppl 3():S18.
2012: Yin Wang; Yuhua Zhou; Yan Zhu; Xiaokui Guo; Yixue Li; Zongxin Ling; Hong Sun
An improved dimensionality reduction method for meta-transcriptome indexing based diseases classification.
BMC systems biology 2012;6 Suppl 3():S12.
2012: Chuanli Wang; Longyun Guo; Yixue Li; Zhuo Wang
Systematic comparison of C3 and C4 plants based on metabolic network analysis.
BMC systems biology 2012;6 Suppl 2():S9.
2012: Yan Zhu; Biqing Li; Qianqian Ning; Geir Skogerbø; Hong Sun; Zhen Wang; Shuang Yang; Yixue Li
Evolutionary relationships between miRNA genes and their activity.
BMC genomics 2012;13():718.
2012: Guangyong Zheng; Guohui Ding; Qi Liu; Chaochun Wei; Yixue Li
Towards biological characters of interactions between transcription factors and their DNA targets in mammals.
BMC genomics 2012;13():388.
2012: Jian Yu; Lingyao Zeng; Guoqing Zhang; Xiaobin Xing; Ying He; Jing Li; Wei Li; Yixue Li; Han Sun; Jiehuan Sun; Chuan Wang; Lu Xie
SyStemCell: a database populated with multiple levels of experimental data from stem cell differentiation research.
PloS one 2012;7(7):e35230.
2012: Liang Sun; Jun Xue; Danxia Yu; Yu Yu; Zhijie Yu; Peng An; Lu Cai; Tao Huang; Miao Jing; Huaixing Li; Yixue Li; Xu Lin; Hongguang Sheng; Fudi Wang
Associations between ionomic profile and metabolic abnormalities in human population.
PloS one 2012;7(6):e38845.
2012: Shuhao Yu; Yan Guan; Zhizhong Guo; Pei Hao; Yixue Li; Yi-Yu Lu; Shi-Bing Su
Combining ZHENG Theory and High-Throughput Expression Data to Predict New Effects of Chinese Herbal Formulae.
Evidence-based complementary and alternative medicine : eCAM 2012;2012():986427.
2012: Wei Ye; Qingfen Yu; Jian Zhang; Yue Chen; Yixue Li; Wei Wang; Hai-Feng Chen
Insight into the stability of cross-β amyloid fibril from VEALYL short peptide with molecular dynamics simulation.
PloS one 2012;7(5):e36382.
2012: Tao Huang; Chuan Wang; Lu Xie; Guoqing Zhang; Yixue Li
SySAP: a system-level predictor of deleterious single amino acid polymorphisms.
Protein & cell 2012;3(1):38-43.
2012: Michael Hecker; Li Hong; Yixue Li; Peter Lorenz; Gabriela Riemekasten; Felix Steinbeck; Uwe K Zettl; Hans-Jürgen Thiesen
Computational analysis of high-density peptide microarray data with application from systemic sclerosis to multiple sclerosis.
Autoimmunity reviews 2012;11(3):180-90.
2011: Youyuan Li; Siliang Zhang; Pei Hao; Yixue Li
Feature-matching pattern-based support vector machines for robust peptide mass fingerprinting.
Molecular & cellular proteomics : MCP 2011;10(12):M110.005785.
2011: Hao Zhang; Jian Zhang; Jiayi Zhu; Yi Jiang; Yixue Li; Zeng Li; Songyao Ma; Fang Qin; Yan Xia; Wei Ye; Hai-Feng Chen
Revealing the drug-resistant mechanism for diarylpyrimidine analogue inhibitors of HIV-1 reverse transcriptase.
Chemical biology & drug design 2011;78(3):427-37.
2011: Yun Li; Yixue Li; Kang Tu; Jingfang Wang; Siyuan Zheng; Pei Hao; Xuan Li
Association of feature gene expression with structural fingerprints of chemical compounds.
Journal of bioinformatics and computational biology 2011;9(4):503-19.
2011: Jing Jiang; Guohui Ding; Jiangwei Lin; Man Zhang; Linyu Shi; Wenjian Lv; Hui Yang; Huasheng Xiao; Gang Pei; Yixue Li; Jiarui Wu; Jinsong Li
Different developmental potential of pluripotent stem cells generated by different reprogramming strategies.
Journal of molecular cell biology 2011;3(3):197-9.
2011: 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 (Oxford, England) 2011;27(11):1521-8.
2011: Zhen Wang; Guohui Ding; Ludwig Geistlinger; Hong Li; Lei Liu; Rong Zeng; Yoshio Tateno; Yixue Li
Evolution of protein phosphorylation for distinct functional modules in vertebrate genomes.
Molecular biology and evolution 2011;28(3):1131-40.
2011: Fang Qin; Yaobin Jiang; Yue Chen; Maoying Wu; Guanwen Yan; Wenjun Ye; Yixue Li; Jian Zhang; Hai-Feng Chen
Conformational selection or induced fit for Brinker and DNA recognition.
Physical chemistry chemical physics : PCCP 2011;13(4):1407-12.
2011: Guangyong Zheng; Haibo Wang; Chaochun Wei; Yixue Li
iGepros: an integrated gene and protein annotation server for biological nature exploration.
BMC bioinformatics 2011;12 Suppl 14():S6.
2011: Yan Ji; Guohui Ding; Yixiang Shi; Yixue Li
A new strategy for better genome assembly from very short reads.
BMC bioinformatics 2011;12():493.
2011: Kailin Tang; Ruixin Zhu; Yixue Li; Zhiwei Cao
Discrimination of approved drugs from experimental drugs by learning methods.
BMC bioinformatics 2011;12():157.
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.
International journal of computational biology and drug design 2011;4(1):5-18.
2011: Zeng Li; Hao Zhang; Yixue Li; Jian Zhang; Hai-Feng Chen
Drug resistant mechanism of diaryltriazine analog inhibitors of HIV-1 reverse transcriptase using molecular dynamics simulation and 3D-QSAR.
Chemical biology & drug design 2011;77(1):63-74.
2011: Hao Ye; Li Ye; Hong Kang; Duanfeng Zhang; Lin Tao; Kailin Tang; Xueping Liu; Ruixin Zhu; Qi Liu; Y Z Chen; Yixue Li; Zhiwei Cao
HIT: linking herbal active ingredients to targets.
Nucleic acids research 2011;39(Database issue):D1055-9.
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 2011;39(Database issue):D663-9.
2010: Shen Niu; Tao Huang; Kaiyan Feng; Yudong Cai; Yixue Li
Prediction of tyrosine sulfation with mRMR feature selection and analysis.
Journal of proteome research 2010;9(12):6490-7.
2010: Xing-Ming Zhao; Yixue Li; Ming Li; Luonan Chen
Advances in genome informatics.
Journal of bioinformatics and computational biology 2010;8 Suppl 1():v-viii.
2010: Yi Yang; Zili Zhang; Yixue Li; Xin-Guang Zhu; Qi Liu
Identifying cooperative transcription factors by combining ChIP-chip data and knockout data.
Cell research 2010;20(11):1276-8.
2010: Jian Shen; Baorang Zhang; Hua Wei; Chuanyan Che; Dezhong Ding; Xiuguo Hua; Peter Bucheli; Linghua Wang; Yixue Li; Xiaoyan Pang; Liping Zhao
Assessment of the modulating effects of fructo-oligosaccharides on fecal microbiota using human flora-associated piglets.
Archives of microbiology 2010;192(11):959-68.
2010: Lingyi Lu; Ziliang Qian; XiaoHe Shi; Haipeng Li; Yu-Dong Cai; Yixue Li
A knowledge-based method to predict the cooperative relationship between transcription factors.
Molecular diversity 2010;14(4):815-9.
2010: Yue Chen; Yong-Jie He; Maoying Wu; Guanwen Yan; Yixue Li; Jian Zhang; Hai-Feng Chen
Insight into the stability of cross-beta amyloid fibril from molecular dynamics simulation.
Biopolymers 2010;93(6):578-86.
2010: Fang Qin; Yue Chen; Maoying Wu; Yixue Li; Jian Zhang; Hai-Feng Chen
Induced fit or conformational selection for RNA/U1A folding.
RNA (New York, N.Y.) 2010;16(5):1053-61.
2010: Jing Zhao; Chao Geng; Lin Tao; Duanfeng Zhang; Ying Jiang; Kailin Tang; Ruixin Zhu; Hong Yu; Weidong Zhang; Fuchu He; Yixue Li; Zhiwei Cao
Reconstruction and analysis of human liver-specific metabolic network based on CNHLPP data.
Journal of proteome research 2010;9(4):1648-58.
2010: Shimin Zhao; Wei Xu; Wenqing Jiang; Wei Yu; Yan Lin; Tengfei Zhang; Jun Yao; Li Zhou; Yaxue Zeng; Hong Li; Yixue Li; Jiong Shi; Wenlin An; Susan M Hancock; Fuchu He; Lunxiu Qin; Jason Chin; Pengyuan Yang; Xian Chen; Qunying Lei; Yue Xiong; Kun-Liang Guan
Regulation of cellular metabolism by protein lysine acetylation.
Science (New York, N.Y.) 2010;327(5968):1000-4.
2010: J Y Zhang; X F Wang; X D Wang; Z C Fan; Yixue Li; An Ji; F H Yang
Selective and lithography-independent fabrication of 20 nm nano-gap electrodes and nano-channels for nanoelectrofluidics applications.
Nanotechnology 2010;21(7):75303.
2010: Jinsong Zhang; Qiang Liu; Wei Zhang; Jianyuan Li; Zheng Li; Zhongyi Tang; Yixue Li; Chunsheng Han; Susan H Hall; Yonglian Zhang
Comparative profiling of genes and miRNAs expressed in the newborn, young adult, and aged human epididymides.
Acta biochimica et biophysica Sinica 2010;42(2):145-53.
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 2010;11 Suppl 11():S5.
2010: Xiao Dong; Chao Li; Yunqin Chen; Guohui Ding; Yixue Li
Human transcriptional interactome of chromatin contribute to gene co-expression.
BMC genomics 2010;11():704.
2010: Di Wu; Jing Sun; Tianlei Xu; Shuning Wang; Guoqing Li; Yixue Li; Zhiwei Cao
Stacking and energetic contribution of aromatic islands at the binding interface of antibody proteins.
Immunome research 2010;6 Suppl 1():S1.
2010: Tao Huang; Ping Wang; Zhi-Qiang Ye; Heng Xu; Zhisong He; Kai-Yan Feng; Lele Hu; Weiren Cui; Kai Wang; Xiao Dong; Lu Xie; Xiangyin Kong; Yu-Dong Cai; Yixue Li
Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid properties.
PloS one 2010;5(7):e11900.
2010: Zhen Wang; Xiao Dong; Guohui Ding; Yixue Li
Comparing the retention mechanisms of tandem duplicates and retrogenes in human and mouse genomes.
Genetics, selection, evolution : GSE 2010;42():24.
2010: Tao Huang; Lei Liu; Ziliang Qian; Kang Tu; Yixue Li; Lu Xie
Using GeneReg to construct time delay gene regulatory networks.
BMC research notes 2010;3(1):142.
2010: Peter Lorenz; Sabine Dietmann; Thomas Wilhelm; Dirk Koczan; Sandra Autran; Sophie Gad; Gaiping Wen; Guohui Ding; Yixue Li; Marie-Françoise Rousseau-Merck; Hans-Juergen Thiesen
The ancient mammalian KRAB zinc finger gene cluster on human chromosome 8q24.3 illustrates principles of C2H2 zinc finger evolution associated with unique expression profiles in human tissues.
BMC genomics 2010;11():206.
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 2010;38(Database issue):D658-64.
2010: Hui Dong; Yanjun Zhang; Hui Xiong; An Yan; Guohui Ding; Yangyi Chen; Liqun Xie; Jiazheng Chen; Guoqing Zhang; Pei Hao; Liming Cong; Yiyu Lu; Xiaoyan Che; Xiaoning Wang; Yixue Li; Kwok-Yung Yuen; Guoping Zhao; Weirong Jin
Detection of human novel influenza A (H1N1) viruses using multi-fluorescent real-time RT-PCR.
Virus research 2010;147(1):85-90.
2010: Aihua Sun; Ying Jiang; Xue Wang; Qijun Liu; Fan Zhong; Quanyuan He; Wei Guan; Hao Li; Yulin Sun; Liang Shi; Hong Yu; Dong Yang; Yang Xu; Yanping Song; Wei Tong; Dong Li; Chengzhao Lin; Yunwei Hao; Chao Geng; Dong Yun; Xuequn Zhang; Xiaoyan Yuan; Ping Chen; Yunping Zhu; Yixue Li; Songping Liang; Xiaohang Zhao; Siqi Liu; Fuchu He
Liverbase: a comprehensive view of human liver biology.
Journal of proteome research 2010;9(1):50-8.
2009: Tao Huang; WeiRen Cui; Zhi-Song He; Lele Hu; Fang Liu; TieQiao Wen; Yixue Li; Yudong Cai
Functional association between influenza A (H1N1) virus and human.
Biochemical and biophysical research communications 2009;390(4):1111-3.
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 : a journal of computational molecular cell biology 2009;16(8):1183-93.
2009: Hong Li; Xiaobin Xing; Guohui Ding; QR Li; Chuan Wang; Lu Xie; Rong Zeng; Yixue Li
SysPTM: a systematic resource for proteomic research on post-translational modifications.
Molecular & cellular proteomics : MCP 2009;8(8):1839-49.
2009: Bing Niu; Yuhuan Jin; Lin Lu; Kaiyan Fen; Lei Gu; Zhisong He; Wencong Lu; Yixue Li; Yudong Cai
Prediction of interaction between small molecule and enzyme using AdaBoost.
Molecular diversity 2009;13(3):313-20.
2009: Xiaoyan Hui; Weidong Zhu; Yu Wang; Karen S L Lam; Jialiang Zhang; Donghai Wu; Edward W Kraegen; Yixue Li; Aimin Xu
Major urinary protein-1 increases energy expenditure and improves glucose intolerance through enhancing mitochondrial function in skeletal muscle of diabetic mice.
The Journal of biological chemistry 2009;284(21):14050-7.
2009: Hong Li; Guohui Ding; Lu Xie; Yixue Li
PAnnBuilder: an R package for assembling proteomic annotation data.
Bioinformatics (Oxford, England) 2009;25(8):1094-5.
2009: Zhen Wang; Guohui Ding; Zhonghao Yu; Lei Liu; Yixue Li
Modeling the age distribution of gene duplications in vertebrate genome using mixture density.
Genomics 2009;93(2):146-51.
2009: Ruoyu Luo; Haibin Wei; Lin Ye; Kankan Wang; Fan Chen; Lijun Luo; Lei Liu; Yuanyuan Li; M James C Crabbe; Li Jin; Yixue Li; Yang Zhong
Photosynthetic metabolism of C3 plants shows highly cooperative regulation under changing environments: a systems biological analysis.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(3):847-52.
2009: Yao Yu; Kang Tu; Siyuan Zheng; Yixue 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 2009;10():264.
2009: Songling Li; Hong Li; Mingfa Li; Yu Shyr; Lu Xie; Yixue Li
Improved prediction of lysine acetylation by support vector machines.
Protein and peptide letters 2009;16(8):977-83.
2009: Xing Yang; Lu Xie; Yixue Li; Chaochun Wei
More than 9,000,000 unique genes in human gut bacterial community: estimating gene numbers inside a human body.
PloS one 2009;4(6):e6074.
2009: Xing Fu; Ning Fu; Song Guo; Zheng Yan; Ying Xu; Hao Hu; Corinna Menzel; Wei Chen; Yixue Li; Rong Zeng; Philipp Khaitovich
Estimating accuracy of RNA-Seq and microarrays with proteomics.
BMC genomics 2009;10():161.
2009: Hong Sun; Geir Skogerbø; Xiaohui Zheng; Wei Liu; Yixue Li
Genomic regions with distinct genomic distance conservation in vertebrate genomes.
BMC genomics 2009;10():133.
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 2009;10 Suppl 1():S56.
2009: Zhen Wang; Guohui Ding; Zhonghao Yu; Lei Liu; Yixue Li
CHSMiner: a GUI tool to identify chromosomal homologous segments.
Algorithms for molecular biology : AMB 2009;4():2.
2009: Changyu Shen; Quanhu SHENG; Jie Dai; Yixue Li; Rong Zeng; Haixu Tang
On the estimation of false positives in peptide identifications using decoy search strategy.
Proteomics 2009;9(1):194-204.
2008: Quanhu SHENG; Yehia Mechref; Yixue Li; Milos V Novotny; Haixu Tang
A computational approach to characterizing bond linkages of glycan isomers using matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry.
Rapid communications in mass spectrometry : RCM 2008;22(22):3561-9.
2008: Yixue Li; Pei Hao; Siyuan Zheng; Kang Tu; Haiwei Fan; Ruixin Zhu; Guohui Ding; Changzheng Dong; Chuan Wang; Xuan Li; H-J Thiesen; Y Eugene Chen; Hualiang Jiang; Lei Liu; Yixue Li
Gene expression module-based chemical function similarity search.
Nucleic acids research 2008;36(20):e137.
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 (Oxford, England) 2008;24(20):2416-7.
2008: Siyuan Zheng; Jia Sheng; Chuan Wang; Xiaojing Wang; Yao Yu; Yixue Li; Alex Michie; Jianliang Dai; Yang Zhong; Pei Hao; Lei Liu; Yixue Li
MPSQ: a web tool for protein-state searching.
Bioinformatics (Oxford, England) 2008;24(20):2412-3.
2008: Wenxi Li; Lu Xie; Xianghuo He; Jinjun Li; Kang Tu; Lin Wei; Jun Wu; Yong Guo; Xi Ma; Pingping Zhang; Zhimei Pan; Xin Hu; Yingjun Zhao; Haiyang Xie; Guoping Jiang; Taoyang Chen; Jianneng Wang; Shusen Zheng; Jing Cheng; Dafang Wan; Shengli Yang; Yixue Li; Jianren Gu
Diagnostic and prognostic implications of microRNAs in human hepatocellular carcinoma.
International journal of cancer. Journal international du cancer 2008;123(7):1616-22.
2008: Chao Yuan; Quanhu SHENG; Haixu Tang; Yixue Li; Rong Zeng; R John Solaro
Quantitative comparison of sarcomeric phosphoproteomes of neonatal and adult rat hearts.
American journal of physiology. Heart and circulatory physiology 2008;295(2):H647-56.
2008: Peilin Jia; Ziliang Qian; Kaiyan Feng; Wencong Lu; Yixue Li; Yudong Cai
Prediction of membrane protein types in a hybrid space.
Journal of proteome research 2008;7(3):1131-7.
2008: Fudong Yu; Yixue Li; Lei Liu; Yuanyuan Li
Comparative genomics of human-like Schistosoma japonicum genes indicates a putative mechanism for host-parasite relationship.
Genomics 2008;91(2):152-7.
2008: Changzheng Dong; Xun Chu; Ying Wang; Yi Wang; Li Jin; Tieliu Shi; Wei Huang; Yixue Li
Exploration of gene-gene interaction effects using entropy-based methods.
European journal of human genetics : EJHG 2008;16(2):229-35.
2008: Xiaojing Wang; Di Wu; Siyuan Zheng; Jing Sun; Lin Tao; Yixue Li; Zhiwei Cao
Ab-origin: an enhanced tool to identify the sourcing gene segments in germline for rearranged antibodies.
BMC bioinformatics 2008;9 Suppl 12():S20.
2008: Rui Wang-Sattler; Yao Yu; Kirstin Mittelstrass; Eva Lattka; Elisabeth Altmaier; Christian Gieger; Karl H Ladwig; Norbert Dahmen; Klaus M Weinberger; Pei Hao; Lei Liu; Yixue Li; H-Erich Wichmann; Jerzy Adamski; Karsten Suhre; Thomas Illig
Metabolic profiling reveals distinct variations linked to nicotine consumption in humans--first results from the KORA study.
PloS one 2008;3(12):e3863.
2008: Hong Sun; Geir Skogerbø; Zhen Wang; Wei Liu; Yixue Li
Structural relationships between highly conserved elements and genes in vertebrate genomes.
PloS one 2008;3(11):e3727.
2008: Guohui Ding; Zhonghao Yu; Jing Zhao; Zhen Wang; Yixue Li; Xiaobin Xing; Chuan Wang; Lei Liu; Yixue Li
Tree of life based on genome context networks.
PloS one 2008;3(10):e3357.
2008: Siyuan Ren; Guang Yang; Youyu He; Yiguo Wang; Yixue Li; Zhengjun Chen
The conservation pattern of short linear motifs is highly correlated with the function of interacting protein domains.
BMC genomics 2008;9():452.
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 2008;9():282.
2008: Qingwei Xu; Yixiang Shi; Qiang Lu; Guoqing Zhang; Qingming Luo; Yixue Li
GORouter: an RDF model for providing semantic query and inference services for Gene Ontology and its associations.
BMC bioinformatics 2008;9 Suppl 1():S6.
2008: Jing-Fang Wang; Dong-Qing Wei; Chao Chen; Yixue Li; Kuo-Chen Chou
Molecular modeling of two CYP2C19 SNPs and its implications for personalized drug design.
Protein and peptide letters 2008;15(1):27-32.
2008: Pedro Alves; Randy J Arnold; David E Clemmer; Yixue Li; James P Reilly; Quanhu SHENG; Haixu Tang; Zhiyin (Ella) Xun; Rong Zeng; Predrag Radivojac
Fast and accurate identification of semi-tryptic peptides in shotgun proteomics.
Bioinformatics (Oxford, England) 2008;24(1):102-9.
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 2008;36(Database issue):D255-62.
2008: Jian Cui; Peng Li; Guang Li; Feng Xu; Chen Zhao; Yixue Li; Zhongnan Yang; Guang Wang; Qingbo Yu; Yixue Li; Tieliu Shi
AtPID: Arabidopsis thaliana protein interactome database--an integrative platform for plant systems biology.
Nucleic acids research 2008;36(Database issue):D999-1008.
2007: Jian Yu; Tongyu Zhu; Zhirou Wang; Hongyu Zhang; Ziliang Qian; Huili Xu; Baomei Gao; Wei Wang; Lianping Gu; Jun Meng; Jina Wang; Xu Feng; Yixue Li; Xuebiao Yao; Jingde Zhu
A novel set of DNA methylation markers in urine sediments for sensitive/specific detection of bladder cancer.
Clinical cancer research : an official journal of the American Association for Cancer Research 2007;13(24):7296-304.
2007: Ziliang Qian; Lingyi Lu; XiaoJun 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 (Oxford, England) 2007;23(18):2449-54.
2007: Sujun Li; Boshu Liu; Yudong Cai; Yixue Li
Predicting protein N-glycosylation by combining functional domain and secretion information.
Journal of biomolecular structure & dynamics 2007;25(1):49-54.
2007: Wu Wei; John H McCusker; Richard W Hyman; Ted Jones; Ye Ning; Zhiwei Cao; Zhenglong Gu; Dan Bruno; Molly Miranda; Michelle Nguyen; Julie Wilhelmy; Caridad Komp; Raquel Tamse; Xiaojing Wang; Peilin Jia; Philippe Luedi; Peter J Oefner; Lior David; Fred S Dietrich; Yixue Li; Ronald W Davis; Lars M Steinmetz
Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(31):12825-30.
2007: Boshu Liu; Sujun Li; Yinglin Wang; Lin Lu; Yixue Li; Yudong Cai
Predicting the protein SUMO modification sites based on Properties Sequential Forward Selection (PSFS).
Biochemical and biophysical research communications 2007;358(1):136-9.
2007: Lingyi Lu; Ziliang Qian; Yu-Dong Cai; Yixue Li
ECS: an automatic enzyme classifier based on functional domain composition.
Computational biology and chemistry 2007;31(3):226-32.
2007: Peilin Jia; Ziliang Qian; Zhenbin Zeng; Yudong Cai; Yixue Li
Prediction of subcellular protein localization based on functional domain composition.
Biochemical and biophysical research communications 2007;357(2):366-70.
2007: Wu Wei; Weihua Wang; Zhiwei Cao; Hong Yu; Xiaojing Wang; Jing Zhao; Hao Tan; Hao Xu; Weihong Jiang; Yixue Li
Comparative analysis of two-component signal transduction system in two streptomycete genomes.
Acta biochimica et biophysica Sinica 2007;39(5):317-25.
2007: Juwen Shen; Zhang Jian; Xiaomin Luo; Weiliang Zhu; Kunqian Yu; Kaixian Chen; Yixue Li; Hualiang Jiang
Predicting protein-protein interactions based only on sequences information.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(11):4337-41.
2007: Jingchun Sun; Yixue Li; Zhongming Zhao
Phylogenetic profiles for the prediction of protein-protein interactions: how to select reference organisms?
Biochemical and biophysical research communications 2007;353(4):985-91.
2007: Ziliang Qian; Lingyi Lu; Liu Qi; Yixue Li
An efficient method for statistical significance calculation of transcription factor binding sites.
Bioinformation 2007;2(5):169-74.
2007: Changzheng Dong; Ziliang Qian; Peilin Jia; Ying Wang; Wei Huang; Yixue Li
Gene-centric characteristics of genome-wide association studies.
PloS one 2007;2(12):e1262.
2007: Jing Li; Zijing J Liu; Yuchun C Pan; Qi Liu; Xing Fu; nigel cooper; Yixue Li; Mengsheng Qiu; Tieliu Shi
Regulatory module network of basic/helix-loop-helix transcription factors in mouse brain.
Genome biology 2007;8(11):R244.
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 2007;8():414.
2007: Tao Liu; Qian Zhang; Lingling Wang; Lu Yu; Wenchuan Leng; Juhua Yang; Lihong Chen; Junping Peng; Li Ma; Jie Dong; Xingye Xu; Ying Xue; Yafang Zhu; Wenliang Zhang; Li Yang; Weijun Li; Lilian Sun; Zhe Wan; Guohui Ding; Fudong Yu; Kang Tu; Ziliang Qian; Ruoyu Li; Yan Shen; Yixue Li; Qi Jin
The use of global transcriptional analysis to reveal the biological and cellular events involved in distinct development phases of Trichophyton rubrum conidial germination.
BMC genomics 2007;8():100.
2006: Jing Li; Qi Liu; Mengsheng Qiu; Yuchun Pan; Yixue Li; Tieliu Shi
Identification and analysis of the mouse basic/Helix-Loop-Helix transcription factor family.
Biochemical and biophysical research communications 2006;350(3):648-56.
2006: Ziliang Qian; Yu-Dong Cai; Yixue Li
A novel computational method to predict transcription factor DNA binding preference.
Biochemical and biophysical research communications 2006;348(3):1034-7.
2006: Ziliang Qian; Yu-Dong Cai; Yixue Li
Automatic transcription factor classifier based on functional domain composition.
Biochemical and biophysical research communications 2006;347(1):141-4.
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 2006;2(8):e102.
2006: Zhuo Fang; Jiong Yang; Yixue Li; Qingming Luo; Lei Liu
Knowledge guided analysis of microarray data.
Journal of biomedical informatics 2006;39(4):401-11.
2006: Lianyi Han; Juan Cui; Honghuang Lin; Zhiliang Ji; Zhiwei Cao; Yixue Li; Yuzong Chen
Recent progresses in the application of machine learning approach for predicting protein functional class independent of sequence similarity.
Proteomics 2006;6(14):4023-37.
2006: Lili Wang; Zhong Yang; Yuanyuan Li; Fudong Yu; Paul J Brindley; Donald P McManus; Dongzhi Wei; Zeguang Han; Zheng Feng; Yixue Li; Wei Hu
Reconstruction and in silico analysis of the MAPK signaling pathways in the human blood fluke, Schistosoma japonicum.
FEBS letters 2006;580(15):3677-86.
2006: Sujun Li; Boshu Liu; Rong Zeng; Yudong Cai; Yixue Li
Predicting O-glycosylation sites in mammalian proteins by using SVMs.
Computational biology and chemistry 2006;30(3):203-8.
2006: Xiaojing Yu; Jianping Cao; Yudong Cai; Tieliu Shi; Yixue Li
Predicting rRNA-, RNA-, and DNA-binding proteins from primary structure with support vector machines.
Journal of theoretical biology 2006;240(2):175-84.
2006: Pei Hao; Min Chen; Guoqing Zhang; Weizhong He; Yixue Li
Bioinformatics research on the SARS coronavirus (SARS_CoV) in China.
Current pharmaceutical design 2006;12(35):4565-72.
2006: Lingling Wang; Li Ma; Wenchuan Leng; Tao Liu; Lu Yu; Juhua Yang; Li Yang; Wenliang Zhang; Qian Zhang; Jie Dong; Ying Xue; Yafang Zhu; Xingye Xu; Zhe Wan; Guohui Ding; Fudong Yu; Kang Tu; Yixue Li; Ruoyu Li; Yan Shen; Qi Jin
Analysis of the dermatophyte Trichophyton rubrum expressed sequence tags.
BMC genomics 2006;7():255.
2006: Peilin Jia; Tieliu Shi; Yudong Cai; Yixue Li
Demonstration of two novel methods for predicting functional siRNA efficiency.
BMC bioinformatics 2006;7():271.
2006: Wu Wei; ZhiWei Cao; Yu-Li Zhu; XiaoJing Wang; GuoHui Ding; Hao Xu; PeiLin Jia; Di Qu; Antoine Danchin; Yixue Li
Conserved genes in a path from commensalism to pathogenicity: comparative phylogenetic profiles of Staphylococcus epidermidis RP62A and ATCC12228.
BMC genomics 2006;7():112.
2006: Zhuo Wang; Xin-Guang Zhu; Yazhu Chen; Yuanyuan Li; Jing Hou; Yixue Li; Lei Liu
Exploring photosynthesis evolution by comparative analysis of metabolic networks between chloroplasts and photosynthetic bacteria.
BMC genomics 2006;7():100.
2006: Ziliang Qian; Yanbin Yin; Yong Zhang; Lingyi Lu; Yixue Li; Ying Jiang
Genomic characterization of ribitol teichoic acid synthesis in Staphylococcus aureus: genes, genomic organization and gene duplication.
BMC genomics 2006;7():74.
2006: Xiaojing Yu; Chuan Wang; Yixue Li
Classification of protein quaternary structure by functional domain composition.
BMC bioinformatics 2006;7():187.
2005: Zuofeng Li; Qi Liu; Mangen Song; Ying Zheng; Peng Nan; Ying Cao; Guoqiang Chen; Yixue Li; Yang Zhong
Detecting correlation between sequence and expression divergences in a comparative analysis of human serpin genes.
Bio Systems 2005;82(3):226-34.
2005: Jingchun Sun; Jinlin Xu; Zhen Liu; Qi Liu; Aimin Zhao; Tieliu Shi; Yixue Li
Refined phylogenetic profiles method for predicting protein-protein interactions.
Bioinformatics (Oxford, England) 2005;21(16):3409-15.
2004: Zhuo Wang; Yazhu Chen; Yixue Li
A brief review of computational gene prediction methods.
Genomics, proteomics & bioinformatics 2004;2(4):216-21.
2004: Cheng Luo; Haibin Luo; Suxin Zheng; Chunshan Gui; Liduo Yue; Changying Yu; Tao Sun; Peilan He; Jing Chen; Jianhua Shen; Xiaomin Luo; Yixue Li; Hong Liu; Donglu Bai; Jingkang Shen; Yiming Yang; Fangqiu Li; Jianping Zuo; Rolf Hilgenfeld; Gang Pei; Kaixian Chen; Xu Shen; Hualiang Jiang
Nucleocapsid protein of SARS coronavirus tightly binds to human cyclophilin A.
Biochemical and biophysical research communications 2004;321(3):557-65.
2004: Lijian Hui; Xin Zhang; Xin Wu; Zhixin Lin; Qingkang Wang; Yixue Li; Gengxi Hu
Identification of alternatively spliced mRNA variants related to cancers by genome-wide ESTs alignment.
Oncogene 2004;23(17):3013-23.
2003: Qi Liu; Yisheng Zhu; Baohua Wang; Yixue Li
Identification of beta-barrel membrane proteins based on amino acid composition properties and predicted secondary structure.
Computational biology and chemistry 2003;27(3):355-61.
2001: Yixue Li; John R Kusel; Malcolm W Kennedy; Andreas Ruppel
Diversity among schistosomes: perspectives for control.
Trends in parasitology 2001;17(3):113-5.