Yu Dong Cai

Summary

Country: China

Publications

  1. pmc Predicting biological functions of compounds based on chemical-chemical interactions
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 6:e29491. 2011
  2. pmc Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property
    Tao Huang
    Institute of Systems Biology, Shanghai University, Shanghai, People s Republic of China
    PLoS ONE 6:e25297. 2011
  3. pmc Computational analysis of HIV-1 resistance based on gene expression profiles and the virus-host interaction network
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 6:e17291. 2011
  4. pmc Prediction of body fluids where proteins are secreted into based on protein interaction network
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 6:e22989. 2011
  5. pmc Predicting Anatomical Therapeutic Chemical (ATC) classification of drugs by integrating chemical-chemical interactions and similarities
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, China
    PLoS ONE 7:e35254. 2012
  6. pmc Prediction and analysis of protein hydroxyproline and hydroxylysine
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 5:e15917. 2010
  7. pmc Prediction of protein cleavage site with feature selection by random forest
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, PR China
    PLoS ONE 7:e45854. 2012
  8. pmc Analysis and prediction of translation rate based on sequence and functional features of the mRNA
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 6:e16036. 2011
  9. pmc Hepatitis C virus network based classification of hepatocellular cirrhosis and carcinoma
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 7:e34460. 2012
  10. pmc Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties
    Lele Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 6:e14556. 2011

Collaborators

Detail Information

Publications84

  1. pmc Predicting biological functions of compounds based on chemical-chemical interactions
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 6:e29491. 2011
    ....
  2. pmc Classification and analysis of regulatory pathways using graph property, biochemical and physicochemical property, and functional property
    Tao Huang
    Institute of Systems Biology, Shanghai University, Shanghai, People s Republic of China
    PLoS ONE 6:e25297. 2011
    ..It is anticipated that our report may stimulate a series of follow-up investigations in this new and challenging area...
  3. pmc Computational analysis of HIV-1 resistance based on gene expression profiles and the virus-host interaction network
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 6:e17291. 2011
    ..These proteins may be useful targets for AIDS prevention or therapy, as intervention in these pathways could disrupt communication with virus-targeted proteins and HIV-1 infection...
  4. pmc Prediction of body fluids where proteins are secreted into based on protein interaction network
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 6:e22989. 2011
    ..These encouraging results indicate that the network-based prediction method is quite promising. It is anticipated that the method will benefit the relevant areas for both basic research and drug development...
  5. pmc Predicting Anatomical Therapeutic Chemical (ATC) classification of drugs by integrating chemical-chemical interactions and similarities
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, China
    PLoS ONE 7:e35254. 2012
    ....
  6. pmc Prediction and analysis of protein hydroxyproline and hydroxylysine
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 5:e15917. 2010
    ..Hydroxylation is an important post-translational modification and closely related to various diseases. Besides the biotechnology experiments, in silico prediction methods are alternative ways to identify the potential hydroxylation sites...
  7. pmc Prediction of protein cleavage site with feature selection by random forest
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences Chinese Academy of Sciences, Shanghai, PR China
    PLoS ONE 7:e45854. 2012
    ..It is shown that our method makes much more reliable predictions in terms of the overall prediction accuracy. In addition, this predictor allows the use of a wide range of proteinases...
  8. pmc Analysis and prediction of translation rate based on sequence and functional features of the mRNA
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 6:e16036. 2011
    ..Our translation rate prediction model might become a high throughput tool for annotating the translation rate of mRNAs in large-scale...
  9. pmc Hepatitis C virus network based classification of hepatocellular cirrhosis and carcinoma
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 7:e34460. 2012
    ..It may also provide useful insights for in-depth study of the biological mechanisms of HCV-induced cirrhosis and hepatocellular carcinoma...
  10. pmc Predicting functions of proteins in mouse based on weighted protein-protein interaction network and protein hybrid properties
    Lele Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 6:e14556. 2011
    ..The information thus obtained would be very useful for both basic research and drug development in a timely manner...
  11. pmc An information-theoretic machine learning approach to expression QTL analysis
    Tao Huang
    Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, United States of America
    PLoS ONE 8:e67899. 2013
    ..2% of R/qtl result can be confirmed by at least two other methods. Our methods provide a new way to identify the association between genetic markers and gene expression. Our software is available from supporting information. ..
  12. pmc Prediction of protein modification sites of pyrrolidone carboxylic acid using mRMR feature selection and analysis
    Lu Lu Zheng
    Hubei Bioinformatics and Molecular Imaging Key Laboratory, Huazhong University of Science and Technology, Wuhan, China
    PLoS ONE 6:e28221. 2011
    ..The detailed feature analysis in this paper might provide important clues for understanding the mechanism of the PCA formation and guide relevant experimental validations...
  13. pmc A comparison of computational methods for identifying virulence factors
    Lu Lu Zheng
    Hubei Bioinformatics and Molecular Imaging Key Laboratory, Huazhong University of Science and Technology, Wuhan, Hubei, China
    PLoS ONE 7:e42517. 2012
    ....
  14. ncbi Prediction of carbamylated lysine sites based on the one-class k-nearest neighbor method
    Guohua Huang
    Institute of Systems Biology, Shanghai University, Shanghai, China
    Mol Biosyst 9:2729-40. 2013
    ..It is anticipated that our method could be a potentially useful and essential tool for biologists to theoretically investigate carbamylated lysine sites...
  15. doi Prediction of lysine ubiquitination with mRMR feature selection and analysis
    Yudong Cai
    Institute of Systems Biology, Shanghai University, Shanghai, 200444, People s Republic of China
    Amino Acids 42:1387-95. 2012
    ..These findings might provide useful insights for studying the mechanisms of ubiquitination and modulating the ubiquitination pathway, potentially leading to potential therapeutic strategies in the future...
  16. pmc A unified 35-gene signature for both subtype classification and survival prediction in diffuse large B-cell lymphomas
    Yu Dong Cai
    Institute of Systems Biology, Shanghai University, Shanghai, People s Republic of China
    PLoS ONE 5:e12726. 2010
    ..Our results suggest that for some diseases, especially cancer, subtype classification may be used to predict survival, and, conversely, survival prediction features may shed light on subtype features...
  17. ncbi A novel sequence-based method of predicting protein DNA-binding residues, using a machine learning approach
    Yudong Cai
    Institute of System Biology, Shanghai University, Shanghai, 200244, People s Republic of China
    Mol Cells 30:99-105. 2010
    ..89%. Our method shows that the amino acid micro-environment is important for DNA binding, and that it is possible to identify the protein-DNA binding sites with it...
  18. ncbi Inter- and intra-chain disulfide bond prediction based on optimal feature selection
    Shen Niu
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P R China
    Protein Pept Lett 20:324-35. 2013
    ....
  19. ncbi Automatic transcription factor classifier based on functional domain composition
    Ziliang Qian
    Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Biochem Biophys Res Commun 347:141-4. 2006
    ..4% for TF/non-TF identification and 97.2% for classifications of TF classes: basic domains, zinc-coordinating DNA-binding domains, helix-turn-helix, and beta-scaffold factors...
  20. doi Deciphering the effects of gene deletion on yeast longevity using network and machine learning approaches
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    Biochimie 94:1017-25. 2012
    ..Moreover, it has not escaped our notice that, after some modification, the current model can also be used to study many other phenotype prediction problems from the angle of systems biology...
  21. doi A knowledge-based method to predict the cooperative relationship between transcription factors
    Lingyi Lu
    Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai, 200031, China
    Mol Divers 14:815-9. 2010
    ..The corresponding online service TFIPS (Transcription Factor Interaction Prediction System) is available on http://pcal.biosino.org/cgi-bin/TFIPS/TFIPS.pl...
  22. pmc Prediction of effective drug combinations by chemical interaction, protein interaction and target enrichment of KEGG pathways
    Lei Chen
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
    Biomed Res Int 2013:723780. 2013
    ..These important features may help to gain insights into the mechanisms of drug combinations, and the proposed prediction model could become a useful tool for screening possible drug combinations. ..
  23. doi Predicting protein oxidation sites with feature selection and analysis approach
    Shen Niu
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P R China
    J Biomol Struct Dyn 29:650-8. 2012
    ..Also, the 16 optimal features obtained through this study may provide useful clues and insights for in-depth understanding the action mechanism of protein oxidation...
  24. pmc Identifying chemicals with potential therapy of HIV based on protein-protein and protein-chemical interaction network
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China
    PLoS ONE 8:e65207. 2013
    ..All these indicate that our method as presented in this paper is quite promising. The method may become a useful tool, or at least plays a complementary role to the existing method, for identifying novel anti-HIV drugs...
  25. pmc Predicting drug-target interaction networks based on functional groups and biological features
    Zhisong He
    CAS MPG Partner Institute of Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 5:e9603. 2010
    ..As a complement, the in silico prediction methods can provide us with very useful information in a timely manner...
  26. doi Protein sumoylation sites prediction based on two-stage feature selection
    Lin Lu
    Department of Biomedical Engineering, Shanghai Jiao Tong University, 200240, Shanghai, China
    Mol Divers 14:81-6. 2010
    ..Based on the feature selection strategy, our prediction system can not only be used for high throughput prediction of sumoylation sites but also as a tool to investigate the mechanism of sumoylation...
  27. pmc Analysis and prediction of the metabolic stability of proteins based on their sequential features, subcellular locations and interaction networks
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 5:e10972. 2010
    ..The computational method can also be used as a large-scale tool for annotating the metabolic stability for the avalanche of protein sequences generated in the post-genomic age...
  28. pmc Predicting the network of substrate-enzyme-product triads by combining compound similarity and functional domain composition
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, PR China
    BMC Bioinformatics 11:293. 2010
    ....
  29. ncbi Using protein-protein interaction network information to predict the subcellular locations of proteins in budding yeast
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    Protein Pept Lett 19:644-51. 2012
    ..As a user-friendly web-server, Yeast-PLoc is freely accessible at http://yeastloc.biosino.org/...
  30. pmc Identification of lung-cancer-related genes with the shortest path approach in a protein-protein interaction network
    Bi Qing Li
    The Key Laboratory of Stem Cell Biology, Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Biomed Res Int 2013:267375. 2013
    ..Furthermore, these genes possessed more functional similarity with the known cancer genes than those identified from the gene expression profiles. This study proved the efficiency of the proposed method and showed promising results...
  31. doi HIV-1 protease cleavage site prediction based on amino acid property
    Bing Niu
    School of Materials Science and Engineering, Shanghai University, 149 Yan Chang Road, Shanghai 200072, People s Republic of China
    J Comput Chem 30:33-9. 2009
    ..3% for independent-set test. It is expected that our feature selection scheme can be referred to as a useful assistant technique for finding effective inhibitors of HIV protease, especially for the scientists in this field...
  32. pmc Predicting transcriptional activity of multiple site p53 mutants based on hybrid properties
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 6:e22940. 2011
    ..Our study has provided a new and promising approach for finding functionally important sites and the relevant features for in-depth study of p53 protein and its action mechanism...
  33. ncbi Predicting DNA-binding sites of proteins based on sequential and 3D structural information
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200031, People s Republic of China
    Mol Genet Genomics 289:489-99. 2014
    ....
  34. ncbi Support vector machine for predicting alpha-turn types
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, Shanghai, China
    Peptides 24:629-30. 2003
    ....
  35. ncbi Using LogitBoost classifier to predict protein structural classes
    Yu Dong Cai
    Department of Chemistry, College of Sciences, Shanghai University, 99 Shang Da Road, Shanghai 200436, China
    J Theor Biol 238:172-6. 2006
    ....
  36. pmc Predicting drugs side effects based on chemical-chemical interactions and protein-chemical interactions
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
    Biomed Res Int 2013:485034. 2013
    ....
  37. ncbi Support Vector Machines for predicting HIV protease cleavage sites in protein
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, People s Republic of China
    J Comput Chem 23:267-74. 2002
    ..The principle of the Support Vector Machine method can also be applied to analyzing the specificity of other multisubsite enzymes...
  38. pmc Identification of colorectal cancer related genes with mRMR and shortest path in protein-protein interaction network
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 7:e33393. 2012
    ..It has not escaped our notice that the method can be applied to identify the genes of other diseases as well...
  39. ncbi Predicting subcellular localization with AdaBoost Learner
    Yu Huan Jin
    Department of Chemistry, College of Sciences, Shanghai University, 99 Shang Da Road, Shanghai, China 200444
    Protein Pept Lett 15:286-9. 2008
    ..An online server for predicting subcellular localization of proteins based on AdaBoost classifier was available on http://chemdata.shu. edu.cn/sl12...
  40. ncbi Using AdaBoost for the prediction of subcellular location of prokaryotic and eukaryotic proteins
    Bing Niu
    School of Materials Science and Engineering, Shanghai University, Shanghai, 200444, China
    Mol Divers 12:41-5. 2008
    ..An online web server for predicting subcellular location of prokaryotic and eukaryotic proteins is available at http://chemdata.shu.edu.cn/subcell/ ...
  41. ncbi Prediction of protein-protein interactions based on feature selection and data balancing
    Liang Liu
    Department of Chemistry, College of Sciences, Shanghai University, Shanghai, People s Republic of China
    Protein Pept Lett 20:336-45. 2013
    ..8369 with sensitivity of 0.7356. The predictor, developed by this research for the prediction of the fruit fly PPI-nesses, is available for public use at http://chemdata.shu.edu.cn/ppip...
  42. ncbi Prediction of beta-turns with learning machines
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, 200233 Shanghai, China
    Peptides 24:665-9. 2003
    ..1 and 97.3%, respectively. The results obtained from this study support the conclusion that the residue-coupled effect along a tetrapeptide is important for the formation of a beta-turn...
  43. ncbi Support vector machines for prediction of protein domain structural class
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, Shanghai 200233, China
    J Theor Biol 221:115-20. 2003
    ....
  44. ncbi Selection of reprogramming factors of induced pluripotent stem cells based on the protein interaction network and functional profiles
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P R China
    Protein Pept Lett 19:113-9. 2012
    ..It can be used to select reprogramming factors from millions of possibilities. It is anticipated that the novel approach will become a very useful tool for both basic research and drug development...
  45. doi Prediction and analysis of protein palmitoylation sites
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    Biochimie 93:489-96. 2011
    ..Meanwhile, the protein disorder region might also play an import role in the post-translational modification. These findings may provide useful insights for revealing the mechanisms of palmitoylation...
  46. pmc Prediction of protein-protein interaction sites by random forest algorithm with mRMR and IFS
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 7:e43927. 2012
    ..It is anticipated that our prediction method will become a useful tool for identifying PPI sites, and that the feature analysis described in this paper will provide useful insights into the mechanisms of interaction...
  47. pmc Support vector machines for predicting membrane protein types by using functional domain composition
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, Shanghai 200233, China
    Biophys J 84:3257-63. 2003
    ..C. Chou (2001), may become a very useful high-throughput tool in the area of bioinformatics and proteomics...
  48. ncbi Predicting membrane protein types with bragging learner
    Bing Niu
    School of Materials Science and Engineering, Shanghai University, Shanghai, People s Republic of China
    Protein Pept Lett 15:590-4. 2008
    ..An online membrane protein type prediction web server developed in our lab is available at http://chemdata.shu.edu.cn/protein/protein.jsp...
  49. ncbi A novel computational method to predict transcription factor DNA binding preference
    Ziliang Qian
    Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
    Biochem Biophys Res Commun 348:1034-7. 2006
    ....
  50. ncbi ECS: an automatic enzyme classifier based on functional domain composition
    Lingyi Lu
    Bioinformatics Center, Key Lab of Molecular Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
    Comput Biol Chem 31:226-32. 2007
    ..Moreover, a web-based software Enzyme Classification System (ECS) for identification as well as classification of enzymes can be accessed at: http://pcal.biosino.org/...
  51. pmc Prediction of deleterious non-synonymous SNPs based on protein interaction network and hybrid properties
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 5:e11900. 2010
    ..Our results suggest that the protein interaction context could provide important clues to help better illustrate SAP's functional association. This research will facilitate the post genome-wide association studies...
  52. pmc Prediction of protein domain with mRMR feature selection and analysis
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    PLoS ONE 7:e39308. 2012
    ..Finally, it has not escaped our notice that the current approach can also be utilized to study protein signal peptides, B-cell epitopes, HIV protease cleavage sites, among many other important topics in protein science and biomedicine...
  53. pmc A novel method of predicting protein disordered regions based on sequence features
    Tong Hui Zhao
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China
    Biomed Res Int 2013:414327. 2013
    ..The selected features may shed some light on the understanding of the formation mechanism of disordered structures, providing guidelines for experimental validation...
  54. ncbi Classification of transcription factors using protein primary structure
    Xin Yi Yang
    CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, China
    Protein Pept Lett 17:899-908. 2010
    ..A free online classifier is available at http://app3.biosino.org/132dvc/tf/...
  55. ncbi A sequence-based approach for predicting protein disordered regions
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
    Protein Pept Lett 20:243-8. 2013
    ..371 on a rigorous benchmark dataset tested by 5-fold cross-validation and 0.219 on an independent test dataset. Our results suggest that conservation and secondary structure play important roles in intrinsically disordered proteins...
  56. ncbi Predicting subcellular location of proteins using integrated-algorithm method
    Yu Dong Cai
    Institute of System Biology, Shanghai University, 99 Shangda Road, 200244 Shanghai, China
    Mol Divers 14:551-8. 2010
    ..It can achieve correct rate of 77.83 and 80.56% for the training set and test set, respectively, which is better than all of the 60 algorithms collected in Weka. This predicting software is available upon request...
  57. pmc Prediction of pharmacological and xenobiotic responses to drugs based on time course gene expression profiles
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 4:e8126. 2009
    ..9%. Our method can be used for pharmacological and xenobiotic responses prediction of new compounds and accelerate drug development...
  58. ncbi Nearest neighbour algorithm for predicting protein subcellular location by combining functional domain composition and pseudo-amino acid composition
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, Shanghai 200233, China
    Biochem Biophys Res Commun 305:407-11. 2003
    ..Very high success rates were observed, suggesting that such a hybrid approach may become a useful high-throughput tool in the area of bioinformatics and proteomics...
  59. ncbi An approach to predict transcription factor DNA binding site specificity based upon gene and transcription factor functional categorization
    Ziliang Qian
    CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 19 Yuquan Road, Beijing 100039, China
    Bioinformatics 23:2449-54. 2007
    ..We noted that the generally acknowledged information of functional annotations of TFs as well as that of their target genes should provide useful hints in determining TF DNA binding preferences...
  60. ncbi Analysis of protein pathway networks using hybrid properties
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai 201306, China
    Molecules 15:8177-92. 2010
    ..88%. It is anticipated that, this novel approach and encouraging result, although preliminary yet, may stimulate extensive investigations into this important topic...
  61. doi Crosstissue coexpression network of aging
    Tao Huang
    Department of Ophthalmology, Yangpu District Central Hospital, Shanghai, People s Republic of China
    OMICS 15:665-71. 2011
    ..By bridging gene-level and tissue-level research, this study could help identify targets for attenuation of critical aging-related genes, pathways, or networks for antiaging intervention...
  62. ncbi Predicting protein structural class with AdaBoost Learner
    Bing Niu
    Department of Chemistry, College of Sciences, Shanghai University, 99 Shang Da Road, Shanghai 200436, China
    Protein Pept Lett 13:489-92. 2006
    ..Or at the very least, it will play a complementary role to many of the existing algorithms in this regard...
  63. ncbi Support vector machines for prediction of protein signal sequences and their cleavage sites
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, Shanghai 200233, China
    Peptides 24:159-61. 2003
    ..It has not escaped our attention that the new method may also serve as a useful tool for further investigating many unclear details regarding the molecular mechanism of the ZIP code protein-sorting system in cells...
  64. ncbi Analysis of metabolic pathway using hybrid properties
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, People s Republic of China
    Protein Pept Lett 19:99-107. 2012
    ..26%. It is anticipated that this novel approach and encouraging result may give meaningful illumination to investigate this important topic...
  65. ncbi Predict and analyze S-nitrosylation modification sites with the mRMR and IFS approaches
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Science, Chinese Academy of Science, Shanghai 200031, PR China
    J Proteomics 75:1654-65. 2012
    ....
  66. ncbi Identify catalytic triads of serine hydrolases by support vector machines
    Yu Dong Cai
    Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, Shanghai 200233, China
    J Theor Biol 228:551-7. 2004
    ..The success rate by jackknife test for the 139 serine hydrolases was 85%, implying that the method is quite promising and may become a useful tool in structural bioinformatics...
  67. pmc An ensemble prognostic model for colorectal cancer
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, PR China
    PLoS ONE 8:e63494. 2013
    ..This method could be applied to the studies of other diseases and it could significantly improve the prediction performance by ensembling heterogeneous information...
  68. ncbi Computational methods for protein-protein interaction and their application
    Tie Liu Shi
    Bioinformatics Center, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Curr Protein Pept Sci 6:443-9. 2005
    ..This review highlights the recent advances of the bioinformatics methods in protein-protein interaction researches. In the end, the application of the protein-protein interaction has also been discussed...
  69. pmc Cooperativity among short amyloid stretches in long amyloidogenic sequences
    Lele Hu
    Institute of Systems Biology, Shanghai University, Shanghai, People s Republic of China
    PLoS ONE 7:e39369. 2012
    ..Our study revealed that genome-wide amyloid segments are not only dependent on short high propensity stretches, but also on nearby residues...
  70. doi Predicting N-terminal acetylation based on feature selection method
    Yu Dong Cai
    Department of Combinatorics and Geometry, CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 320 Yueyang Road, Shanghai 200031, People s Republic of China
    Biochem Biophys Res Commun 372:862-5. 2008
    ..The software is available upon request...
  71. ncbi Application of SVM to predict membrane protein types
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, Shanghai 200233, China
    J Theor Biol 226:373-6. 2004
    ..12 (1999) 107) and SVM, if effectively complemented with each other, will become a powerful tool for predicting membrane protein types and the other protein attributes as well...
  72. doi Identification of retinoblastoma related genes with shortest path in a protein-protein interaction network
    Bi Qing Li
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, People s Republic of China
    Biochimie 94:1910-7. 2012
    ..This study shows promising results and proves the efficiency of the proposed methods...
  73. ncbi Support vector machines for predicting rRNA-, RNA-, and DNA-binding proteins from amino acid sequence
    Yu Dong Cai
    Shanghai Research Center of Biotechnology, Chinese Academy of Sciences, China
    Biochim Biophys Acta 1648:127-33. 2003
    ..The RNA- and DNA-binding SVMs demonstrate more diverse accuracy, ranging from approximately 76% to approximately 97%. Analysis of the test results suggests the directions of improving the SVMs...
  74. doi Prediction and analysis of protein methylarginine and methyllysine based on Multisequence features
    Le Le Hu
    Institute of Systems Biology, Shanghai University, Shanghai 200444, China Department of Chemistry, College of Sciences, Shanghai University, China
    Biopolymers 95:763-71. 2011
    ..These findings may provide valuable information for exploiting the mechanisms of methylation. Our method may serve as a useful tool for biologists to find the potential methylated sites of proteins...
  75. pmc Predicting protein phenotypes based on protein-protein interaction network
    Lele Hu
    Institute of Systems Biology, Shanghai University, Shanghai, China
    PLoS ONE 6:e17668. 2011
    ..Besides the high-through phenotype assays, the computational methods are alternative ways to identify the phenotypes of proteins...
  76. ncbi Prediction of protein secondary structure content by artificial neural network
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, Shanghai, 200233, China
    J Comput Chem 24:727-31. 2003
    ..C. Chou [J Protein Chem 1999, 18, 473] was adopted as the input. Self-consistency and independent-dataset tests were used to appraise the performance of the neural network. Results of both tests indicated high performance of the method...
  77. ncbi Support vector machines for prediction of protein subcellular location by incorporating quasi-sequence-order effect
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, Shanghai, 200233, China
    J Cell Biochem 84:343-8. 2002
    ..Furthermore, tests for correct prediction rates were undertaken with three independent testing datasets containing 2,148 proteins, 2,417 proteins, and 2,494 proteins producing values of 84, 77, and 74%, respectively...
  78. ncbi Prediction of compounds' biological function (metabolic pathways) based on functional group composition
    Yu Dong Cai
    CAS MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    Mol Divers 12:131-7. 2008
    ..The overall prediction rate reached 73.3%, indicating that functional group composition of compounds was really related to their biological metabolic functions...
  79. ncbi Using compound similarity and functional domain composition for prediction of drug-target interaction networks
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, China
    Med Chem 6:388-95. 2010
    ..23%, 94.74%, 97.80%, and 97.51%, respectively, indicating that compound similarity and functional domain composition are very effective to predict drug-target interaction networks...
  80. pmc Predicting chemical toxicity effects based on chemical-chemical interactions
    Lei Chen
    College of Information Engineering, Shanghai Maritime University, Shanghai, China
    PLoS ONE 8:e56517. 2013
    ..50%, substantially higher than the rate of 25.43% achieved by random guesses. Encouraged by the promising results, we expect that our method will become a useful tool in screening out drugs with high toxicity...
  81. pmc Dysfunctions associated with methylation, microRNA expression and gene expression in lung cancer
    Tao Huang
    Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, People s Republic of China
    PLoS ONE 7:e43441. 2012
    ..Our results provide a systematic view of the functional alterations during tumorigenesis that may help to elucidate the mechanisms of lung cancer and lead to improved treatments for patients...
  82. pmc Prediction of antimicrobial peptides based on sequence alignment and feature selection methods
    Ping Wang
    Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
    PLoS ONE 6:e18476. 2011
    ..For the convenience of most experimental scientists who want to use the prediction method without the interest to follow the mathematical details, a user-friendly web-server is provided at http://amp.biosino.org/...
  83. ncbi Support vector machines for predicting the specificity of GalNAc-transferase
    Yu Dong Cai
    Shanghai Research Centre of Biotechnology, Chinese Academy of Sciences, 200233, Shanghai, China
    Peptides 23:205-8. 2002
    ..9%, respectively. Furthermore, the prediction of the independent testing dataset (30 oligopeptides) was tested, the rate reaches 76.67%...