Jian Huang

Summary

Affiliation: Kyoto University
Country: Japan

Publications

  1. ncbi request reprint Predicting B cell epitope residues with network topology based amino acid indices
    Jian Huang
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611 0011, Japan
    Genome Inform 19:40-9. 2007
  2. ncbi request reprint New amino acid indices based on residue network topology
    Jian Huang
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611 0011, Japan
    Genome Inform 18:152-61. 2007
  3. pmc MIMOX: a web tool for phage display based epitope mapping
    Jian Huang
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    BMC Bioinformatics 7:451. 2006
  4. pmc CED: a conformational epitope database
    Jian Huang
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    BMC Immunol 7:7. 2006
  5. pmc Penalized feature selection and classification in bioinformatics
    Shuangge Ma
    Department of Epidemiology and Public Health, Yale University, USA
    Brief Bioinform 9:392-403. 2008
  6. pmc A robust two-way semi-linear model for normalization of cDNA microarray data
    Deli Wang
    Biostatistics and Bioinformatics Unit, Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
    BMC Bioinformatics 6:14. 2005
  7. ncbi request reprint Regularized ROC method for disease classification and biomarker selection with microarray data
    Shuangge Ma
    Department of Biostatistics, University of Washington, Washington, USA
    Bioinformatics 21:4356-62. 2005
  8. ncbi request reprint [Immune responses of dendritic cells after loaded with cytotoxicity T lymphocyte epitope based peptide of human alpha-fetoprotein (hAFP)]
    Jianwei Guo
    Department of Immunology, School of Basic Medical Sciences, Sichuan University or West China University of Medical Science, Chengdu 610041, China
    Zhonghua Gan Zang Bing Za Zhi 10:178-80. 2002
  9. pmc Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS)
    Jian Huang
    Department of Chemistry of Fudan University and Shanghai Ministry Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
    BMC Genomics 8:207. 2007
  10. pmc Supervised group Lasso with applications to microarray data analysis
    Shuangge Ma
    Department of Epidemiology and Public Health, Yale University, New Haven, CT 06520, USA
    BMC Bioinformatics 8:60. 2007

Collaborators

Detail Information

Publications32

  1. ncbi request reprint Predicting B cell epitope residues with network topology based amino acid indices
    Jian Huang
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611 0011, Japan
    Genome Inform 19:40-9. 2007
    ..It is suggested that the performance in surface residue prediction might form a theoretical upper limit for the performance of B cell epitope residue prediction methods...
  2. ncbi request reprint New amino acid indices based on residue network topology
    Jian Huang
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho Uji, Kyoto 611 0011, Japan
    Genome Inform 18:152-61. 2007
    ..75. It indicates that the network property based amino acid indices can be useful complements to the existing physicochemical property based amino acid indices...
  3. pmc MIMOX: a web tool for phage display based epitope mapping
    Jian Huang
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    BMC Bioinformatics 7:451. 2006
    ..Most of the existing tools have not been implemented as an online service until now however, making it less convenient for the community to access, utilize, and evaluate them...
  4. pmc CED: a conformational epitope database
    Jian Huang
    Bioinformatics Center, Institute for Chemical Research, Kyoto University, Uji, Kyoto 611 0011, Japan
    BMC Immunol 7:7. 2006
    ..These epitopes have implicit structural information, making them attractive for both theoretical and applied biomedical research. However, most existing databases focus on linear rather than conformational epitopes...
  5. pmc Penalized feature selection and classification in bioinformatics
    Shuangge Ma
    Department of Epidemiology and Public Health, Yale University, USA
    Brief Bioinform 9:392-403. 2008
    ..Our goal is to make interested researchers aware of these feature selection and classification methods that are applicable to high-dimensional bioinformatics data...
  6. pmc A robust two-way semi-linear model for normalization of cDNA microarray data
    Deli Wang
    Biostatistics and Bioinformatics Unit, Comprehensive Cancer Center, The University of Alabama at Birmingham, Birmingham, AL 35294, USA
    BMC Bioinformatics 6:14. 2005
    ..Normalization is a basic step in microarray data analysis. A proper normalization procedure ensures that the intensity ratios provide meaningful measures of relative expression values...
  7. ncbi request reprint Regularized ROC method for disease classification and biomarker selection with microarray data
    Shuangge Ma
    Department of Biostatistics, University of Washington, Washington, USA
    Bioinformatics 21:4356-62. 2005
    ..However, due to computational difficulties, the ROC-based classification has not been used with microarray data. Moreover, the standard ROC technique does not incorporate built-in biomarker selection...
  8. ncbi request reprint [Immune responses of dendritic cells after loaded with cytotoxicity T lymphocyte epitope based peptide of human alpha-fetoprotein (hAFP)]
    Jianwei Guo
    Department of Immunology, School of Basic Medical Sciences, Sichuan University or West China University of Medical Science, Chengdu 610041, China
    Zhonghua Gan Zang Bing Za Zhi 10:178-80. 2002
    ..To study the immune responses of lymphocytes after activated by dendritic cells (DCs) loaded with cytotoxicity T lymphocyte (CTL) epitope based peptide of human alpha-fetoprotein (hAFP, 218-226 LLNQHACAV)...
  9. pmc Discovering multiple transcripts of human hepatocytes using massively parallel signature sequencing (MPSS)
    Jian Huang
    Department of Chemistry of Fudan University and Shanghai Ministry Key Laboratory of Disease and Health Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China
    BMC Genomics 8:207. 2007
    ..To discover the molecular basis of hepatocyte function, we employed Massively Parallel Signature Sequencing (MPSS) to determine the transcriptomic profile of adult human hepatocytes obtained by laser capture microdissection (LCM)...
  10. pmc Supervised group Lasso with applications to microarray data analysis
    Shuangge Ma
    Department of Epidemiology and Public Health, Yale University, New Haven, CT 06520, USA
    BMC Bioinformatics 8:60. 2007
    ..However, most available statistical methods for gene selection do not take into consideration the cluster structure...
  11. ncbi request reprint Dynamic sharing of large-scale visualization
    Jian Huang
    University of Tennessee, Knoxville, USA
    IEEE Comput Graph Appl 27:20-5. 2007
  12. ncbi request reprint A multi-level cache model for run-time optimization of remote visualization
    Robert Sisneros
    Department of Computer Science, University of Tennessee, Knoxville, TN 37996, USA
    IEEE Trans Vis Comput Graph 13:991-1003. 2007
    ..The lower bound of achievable latency discovered with our approach can aid the design of remote visualization algorithms and the selection of suitable network layouts for a remote visualization system...
  13. ncbi request reprint [Screening and characterization of human phage Fab antibody gene to prostate specific membrane antigen]
    Hai Huang
    Department of Urology, Second Affiliated Hospital of Sun Yat Sen University, Guangzhou, Guangdong 510120, China
    Zhonghua Nan Ke Xue 13:601-4. 2007
    ..To screen and characterize the variable region gene about prostate specific membrane antigen (PSMA) of the Chinese Fab fragment, and to establish a new approach to researches on PSMA and prostate gene therapy...
  14. ncbi request reprint Combining multiple markers for classification using ROC
    Shuangge Ma
    Division of Biostatistics, Yale University, New Haven, Connecticut 06520, USA
    Biometrics 63:751-7. 2007
    ..We also propose Monte Carlo methods to assess the overall prediction performance and the relative importance of individual markers. Finite sample performance is evaluated using simulation studies and two public data sets...
  15. ncbi request reprint BMI-1 autoantibody in serum as a new potential biomarker of nasopharyngeal carcinoma
    Yong qing Tong
    Cancer Research Institute, Xiang Ya School of Medicine, Central South University, Changsha, Hunan, PR China
    Cancer Biol Ther 7:340-4. 2008
    ..74 and specificity 0.73; AUC = 0.8044). The showed that BMI-1 antibody as a potential marker of NPC may be rational, and could have diagnostic and prognostic value...
  16. ncbi request reprint Apoptosis-inducing effect and structural basis of Polygonatum cyrtonema lectin and chemical modification properties on its mannose-binding sites
    Bo Liu
    College of Life Sciences, Sichuan University, Chengdu, China
    BMB Rep 41:369-75. 2008
    ..g., hemagglutinating and mitogenic activity assays, fluorescence and Circular Dichrosim (CD) spectroscopy) to profoundly identify the role of some key amino acids in the structure-function relationship of PCL...
  17. doi request reprint Dynamic visualization of coexpression in systems genetics data
    Joshua New
    Department of Electrical Engineering and Computer Science, University of Tennesee, Knoxville, TN 37996, USA
    IEEE Trans Vis Comput Graph 14:1081-94. 2008
    ..We demonstrate our system using a real-world workflow from a large-scale, systems genetics study of mammalian gene co-expression...
  18. ncbi request reprint A fully human chimeric immune receptor for retargeting T-cells to CEA-expressing tumor cells
    Hirotomo Shibaguchi
    Department of Biochemistry, Faculty of Medicine, Fukuoka University, 7 45 1 Nanakuma, Jonan ku, Fukuoka 814 0180, Japan
    Anticancer Res 26:4067-72. 2006
    ..To reduce the immunogenicity of conventional CIR in humans, an attempt was made to generate a CIR encoded by all human genes...
  19. ncbi request reprint Clustering threshold gradient descent regularization: with applications to microarray studies
    Shuangge Ma
    Department of Epidemiology and Public Health, Yale University, New Haven, CT, USA
    Bioinformatics 23:466-72. 2007
    ..First, the model is sparse in the sense that only a subset of the parameter vector is non-zero. Second, the cluster structures of gene expressions are properly accounted for...
  20. pmc Genetic linkage analysis of a dichotomous trait incorporating a tightly linked quantitative trait in affected sib pairs
    Jian Huang
    Department of Statistics and Actuarial Science, Division of Statistical Genetics, University of Iowa, Iowa City, IA 52242, USA
    Am J Hum Genet 72:949-60. 2003
    ..We also apply the proposed new method to an asthma genome-scan data set and incorporate the total serum immunoglobulin E level in the analysis...
  21. ncbi request reprint Hepatitis B virus (HBV) vaccine-induced escape mutants of HBV S gene among children from Qidong area, China
    Xinghua Huang
    Institute of Genetics, School of Life Sciences, Fudan University, 200433 Shanghai, PR China
    Virus Res 99:63-8. 2004
    ..The structure of double loop conformation in "a" epitope was conservative, and important for HBV antigenicity. These changes in a double loop conformation would escape neutralization by vaccine-induced antibody...
  22. ncbi request reprint MProbe: computer aided probe design for oligonucleotide microarrays
    Wuju Li
    Beijing Institute of Basic Medical Sciences, Beijing, PR China
    Appl Bioinformatics 1:163-6. 2002
    ....
  23. ncbi request reprint [Computer aid vaccine design: new area of biomedical engineering]
    Jian Huang
    School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054
    Sheng Wu Yi Xue Gong Cheng Xue Za Zhi 21:1039-42. 2004
    ..This article reviewed the background of the coming of CAVD and its main research contents, methods and applications. Free tools of the trade in CAVD are listed; the implication and the perspective of CAVD are also suggested...
  24. ncbi request reprint Kernel machine-based one-parameter regularized fisher discriminant method for face recognition
    Wen Sheng Chen
    Department of Mathematics, Shenzhen University, Shenzhen 518060, China
    IEEE Trans Syst Man Cybern B Cybern 35:659-69. 2005
    ..Three databases, namely FERET, Yale Group B, and CMU PIE, are selected for evaluation. The results are encouraging. Comparing with the existing LDA-based methods, the proposed method gives superior results...
  25. ncbi request reprint A semiparametric approach for the nonparametric transformation survival model with multiple covariates
    Xiao Song
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    Biostatistics 8:197-211. 2007
    ..The estimator is evaluated via simulation studies and illustrated with the Veterans Administration lung cancer data set...
  26. pmc Regularized binormal ROC method in disease classification using microarray data
    Shuangge Ma
    Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
    BMC Bioinformatics 7:253. 2006
    ..It is also of interest to develop methods for evaluation of classification performance and ranking of identified biomarkers...
  27. ncbi request reprint Copper(II)-catalyzed amidations of alkynyl bromides as a general synthesis of ynamides and Z-enamides. An intramolecular amidation for the synthesis of macrocyclic ynamides
    Xuejun Zhang
    Division of Pharmaceutical Sciences, 777 Highland Avenue, University of Wisconsin, Madison, Wisconsin 53705, USA
    J Org Chem 71:4170-7. 2006
    ..Given the surging interest in ynamide chemistry, this atom economical synthesis of ynamides should invoke further attention from the synthetic organic community...
  28. ncbi request reprint Robust semiparametric microarray normalization and significance analysis
    Shuangge Ma
    Department of Biostatistics, University of Washington, Seattle, Washington 98115, USA
    Biometrics 62:555-61. 2006
    ..A small simulation study is used to compare finite sample performance of the proposed approach with alternatives. We also demonstrate the proposed method with a real dataset...
  29. ncbi request reprint Regularized estimation in the accelerated failure time model with high-dimensional covariates
    Jian Huang
    Department of Statistics and Actuarial Science, University of Iowa, Iowa City, Iowa 52242, USA
    Biometrics 62:813-20. 2006
    ..The proposed method is evaluated using simulations and demonstrated on a real data example...
  30. ncbi request reprint Development and clinical evaluation of oligonucleotide microarray for HLA-AB genotyping
    Fan Zhang
    Beijing Institute of Radiation Medicine, Beijing 100850, China
    Pharmacogenomics 7:973-85. 2006
    ..In this study, oligonucleotide microarray for HLA-AB genotyping was prepared and evaluated...
  31. ncbi request reprint Scalable data servers for large multivariate volume visualization
    Markus Glatter
    The University of Tennessee, USA
    IEEE Trans Vis Comput Graph 12:1291-8. 2006
    ..We demonstrate our system of scalable data servers using two large time-varying simulation datasets...
  32. ncbi request reprint Predicting subcellular localization of mycobacterial proteins by using Chou's pseudo amino acid composition
    Hao Lin
    Center for Bioinformatics, School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, 610054, China
    Protein Pept Lett 15:739-44. 2008
    ..2% and 79.1%, respectively. Compared with other existing methods, SVM combined with PseAAC display higher accuracies...