Research Topics
| Jian HuangSummaryAffiliation: Kyoto University Country: Japan Publications
| Collaborators
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Detail Information
Publications
Predicting B cell epitope residues with network topology based amino acid indicesJian 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...- New amino acid indices based on residue network topologyJian 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... 
MIMOX: a web tool for phage display based epitope mappingJian 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...- CED: a conformational epitope databaseJian 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... - Penalized feature selection and classification in bioinformaticsShuangge 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... - A robust two-way semi-linear model for normalization of cDNA microarray dataDeli 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... - Regularized ROC method for disease classification and biomarker selection with microarray dataShuangge Ma
Department of Biostatistics, University of Washington, Washington, USA
Bioinformatics 21:4356-62. 2005..The proposed approach is demonstrated with a simulation study, the Colon data and the Estrogen data. The proposed approach yields parsimonious models with excellent classification performance... - [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..CONCLUSIONS: The results of this research supply the basic materials for the DC based vaccine with HLA-A2 restricted peptide epitope derived from hAFP against AFP positive primary hepatocellular carcinoma... - 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)... - Supervised group Lasso with applications to microarray data analysisShuangge 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... - Dynamic sharing of large-scale visualizationJian Huang
University of Tennessee, Knoxville, USA
IEEE Comput Graph Appl 27:20-5. 2007 - A multi-level cache model for run-time optimization of remote visualizationRobert 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... - [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... - Combining multiple markers for classification using ROCShuangge 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... - BMI-1 autoantibody in serum as a new potential biomarker of nasopharyngeal carcinomaYong 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... - Apoptosis-inducing effect and structural basis of Polygonatum cyrtonema lectin and chemical modification properties on its mannose-binding sitesBo 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... 
Dynamic visualization of coexpression in systems genetics dataJoshua 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...- A fully human chimeric immune receptor for retargeting T-cells to CEA-expressing tumor cellsHirotomo 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... - Clustering threshold gradient descent regularization: with applications to microarray studiesShuangge 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... - Genetic linkage analysis of a dichotomous trait incorporating a tightly linked quantitative trait in affected sib pairsJian 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... - Hepatitis B virus (HBV) vaccine-induced escape mutants of HBV S gene among children from Qidong area, ChinaXinghua 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... - MProbe: computer aided probe design for oligonucleotide microarraysWuju Li
Beijing Institute of Basic Medical Sciences, Beijing, PR China
Appl Bioinformatics 1:163-6. 2002.... - [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... - Kernel machine-based one-parameter regularized fisher discriminant method for face recognitionWen 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... - A semiparametric approach for the nonparametric transformation survival model with multiple covariatesXiao 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... - Regularized binormal ROC method in disease classification using microarray dataShuangge 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... - Copper(II)-catalyzed amidations of alkynyl bromides as a general synthesis of ynamides and Z-enamides. An intramolecular amidation for the synthesis of macrocyclic ynamidesXuejun 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... - Robust semiparametric microarray normalization and significance analysisShuangge 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... - Regularized estimation in the accelerated failure time model with high-dimensional covariatesJian 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... - Development and clinical evaluation of oligonucleotide microarray for HLA-AB genotypingFan Zhang
Beijing Institute of Radiation Medicine, Beijing 100850, China
Pharmacogenomics 7:973-85. 2006..CONCLUSION: The microarray for HLA-AB genotyping is satisfactory for clinical use in HLA-AB genotyping with its good specificity, sensitivity and reproducibility... - Scalable data servers for large multivariate volume visualizationMarkus 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... - Predicting subcellular localization of mycobacterial proteins by using Chou's pseudo amino acid compositionHao 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...