Now showing items 1-20 of 34

    • BADGE: A novel Bayesian model for accurate abundance quantification and differential analysis of RNA-Seq data 

      Gu, Jinghua; Wang, Xiao; Hilakivi-Clarke, Leena; Clarke, Robert; Xuan, Jianhua (2014-09-10)
      Abstract Background Recent advances in RNA sequencing (RNA-Seq) technology have offered unprecedented scope and resolution for transcriptome analysis. However, precise quantification of mRNA abundance and identification ...
    • Bayesian Alignment Model for Analysis of LC-MS-based Omic Data 

      Tsai, Tsung-Heng (Virginia Tech, 2014-05-22)
      Liquid chromatography coupled with mass spectrometry (LC-MS) has been widely used in various omic studies for biomarker discovery. Appropriate LC-MS data preprocessing steps are needed to detect true differences between ...
    • caBIG VISDA: modeling, visualization, and discovery for cluster analysis of genomic data 

      Zhu, Yitan; Li, Huai; Miller, David J; Wang, Zuyi; Xuan, Jianhua; Clarke, Robert; Hoffman, Eric P; Wang, Yue (2008-09-18)
      Abstract Background The main limitations of most existing clustering methods used in genomic data analysis include heuristic or random algorithm initialization, the potential of finding poor local optima, the lack of cluster ...
    • caBIG VISDA: modeling, visualization, and discovery for cluster analysis of genomic data 

      Zhu, Yitan; Li, Huai; Miller, David J; Wang, Zuyi; Xuan, Jianhua; Clarke, Robert; Hoffman, Eric P; Wang, Yue (2008-09-18)
      Abstract Background The main limitations of most existing clustering methods used in genomic data analysis include heuristic or random algorithm initialization, the potential of finding poor local optima, the lack of cluster ...
    • Collimator width Optimization in X-ray Luminescent Computed Tomography 

      Mishra, Sourav (Virginia Tech, 2013-06-17)
      X-ray Luminescent Computed Tomography (XLCT) is a new imaging modality which is under extensive trials at present. The modality works by selective excitation of X-ray sensitive nanophosphors and detecting the optical signal ...
    • Computational Analysis of Genome-Wide DNA Copy Number Changes 

      Song, Lei (Virginia Tech, 2011-05-03)
      DNA copy number change is an important form of structural variation in human genome. Somatic copy number alterations (CNAs) can cause over expression of oncogenes and loss of tumor suppressor genes in tumorigenesis. Recent ...
    • Concurrency Optimization for Integrative Network Analysis 

      Barnes II, Robert Otto (Virginia Tech, 2013-06-12)
      Virginia Tech\'s Computational Bioinformatics and Bio-imaging Laboratory (CBIL) is exploring integrative network analysis techniques to identify subnetworks or genetic pathways that contribute to various cancers. Chen et. ...
    • Design and Implementation of Convex Analysis of Mixtures Software Suite 

      Meng, Fan (Virginia Tech, 2012-08-07)
      Various convex analysis of mixtures (CAM) based algorithms have been developed to address real world blind source separation (BSS) problems and proven to have good performances in previous papers. This thesis reported the ...
    • Detection and Characterization of Multilevel Genomic Patterns 

      Feng, Yuanjian (Virginia Tech, 2010-05-26)
      DNA microarray has become a powerful tool in genetics, molecular biology, and biomedical research. DNA microarray can be used for measuring the genotypes, structural changes, and gene expressions of human genomes. Detection ...
    • Effective Methods of Semantic Analysis in Spatial Contexts 

      Dos Santos Jr., Raimundo Fonseca (Virginia Tech, 2014-08-01)
      With the growing spread of spatial data, exploratory analysis has gained a considerable amount of attention. Particularly in the fields of Information Retrieval and Data Mining, the integration of data points helps uncover ...
    • Gene Selection for Multiclass Prediction by Weighted Fisher Criterion 

      Xuan, Jianhua; Wang, Yue; Dong, Yibin; Feng, Yuanjian; Wang, Bin; Khan, Javed; Bakay, Maria; Wang, Zuyi; Pachman, Lauren; Winokur, Sara; Chen, Yi-Wen; Clarke, Robert; Hoffman, Eric (2007-07-10)
      Gene expression profiling has been widely used to study molecular signatures of many diseases and to develop molecular diagnostics for disease prediction. Gene selection, as an important step for improved diagnostics, ...
    • Identifying cancer biomarkers by network-constrained support vector machines 

      Chen, Li; Xuan, Jianhua; Riggins, Rebecca B; Clarke, Robert; Wang, Yue (2011-10-12)
      Abstract Background One of the major goals in gene and protein expression profiling of cancer is to identify biomarkers and build classification models for prediction of disease prognosis or treatment response. Many ...
    • Identifying cancer biomarkers by network-constrained support vector machines 

      Chen, Li; Xuan, Jianhua; Riggins, Rebecca B; Clarke, Robert; Wang, Yue (2011-10-12)
      Abstract Background One of the major goals in gene and protein expression profiling of cancer is to identify biomarkers and build classification models for prediction of disease prognosis or treatment response. Many ...
    • Identifying protein interaction subnetworks by a bagging Markov random field-based method 

      Chen, Li; Xuan, Jianhua; Riggins, Rebecca B.; Wang, Yue; Clarke, Robert (Nucleic Acids Research, 2013)
      Identification of differentially expressed subnetworks from protein-protein interaction (PPI) networks has become increasingly important to our global understanding of the molecular mechanisms that drive cancer. Several ...
    • Knowledge-fused differential dependency network models for detecting significant rewiring in biological networks 

      Tian, Ye; Zhang, Bai; Hoffman, Eric P; Clarke, Robert; Zhang, Zhen; Shih, Ie-Ming; Xuan, Jianhua; Herrington, David M; Wang, Yue (2014-07-24)
      Modeling biological networks serves as both a major goal and an effective tool of systems biology in studying mechanisms that orchestrate the activities of gene products in cells. Biological networks are context-specific ...
    • Knowledge-fused Identification of Condition-specific Rewiring of Dependencies in Biological Networks 

      Tian, Ye (Virginia Tech, 2014-09-30)
      Gene network modeling is one of the major goals of systems biology research. Gene network modeling targets the middle layer of active biological systems that orchestrate the activities of genes and proteins. Gene network ...
    • Knowledge-guided gene ranking by coordinative component analysis 

      Wang, Chen; Xuan, Jianhua; Li, Huai; Wang, Yue; Zhan, Ming; Hoffman, Eric P; Clarke, Robert (2010-03-30)
      Abstract Background In cancer, gene networks and pathways often exhibit dynamic behavior, particularly during the process of carcinogenesis. Thus, it is important to prioritize those genes that are strongly associated with ...
    • Knowledge-guided multi-scale independent component analysis for biomarker identification 

      Chen, Li; Xuan, Jianhua; Wang, Chen; Shih, Ie-Ming; Wang, Yue; Zhang, Zhen; Hoffman, Eric; Clarke, Robert (2008-10-06)
      Abstract Background Many statistical methods have been proposed to identify disease biomarkers from gene expression profiles. However, from gene expression profile data alone, statistical methods often fail to identify ...
    • Knowledge-guided multi-scale independent component analysis for biomarker identification 

      Chen, Li; Xuan, Jianhua; Wang, Chen; Shih, Ie-Ming; Wang, Yue; Zhang, Zhen; Hoffman, Eric; Clarke, Robert (2008-10-06)
      Abstract Background Many statistical methods have been proposed to identify disease biomarkers from gene expression profiles. However, from gene expression profile data alone, statistical methods often fail to identify ...
    • Machine Learning to Interrogate High-throughput Genomic Data: Theory and Applications 

      Yu, Guoqiang (Virginia Tech, 2011-09-07)
      The missing heritability in genome-wide association studies (GWAS) is an intriguing open scientific problem which has attracted great recent interest. The interaction effects among risk factors, both genetic and environmental, ...