Xinghua Lu

Summary

Affiliation: Medical University of South Carolina
Country: USA

Publications

  1. ncbi Novel metrics for evaluating the functional coherence of protein groups via protein semantic network
    Bin Zheng
    Department of Biostatistics, Bioinformatics and Epidemiology, 135 Cannon Street, Charleston, South Carolina 29425, USA
    Genome Biol 8:R153. 2007
  2. ncbi Automatic annotation of protein motif function with Gene Ontology terms
    Xinghua Lu
    Dept of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon St, Suite 303, Charleston, SC 29425, USA
    BMC Bioinformatics 5:122. 2004
  3. ncbi GOGrapher: A Python library for GO graph representation and analysis
    Brian Muller
    Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon St Suite 303 Charleston, SC 29425, USA
    BMC Res Notes 2:122. 2009
  4. ncbi Enhancing text categorization with semantic-enriched representation and training data augmentation
    Xinghua Lu
    Department of Biostatistics, Bioinformatics and Epidemiology, Charleston, SC 29425, USA
    J Am Med Inform Assoc 13:526-35. 2006
  5. ncbi Multi-label literature classification based on the Gene Ontology graph
    Bo Jin
    Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, Charleston, SC 29425, USA
    BMC Bioinformatics 9:525. 2008
  6. ncbi Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph
    Adam J Richards
    Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
    Bioinformatics 26:i79-87. 2010
  7. ncbi Identifying biological concepts from a protein-related corpus with a probabilistic topic model
    Bin Zheng
    Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, Charleston, SC 29405, USA
    BMC Bioinformatics 7:58. 2006
  8. ncbi Identifying informative subsets of the Gene Ontology with information bottleneck methods
    Bo Jin
    Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 174 Ashley Ave, Charleston, SC 29425, USA
    Bioinformatics 26:2445-51. 2010
  9. ncbi Feature selection for fMRI-based deception detection
    Bo Jin
    Medical University of South Carolina, Charleston, SC, USA
    BMC Bioinformatics 10:S15. 2009
  10. ncbi A multivariate prediction model for microarray cross-hybridization
    Yian A Chen
    Department of Biostatistics, Bioinformatics, and Epidemiology, Medical University of South Carolina, Charleston, SC, USA
    BMC Bioinformatics 7:101. 2006

Research Grants

  1. Automatic Literature-based Protein Annotation
    Xinghua Lu; Fiscal Year: 2009
  2. Statistical methods for integromics discoveries
    Xinghua Lu; Fiscal Year: 2009
  3. Automatic Literature-based Protein Annotation
    Xinghua Lu; Fiscal Year: 2009

Collaborators

Detail Information

Publications14

  1. ncbi Novel metrics for evaluating the functional coherence of protein groups via protein semantic network
    Bin Zheng
    Department of Biostatistics, Bioinformatics and Epidemiology, 135 Cannon Street, Charleston, South Carolina 29425, USA
    Genome Biol 8:R153. 2007
    ..Bipartite protein semantic networks are constructed, so that the functional coherence of a protein group can be evaluated with metrics that measure the closeness and strength of connectivity of the proteins in the network...
  2. ncbi Automatic annotation of protein motif function with Gene Ontology terms
    Xinghua Lu
    Dept of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon St, Suite 303, Charleston, SC 29425, USA
    BMC Bioinformatics 5:122. 2004
    ..The Gene Ontology (GO) project is an endeavor to annotate the function of genes or protein sequences with terms from a dynamic, controlled vocabulary and these annotations serve well as a knowledge base...
  3. ncbi GOGrapher: A Python library for GO graph representation and analysis
    Brian Muller
    Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, 135 Cannon St Suite 303 Charleston, SC 29425, USA
    BMC Res Notes 2:122. 2009
    ..CONCLUSION: The GOGrapher project provides a reusable programming library designed for the manipulation and analysis of Gene Ontology graphs. The library is freely available for the scientific community to use and improve...
  4. ncbi Enhancing text categorization with semantic-enriched representation and training data augmentation
    Xinghua Lu
    Department of Biostatistics, Bioinformatics and Epidemiology, Charleston, SC 29425, USA
    J Am Med Inform Assoc 13:526-35. 2006
    ..Under such a scenario, the performance of information retrieval algorithms is often unsatisfactory, therefore improvements are needed...
  5. ncbi Multi-label literature classification based on the Gene Ontology graph
    Bo Jin
    Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, Charleston, SC 29425, USA
    BMC Bioinformatics 9:525. 2008
    ..The task is usually cast as a text classification problem, and contemporary methods are confronted with unbalanced training data and the difficulties associated with multi-label classification...
  6. ncbi Assessing the functional coherence of gene sets with metrics based on the Gene Ontology graph
    Adam J Richards
    Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC 29425, USA
    Bioinformatics 26:i79-87. 2010
    ..Instead of testing for significance of individual terms, this study is concerned with the task of assessing the global functional coherence of gene sets, for which novel metrics and statistical methods have been devised...
  7. ncbi Identifying biological concepts from a protein-related corpus with a probabilistic topic model
    Bin Zheng
    Department of Biostatistics, Bioinformatics and Epidemiology, Medical University of South Carolina, Charleston, SC 29405, USA
    BMC Bioinformatics 7:58. 2006
    ..The goal of this research is to identify the major biological topics/concepts from a corpus of protein-related MEDLINE titles and abstracts by applying a probabilistic topic model...
  8. ncbi Identifying informative subsets of the Gene Ontology with information bottleneck methods
    Bo Jin
    Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 174 Ashley Ave, Charleston, SC 29425, USA
    Bioinformatics 26:2445-51. 2010
    ....
  9. ncbi Feature selection for fMRI-based deception detection
    Bo Jin
    Medical University of South Carolina, Charleston, SC, USA
    BMC Bioinformatics 10:S15. 2009
    ..In this paper, we investigated the procedures of feature selection to enhance fMRI-based deception detection...
  10. ncbi A multivariate prediction model for microarray cross-hybridization
    Yian A Chen
    Department of Biostatistics, Bioinformatics, and Epidemiology, Medical University of South Carolina, Charleston, SC, USA
    BMC Bioinformatics 7:101. 2006
    ..No comprehensive multivariate predictive modeling has been performed to understand how multiple variables contribute to (cross-) hybridization...
  11. ncbi Revealing a signaling role of phytosphingosine-1-phosphate in yeast
    L Ashley Cowart
    Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, USA
    Mol Syst Biol 6:349. 2010
    ..This approach could be applied to extract meaningful biological information from a similar experimental design that produces multiple sets of high-throughput data...
  12. ncbi A study of statistical methods for function prediction of protein motifs
    Tao Tao
    Department of Computer Science, University of Illinois at Urbana Champaign, 506 S Matthews Avenue, Urbana, IL 61801, USA
    Appl Bioinformatics 3:115-24. 2004
    ..Among the methods tested, a probabilistic translation model with a popularity prior performs the best...
  13. ncbi Genetic polymorphisms in methylenetetrahydrofolate reductase and thymidylate synthase and risk of pancreatic cancer
    Li Wang
    Department of Epidemiology, Institute of Basic Medical Sciences, Cancer Institute and Hospital, Beijing, China
    Clin Gastroenterol Hepatol 3:743-51. 2005
    ..We tested this hypothesis by examining the contribution of functional polymorphisms in methylenetetrahydrofolate reductase (MTHFR) and thymidylate synthase (TS) to risk of cancer...
  14. ncbi Unexpected mobility variation among individual secretory vesicles produces an apparent refractory neuropeptide pool
    Yuen-Keng Ng
    Department of Pharmacology, E1351 Biomedical Science Tower, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
    Biophys J 84:4127-34. 2003
    ..This unexpected variation, which could reflect heterogeneity among vesicles or in their medium, is shown to generate the appearance of a regulated refractory neuropeptide pool...

Research Grants6

  1. Automatic Literature-based Protein Annotation
    Xinghua Lu; Fiscal Year: 2009
    ..The efficient knowledge acquisition and management will enhance biomedical research regarding the mechanisms of diseases and drug discovery. ..
  2. Statistical methods for integromics discoveries
    Xinghua Lu; Fiscal Year: 2009
    ..We expect that the methodologies developed in the project are widely applicable to study a variety of cellular signal transduction systems. ..
  3. Automatic Literature-based Protein Annotation
    Xinghua Lu; Fiscal Year: 2009
    ..The efficient knowledge acquisition and management will enhance biomedical research regarding the mechanisms of diseases and drug discovery. ..