Jianxin Wang

Summary

Affiliation: Central South University
Country: China

Publications

  1. ncbi request reprint UPNT: Uniform Projection and Neighbourhood Thresholding method for motif discovery
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha, 410083, PR China
    Int J Bioinform Res Appl 4:96-106. 2008
  2. doi request reprint A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks
    Jianxin Wang
    Department of Computer Science, School of Information Science and Engineering, Central South University, Changsha 410083, China
    IEEE/ACM Trans Comput Biol Bioinform 8:607-20. 2011
  3. pmc An unsupervised machine learning method for assessing quality of tandem mass spectra
    Wenjun Lin
    Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7N 5A9, Canada
    Proteome Sci 10:S12. 2012
  4. pmc A fast and accurate algorithm for single individual haplotyping
    Minzhu Xie
    College of Physics and Information Science, Hunan Normal University, Changsha 410081, PR China
    BMC Syst Biol 6:S8. 2012
  5. pmc Biological network motif detection and evaluation
    Wooyoung Kim
    Department of Computer Science, Georgia State University, Atlanta, GA, USA
    BMC Syst Biol 5:S5. 2011
  6. pmc An effective method for refining predicted protein complexes based on protein activity and the mechanism of protein complex formation
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha 410083, China
    BMC Syst Biol 7:28. 2013
  7. doi request reprint Symmetry compression method for discovering network motifs
    Jianxin Wang
    School of Information Engineering and Science, Central South University, Computer Building, Changsha, Hunan, P R China
    IEEE/ACM Trans Comput Biol Bioinform 9:1776-89. 2012
  8. doi request reprint Construction and application of dynamic protein interaction network based on time course gene expression data
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha, China
    Proteomics 13:301-12. 2013
  9. doi request reprint Computational approaches to predicting essential proteins: a survey
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha, China
    Proteomics Clin Appl 7:181-92. 2013
  10. doi request reprint Identifying protein complexes from interactome based on essential proteins and local fitness method
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha, 410005, China
    IEEE Trans Nanobioscience 11:324-35. 2012

Collaborators

Detail Information

Publications31

  1. ncbi request reprint UPNT: Uniform Projection and Neighbourhood Thresholding method for motif discovery
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha, 410083, PR China
    Int J Bioinform Res Appl 4:96-106. 2008
    ..This paper further demonstrates its superiority over other projection algorithms by the experiments...
  2. doi request reprint A fast hierarchical clustering algorithm for functional modules discovery in protein interaction networks
    Jianxin Wang
    Department of Computer Science, School of Information Science and Engineering, Central South University, Changsha 410083, China
    IEEE/ACM Trans Comput Biol Bioinform 8:607-20. 2011
    ..Compared to other previous competing algorithms, our algorithm HC-PIN is faster and more accurate...
  3. pmc An unsupervised machine learning method for assessing quality of tandem mass spectra
    Wenjun Lin
    Division of Biomedical Engineering, University of Saskatchewan, 57 Campus Dr, Saskatoon, S7N 5A9, Canada
    Proteome Sci 10:S12. 2012
    ..These methods need the training datasets with knowing the quality of all spectra, which are usually unavailable for the new datasets...
  4. pmc A fast and accurate algorithm for single individual haplotyping
    Minzhu Xie
    College of Physics and Information Science, Hunan Normal University, Changsha 410081, PR China
    BMC Syst Biol 6:S8. 2012
    ..e., Single Individual Haplotyping) has become a practical haplotyping approach...
  5. pmc Biological network motif detection and evaluation
    Wooyoung Kim
    Department of Computer Science, Georgia State University, Atlanta, GA, USA
    BMC Syst Biol 5:S5. 2011
    ..Since network motif discovery involves computationally challenging processes, previous algorithms have focused on computational efficiency. However, we believe that the biological quality of network motifs is also very important...
  6. pmc An effective method for refining predicted protein complexes based on protein activity and the mechanism of protein complex formation
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha 410083, China
    BMC Syst Biol 7:28. 2013
    ....
  7. doi request reprint Symmetry compression method for discovering network motifs
    Jianxin Wang
    School of Information Engineering and Science, Central South University, Computer Building, Changsha, Hunan, P R China
    IEEE/ACM Trans Comput Biol Bioinform 9:1776-89. 2012
    ..Furthermore, SCMD enables us to find larger motifs in biological networks with notable symmetry than previously possible...
  8. doi request reprint Construction and application of dynamic protein interaction network based on time course gene expression data
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha, China
    Proteomics 13:301-12. 2013
    ....
  9. doi request reprint Computational approaches to predicting essential proteins: a survey
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha, China
    Proteomics Clin Appl 7:181-92. 2013
    ..In this paper, we review the state-of-the-art techniques for computational detection of essential proteins, and discuss some challenges for future research in this field...
  10. doi request reprint Identifying protein complexes from interactome based on essential proteins and local fitness method
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha, 410005, China
    IEEE Trans Nanobioscience 11:324-35. 2012
    ..The program and related files available on https://github.com/gangchen/epof...
  11. doi request reprint Identification of hierarchical and overlapping functional modules in PPI networks
    Jianxin Wang
    School of Information Science and Engineering, Central SouthUniversity, Changsha, 410083, China
    IEEE Trans Nanobioscience 11:386-93. 2012
    ..The experimental results show that OH-PIN outperforms the existing algorithms in terms of the functional enrichment and matching with known protein complexes...
  12. doi request reprint Identification of essential proteins based on edge clustering coefficient
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Computer Building, Changsha 410083, China
    IEEE/ACM Trans Comput Biol Bioinform 9:1070-80. 2012
    ..Moreover, the essential proteins discovered by NC show significant cluster effect...
  13. pmc Integration of breast cancer gene signatures based on graph centrality
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha, 410083, China
    BMC Syst Biol 5:S10. 2011
    ..However due to small overlap between different signatures, it is challenging to integrate existing disjoint signatures to provide a unified insight on the association between gene expression and clinical outcome...
  14. pmc A new essential protein discovery method based on the integration of protein-protein interaction and gene expression data
    Min Li
    School of Information Science and Engineering, Central South University, Changsha, Hunan, P R China
    BMC Syst Biol 6:15. 2012
    ..However, the network topology-based centrality measures are very sensitive to the robustness of network. Therefore, a new robust essential protein discovery method would be of great value...
  15. pmc Reordering based integrative expression profiling for microarray classification
    Xiaogang Wu
    School of Informatics, Indiana University, Indianapolis, IN 46202, USA
    BMC Bioinformatics 13:S1. 2012
    ..To implement IXP, ant colony optimization reordering (ACOR) algorithm is used to group functionally related genes in an ordered way...
  16. pmc Modifying the DPClus algorithm for identifying protein complexes based on new topological structures
    Min Li
    School of Information Science and Engineering, Central South University, Changsha, Hunan 410083, PR China
    BMC Bioinformatics 9:398. 2008
    ..As the size of protein-protein interaction set increases, a general trend is to represent the interactions as a network and to develop effective algorithms to detect significant complexes in such networks...
  17. pmc Recent advances in clustering methods for protein interaction networks
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha 410083, China
    BMC Genomics 11:S10. 2010
    ..The predictions of protein functions and interactions based on modules will be covered. Finally, the performance of different clustering methods will be compared and the directions for future research will be discussed...
  18. pmc Identifying protein complexes from interaction networks based on clique percolation and distance restriction
    Jianxin Wang
    School of Information Science and Engineering, Central South University, Changsha 410083, China
    BMC Genomics 11:S10. 2010
    ..Each protein might be subordinate multiple protein complexes in the real protein-protein interaction networks. Identifying overlapping protein complexes from protein-protein interaction networks is a considerable research topic...
  19. doi request reprint A local average connectivity-based method for identifying essential proteins from the network level
    Min Li
    School of Information Science and Engineering, Central South University, Changsha 410083, PR China
    Comput Biol Chem 35:143-50. 2011
    ..The comparison results based on the validations of sensitivity, specificity, F-measure, positive predictive value, negative predictive value, and accuracy consistently show that LAC outweighs these seven previous methods...
  20. pmc A comparison of the functional modules identified from time course and static PPI network data
    Xiwei Tang
    School of Information Science and Engineering, Central South University, Changsha, 410083, China
    BMC Bioinformatics 12:339. 2011
    ..The shift from static to dynamic network analysis is essential for further understanding of molecular systems...
  21. doi request reprint hF-measure: A new measurement for evaluating clusters in protein-protein interaction networks
    Min Li
    School of Information Science and Engineering, Central South University, Changsha, China
    Proteomics 13:291-300. 2013
    ..Especially, hF-measure(Tb) can capture the topology changes in clusters, which can also be used to the analysis of dynamic network...
  22. pmc Towards the identification of protein complexes and functional modules by integrating PPI network and gene expression data
    Min Li
    School of Information Science and Engineering, Central South University, Changsha, China
    BMC Bioinformatics 13:109. 2012
    ..However, most of them considered the PPI networks as static graphs and overlooked the dynamics inherent within these networks. Moreover, few of them can distinguish between protein complexes and functional modules...
  23. ncbi request reprint Identifying the overlapping complexes in protein interaction networks
    Min Li
    School of Information Science and Engineering, Central South University, Changsha 410083, China
    Int J Data Min Bioinform 4:91-108. 2010
    ..The algorithm IPC-MCE is applied to the protein interaction network of Saccharomyces cerevisiae. Many well-known protein complexes are detected...
  24. pmc Iteration method for predicting essential proteins based on orthology and protein-protein interaction networks
    Wei Peng
    School of Information Science and Engineering, Central South University, Changsha, Hunan 410083, People s Republic of China
    BMC Syst Biol 6:87. 2012
    ..However, none of their methods has widely been acknowledged...
  25. pmc A model of higher accuracy for the individual haplotyping problem based on weighted SNP fragments and genotype with errors
    Minzhu Xie
    School of Information Science and Engineering, Central South University, Changsha 410083, China
    Bioinformatics 24:i105-13. 2008
    ..Based on various optimal criteria and including different extra information, many models for the problem have been proposed. Higher accuracy of the models has been an important issue in the study of haplotype reconstruction...
  26. doi request reprint A heuristic algorithm for haplotype reconstruction from aligned weighted SNP fragments
    Jingli Wu
    School of Information Science and Engineering, Central South University, Changsha, 410083, China
    Int J Bioinform Res Appl 9:13-24. 2013
    ..Computational experiments indicate that the algorithm is a good solution for the Weighted Minimum Letter Flips (WMLF) model, and gets better performance than previous works...
  27. ncbi request reprint A practical algorithm for multiplex PCR primer set selection
    Jingli Wu
    School of Information Science and Engineering, Central South University, Changsha 410083, China
    Int J Bioinform Res Appl 5:38-49. 2009
    ..Experimental results show that MG-PGA can not only find a small primer set, but can also satisfy multiple biological constraints. Therefore, MG-PGA is a practical solution for MP-PCR primer design...
  28. pmc Predicting β-turns in protein using kernel logistic regression
    Murtada Khalafallah Elbashir
    School of Information Science and Engineering, Central South University, Changsha 410083, China
    Biomed Res Int 2013:870372. 2013
    ..In addition, KLR yields probabilistic outcome and has a well-defined extension to multiclass case...
  29. ncbi request reprint Research on parameterized algorithms of the individual haplotyping problem
    Minzhu Xie
    School of Information Science and Engineering, Central South University, Changsha, Hunan Province 410083, China
    J Bioinform Comput Biol 5:795-816. 2007
    ..Since, the value of k(1) and k(2) are both small (about 10) in practice, our algorithms are more efficient and applicable compared with the algorithms of V. Bafna et al. of time complexity O(mn(2)) and O(m(2)n + m(3)), respectively...
  30. doi request reprint Evaluation of gene ontology semantic similarities on protein interaction datasets
    Gang Chen
    School of Information Science and Engineering, Central South University, Changsha, People s Republic of China
    Int J Bioinform Res Appl 9:173-83. 2013
    ..Various methods have been proposed for calculating the semantic similarity between GO terms and gene products, therefore evaluating these measurements on protein interaction data is helpful and necessary for related studies...
  31. ncbi request reprint DigiNorthern, digital expression analysis of query genes based on ESTs
    Jianxin Wang
    Department of Cancer Genetics and the Biomathematics and Biostatistics Core Facility, Roswell Park Cancer Institute, Elm and Carlton Streets, Buffalo, NY 14263, USA
    Bioinformatics 19:653-4. 2003
    ....