Bioinformatics

Here is a list of publications that are related to our research in bioinformatics.

  1. fRMSDPred: Predicting local rmsd between structural fragments using sequence information.

    Huzefa Rangwala and George Karypis. Computational Systems Biology (CSB), pp. 311-322, 2007.

  1. Effective Optimization Algorithms for Fragment-Assembly Based Protein Structure Prediction.

    Kevin DeRonne and George Karypis. Journal of Bioinformatics and Computational Biology (JBCB), 2007.

  1. Building Multiclass Classifiers for Remote Homology Detection and Fold Recognition.

    Huzefa Rangwala and George Karypis. BMC Bioinformatics, Jan 15;23(2):e17-23., 2006.

  1. Effective Optimization Algorithms for Fragment-assembly based Protein Structure Prediction.

    Kevin W. DeRonne and George Karypis. Computational Systems Bioinformatics Conference (CSB), 2006.

  1. Acyclic Subgraph-based Descriptor Spaces for Chemical Compound Retrieval and Classification.

    Nikil Wale and George Karypis. IEEE International Conference on Data Mining (ICDM), 2006.

  1. Incremental Window-based Protein Sequence Alignment Algorithms.

    Huzefa Rangwala and George Karypis. 5th European Conference on Computational Biology (ECCB), 2006.

  1. Protein Structure Prediction using String Kernels.

    Huzefa Rangwala, Kevin DeRonne, and George Karypis. UMN CSE 06-005, 2006.

  1. YASSPP: Better Kernels and Coding Schemes Lead to Improvements in SVM-basedSecondary Structure Prediction.

    George Karypis. PROTEINS: Structure, Function, and Bioinformatics, 2006.

  1. Profile Based Direct Kernels for Remote Homology Detection and Fold Recognition.

    Huzefa Rangwala and George Karypis. Bioinformatics, Vol. 31, No. 23, pp. 4239 - 4247, 2005.

  1. Data Clustering in Life Sciences.

    Ying Zhao and George Karypis. Molecular Biotechnology, 31(1), pp. 55--80, 2005.

  1. Gene Classification using Expression Profiles: A Feasibility Study.

    Michihiro Kuramochi and George Karypis. International Journal on Artificial Intelligence Tools. Vol. 14, No. 4, pp. 641 - 660, 2005.

  1. Frequent Sub-structure Based Approaches for Classifying Chemical Compounds.

    Mukund Deshpande, Michihiro Kuramochi, Nikil Wale, and George Karypis. IEEE Trans. Knowl. Data Eng. 17(8): 1036-1050, 2005.