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Publications Related to Bioinformatics

  1. Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor. Salim Charaniya, Sarika Mehra, Wei Lian, Karthik P. Jayapal, George Karypis, Wei-Shou Hu.  Nucleic Acids Research, 35(21):7222-36., 2007.

  1. A Generalized Framework for Protein Sequence Annotation. Huzefa Rangwala, Christopher Kauffman, and George Karypis.  UMN TR# 07-023, 2007.

  1. Methods for Effective Virtual Screening and Scaffold-Hopping in Chemical Compounds. Nikil Wale and George Karypis.  Computational Systems Biology (CSB), pp. 403-416, 2007.

  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.
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