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Bioinformatics

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

  1. Improving Homology Models for Protein-Ligand Binding Sites. Chris Kauffman, Huzefa Rangwala, and George Karypis.  LSS Computational systems Bioinformatics Conference (CSB), 2008.

  1. Improved prediction of protein model quality. Kevin W. DeRonne and George Karypis.  CSE TR# 08-002, 2008.

  1. An Analysis of Information Content Present in Protein-DNA Interactions. Chris Kauffman and George Karypis.  Pacific Symposium on Biocomputing, 2008.

  1. fRMSDAlign: Protein Sequence Alignment Using Predicted Local Structure Information. Huzefa Rangwala and George Karypis.  6th Asia Pacific Bioinformatics Conference, 2008.

  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.
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