George Karypis, PhD

Professor, Department of Computer Science & Engineering, College of Science and Engineering

George Karypis

Contact Info

karypis@umn.edu

Office Phone 612-626-7524

Office Address:
4-203 EE/CS
480 Walter

Mailing Address:
4-192 EE/CS Building
200 Union Street SE
Minneapolis, MN 55455

Professor, Department of Computer Science & Engineering, College of Science and Engineering

Affiliate Faculty, Institute for Health Informatics (IHI)


PhD, University of Minnesota (Computer Science), 1996

BS, University of Minnesota (Computer Science), 1992

Research

Research Summary/Interests

My research interests span the areas of data mining, bio-informatics, parallel processing, CAD, and scientific computing.

My research in data mining is focused on developing innovative new algorithms for a variety of data mining problems including clustering, classification, pattern discovery, and deviation detection, with an emphasis on business applications and information retrieval.

My research in bio-informatics is focused on developing algorithms for understanding the function of genes and proteins in different species using data arising from genome-wide expression profiles. In this work, I'm trying to use data mining techniques to analyze expression profiles of genes and find groups of genes that behave similarly, and determine the underlying genetic regulatory network.

My research in parallel processing is focused on developing scalable parallel algorithms for emerging applications and architectures. This includes research on data intensive applications, scientific computing, architectures with deep memory hierarchies, and architectures with heterogeneous interconnection networks.

My recent research has led to the development of a number of highly efficient and scalable software packages and algorithms such as METIS (a serial sparse graph partitioning software), ParMETIS (an MPI-based parallel graph partitioning software), hMETIS (a circuit partitioning software), PSPASES (a parallel direct solver), and CHAMELEON (a spatial clustering algorithm).

Publications

  • Huzefa Rangwala, Christopher Kauffman, and George Karypis. (2009). A kernel framework for protein residue annotation. PAKDD, pp. 439-451.
  • Rezwan Ahmed, Huzefa Rangwala, and George Karypis. (2009). TOPTMH: Topology Predictor for Transmembrane alpha-Helices. Journal of Bioinformatics and Computational Biolog.
  • Salim Charaniya, Wei-Shou Hu, and George Karypis. (2009). Mining bioprocess data: opportunities and challenges. Trends in Biotechnology.
  • Kevin W. Deronne and George Karypis. (2009). Improved estimation of structure predictor quality. BMC Structural Biology, 9:41.
  • Salim Charaniya, George Karypis, and We-Shou Hu (2009). Mining Transcriptome Data for Function-Trait Relationship of Hyper Productivty of Recombinant Antibody. Biotechnology & Bioengineering, Vol. 102, No. 6, pp. 1654-1669.
  • Chris Kauffman and George Karypis (2009). LIBRUS: Combined Machine Learning and Homology Information for Sequence-based Ligand-Binding Residue Prediction. Bioinformatics.
  • Ruinan Zhang, Huzefa Rangwala, and George Karypis (2008). Genome alignments using MPI-LAGAN. International Conference on Bioinformatics and Biomedicine.
  • Rezwan Ahmed, Huzefa Rangwala, and George Karypis. (2008). TOPTMH: Topology Predictor for Transmembrane a-Helices. ECML-PKDD.
  • Chris Kauffman, Huzefa Rangwala, and George Karypis. (2008). Improving Homology Models for Protein-Ligand Binding Sites. LSS Computational systems Bioinformatics Conference (CSB).
  • Kevin W. DeRonne and George Karypis. (2008). Improved prediction of protein model quality. CSE TR# 08-002.
  • Chris Kauffman and George Karypis. (2008). An Analysis of Information Content Present in Protein-DNA Interactions. Pacific Symposium on Biocomputing.
  • Huzefa Rangwala and George Karypis. (2008). fRMSDAlign: Protein Sequence Alignment Using Predicted Local Structure Information. 6th Asia Pacific Bioinformatics Conference.
  • Salim Charaniya, Sarika Mehra, Wei Lian, Karthik P. Jayapal, George Karypis, Wei-Shou Hu. (2007). Transcriptome dynamics-based operon prediction and verification in Streptomyces coelicolor. Nucleic Acids Research, 35(21):7222-36.
  • Huzefa Rangwala, Christopher Kauffman, and George Karypis. (2007). A Generalized Framework for Protein Sequence Annotation. UMN TR# 07-023.
  • Nikil Wale and George Karypis. (2007). Methods for Effective Virtual Screening and Scaffold-Hopping in Chemical Compounds. Computational Systems Biology (CSB), pp. 403-416.
  • Huzefa Rangwala and George Karypis. (2007). fRMSDPred: Predicting local rmsd between structural fragments using sequence information. Computational Systems Biology (CSB), pp. 311-322.
  • Kevin DeRonne and George Karypis. (2007). Effective Optimization Algorithms for Fragment-Assembly Based Protein Structure Prediction. Journal of Bioinformatics and Computational Biology (JBCB).
  • Huzefa Rangwala and George Karypis. (2006). Building Multiclass Classifiers for Remote Homology Detection and Fold Recognition. BMC Bioinformatics, Jan 15;23(2):e17-23.
  • Kevin W. DeRonne and George Karypis. (2006). Effective Optimization Algorithms for Fragment-assembly based Protein Structure Prediction. Computational Systems Bioinformatics Conference (CSB).
  • Nikil Wale and George Karypis. (2006). Acyclic Subgraph-based Descriptor Spaces for Chemical Compound Retrieval and Classification. IEEE International Conference on Data Mining (ICDM).
  • Huzefa Rangwala and George Karypis. (2006). Incremental Window-based Protein Sequence Alignment Algorithms. 5th European Conference on Computational Biology (ECCB).
  • Huzefa Rangwala, Kevin DeRonne, and George Karypis. (2006). Protein Structure Prediction using String Kernels. UMN CSE 06-005.
  • George Karypis. (2006). YASSPP: Better Kernels and Coding Schemes Lead to Improvements in SVM-basedSecondary Structure Prediction. PROTEINS