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

  1. Augmenting Chinese hamster genome assembly by identifying regions of high confidence.

    Vishwanathan N., Bandyopadhyay A. Fu H. Sharma M., Johnson K., Mudge J. Ramaraj T., Onsongo G., Silverstein K., Jacob N., Le H., Karypis G., and Hu W.. Biotechnology Journal, 11, 2016.

  1. Exploring the Transcriptome Space of a Recombinant BHK Cell Line Through Next Generation Sequencing.

    Kathryn C. Johnson, Andrew Yongky, Nandita Vishwanathan, Nitya M. Jacob, Karthik P. Jayapal, Chetan T. Goudar, George Karypis, Wei-Shou Hu. Biotechnology and Bioengineering, 111: 770–781, 2014.

  1. Pareto Optimal Pairwise Sequence Alignment.

    Kevin DeRonne and George Karypis. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2013.

  1. Multivariate analysis of cell culture bioprocess data--lactate consumption as process indicator.

    Huong Le and Santosh Kabbur and Luciano Pollastrini and Ziran Sun and Keri Mills and Kevin Johnson and George Karypis and Wei-Shou Hu. Journal of Biotechnology, 162, pp. 210-223, 2012.

  1. Function Genomics of Nectar Production in Brassicaceae.

    R. Bender, P. Klinkenberg, Z. Jiang, B. Bauer, G. Karypis, N. Nguyen, M. Perera, B. Nikolau, and C. Carter. Flora: Morphology, Distribution, Functional Ecology of Plants Volume 207, Issue 7, pp. 491-496, 2012.

  1. Computational Tools for Protein-DNA Interactions.

    Chris Kauffman and George Karypis. WIREs Data Mining and Knowledge Discovery, 2(1): 14-28, 2012.

  1. Genome-wide Inference of Regulatory Networks in Streptomyces Coelicolor.

    Marlene Castro-Melchor, Salim Charaniya, George Karypis, Eriko Takano, and Wei-Shou Hu. BMC Genomics, Vol. 11, pp. 578, 2010.

  1. Mining manufacturing data for discovery of high productivity process characteristics.

    Salim Charaniya, Huong Le, Huzefa Rangwala, Keri Mills, Kevin Johnson, George Karypis, and Wei-Shou Hu. Journal of Biotechnology, Vol. 147, pp. 186—197, 2010.

  1. A kernel framework for protein residue annotation.

    Huzefa Rangwala, Christopher Kauffman, and George Karypis. PAKDD, pp. 439-451, 2009.

  1. TOPTMH: Topology Predictor for Transmembrane alpha-Helices.

    Rezwan Ahmed, Huzefa Rangwala, and George Karypis. Journal of Bioinformatics and Computational Biology, 2009.

  1. Mining bioprocess data: opportunities and challenges.

    Salim Charaniya, Wei-Shou Hu, and George Karypis. Trends in Biotechnology, 2009.