Brian R. King

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Understanding protein subcellular localization is a necessary component toward understanding the overall function of a protein. Numerous computational methods have been published over the past decade, with varying degrees of success. Despite the large number of published methods in this area, only a small fraction of them are available for researchers to(More)
We present a method called ngLOC, an n-gram-based Bayesian classifier that predicts the localization of a protein sequence over ten distinct subcellular organelles. A tenfold cross-validation result shows an accuracy of 89% for sequences localized to a single organelle, and 82% for those localized to multiple organelles. An enhanced version of ngLOC was(More)
In protein sequence classification, identification of the sequence motifs or n-grams that can precisely discriminate between classes is a more interesting scientific question than the classification itself. A number of classification methods aim at accurate classification but fail to explain which sequence features indeed contribute to the accuracy. We(More)
Knowledge of specific domain-domain interactions (DDIs) is essential to understand the functional significance of protein interaction networks. Despite the availability of an enormous amount of data on protein-protein interactions (PPIs), very little is known about specific DDIs occurring in them. Here, we present a top-down approach to accurately infer(More)
ii Acknowledgments This thesis would not be possible without the support of many people. I would like to devote this page to thank these individuals for their encouragement and belief in me through my research and life at Bucknell: • First and foremost, Dr. Brian R. King, for his patience, guidance and support in my research and life. Without your knowledge(More)
Digital signal processing (DSP) techniques for biological sequence analysis continue to grow in popularity due to the inherent digital nature of these sequences. DSP methods have demonstrated early success for detection of coding regions in a gene. Recently, these methods are being used to establish DNA gene similarity. We present the inter-coefficient(More)
Human immunodeficiency virus-1 is a complex retrovirus that gradually destroys the body's immune system, making it harder for the individual to fight infections. The worst prognosis for an infected individual is AIDS; however this result does not occur with everyone. Moreover, not every infected person develops AIDS at the same rate [5]. We developed a(More)