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MOTIVATION Modification of proteins via phosphorylation is a primary mechanism for signal transduction in cells. Phosphorylation sites on proteins are determined in part through particular patterns, or motifs, present in the amino acid sequence. RESULTS We describe an algorithm that simultaneously discovers multiple motifs in a set of peptides that were(More)
In this work we present, apply, and evaluate a novel, interactive visualization model for comparative analysis of structural variants and rearrangements in human and cancer genomes, with emphasis on data integration and uncertainty visualization. To support both global trend analysis and local feature detection, this model enables explorations continuously(More)
MOTIVATION Structural variation is common in human and cancer genomes. High-throughput DNA sequencing has enabled genome-scale surveys of structural variation. However, the short reads produced by these technologies limit the study of complex variants, particularly those involving repetitive regions. Recent 'third-generation' sequencing technologies provide(More)
Atmospheric data analysis is an important area of scientific endeavor, with both government and industrial applications. Our work focuses on clustering particle data acquired via an Aerosol Time-of-Flight Mass Spectrometer (ATOFMS), which is sold and marketed by TSI, Inc. Most papers and software tools developed by the single-particle mass spectrometry(More)
Many applications of clustering require the use of normalized data, such as text or mass spectra mining. The spherical K-means algorithm [6], an adaptation of the traditional K-means algorithm, is highly useful for data of this kind because it produces normalized cluster centers. The K-medians clustering algorithm is also an important clustering tool(More)
Networks, known mathematically as graphs, have become ubiquitous in computational biology. These graphs are used to represent systems such as protein interaction networks, transcriptional regulatory networks, or gene ontology. The study of these networks often occur at an interdisciplinary interface of computational and experimental biodlogy, where(More)