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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)
MOTIVATION Structural variation including deletions, duplications and rearrangements of DNA sequence are an important contributor to genome variation in many organisms. In human, many structural variants are found in complex and highly repetitive regions of the genome making their identification difficult. A new sequencing technology called strobe(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)
A cancer genome is derived from the germline genome through a series of somatic mutations. Somatic structural variants - including duplications, deletions, inversions, translocations, and other rearrangements - result in a cancer genome that is a scrambling of intervals, or "blocks" of the germline genome sequence. We present an efficient algorithm for(More)
BACKGROUND Copy number variants (CNVs), including deletions, amplifications, and other rearrangements, are common in human and cancer genomes. Copy number data from array comparative genome hybridization (aCGH) and next-generation DNA sequencing is widely used to measure copy number variants. Comparison of copy number data from multiple individuals reveals(More)
Reversible protein phosphorylation plays a pivotal role in the regulation of cellular signaling pathways. Current approaches in phosphoproteomics focus on analysis of the global phosphoproteome in a single cellular state or of receptor stimulation time course experiments, often with a restricted number of time points. Although these studies have provided(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)