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Filtration techniques in the form of rapid elimination of candidate sequences while retaining the true one are key ingredients of database searches in genomics. Although SEQUEST and Mascot perform a conceptually similar task to the tool BLAST, the key algorithmic idea of BLAST (filtration) was never implemented in these tools. As a result MS/MS protein(More)
Reliable identification of post-translational modifications is key to understanding various cellular regulatory processes. We describe a tool, InsPecT, to identify post-translational modifications using tandem mass spectrometry data. InsPecT constructs database filters that proved to be very successful in genomics searches. Given an MS/MS spectrum S and a(More)
Tandem mass spectrometry (MS/MS) experiments often generate redundant data sets containing multiple spectra of the same peptides. Clustering of MS/MS spectra takes advantage of this redundancy by identifying multiple spectra of the same peptide and replacing them with a single representative spectrum. Analyzing only representative spectra results in(More)
We have employed recently developed blind modification search techniques to generate the most comprehensive map of post-translational modifications (PTMs) in human lens constructed to date. Three aged lenses, two of which had moderate cataract, and one young control lens were analyzed using multidimensional liquid chromatography mass spectrometry. In total,(More)
Post-translational modifications (PTMs) are of great biological importance. Most existing approaches perform a restrictive search that can only take into account a few types of PTMs and ignore all others. We describe an unrestrictive PTM search algorithm that searches for all types of PTMs at once in a blind mode, i.e., without knowing which PTMs exist in a(More)
The central role of protein kinases in signal transduction pathways has generated intense interest in targeting these enzymes for a wide range of therapeutic indications. Here we report a method for identifying and quantifying protein kinases in any biological sample or tissue from any species. The procedure relies on acyl phosphate-containing nucleotides,(More)
MOTIVATION Versatile and efficient variant calling tools are needed to analyze large scale sequencing datasets. In particular, identification of copy number changes remains a challenging task due to their complexity, susceptibility to sequencing biases, variation in coverage data and dependence on genome-wide sample properties, such as tumor polyploidy or(More)
INTRODUCTION Rheumatoid arthritis (RA), a chronic inflammatory disease, is associated with insulin resistance. Experimental evidence indicates that the relationship between insulin resistance and inflammation is bidirectional: Inflammation promotes insulin resistance, and insulin resistance promotes inflammation. Therefore, we examined the hypothesis that(More)
BACKGROUND Adult granulosa cell tumors of the testis (AGCTT) are classified as sex cord-stromal tumors. Only 31 cases have been reported. Typical presentation includes a slowly enlarging, painless testicular mass. Associated findings are gynecomastia, decreased libido, and erectile dysfunction. Immunohistochemistry can be used to confirm the diagnosis. (More)
Motivation: Increased throughput and diverse experimental designs of large-scale sequencing studies necessitate versatile, scalable and robust variant calling tools. In particular, identification of copy number changes remains a challenging task due to their complexity, susceptibility to sequencing biases, variation in coverage data and dependence on(More)