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Label-free quantification of high mass resolution LC-MS data has emerged as a promising technology for proteome analysis. Computational methods are required for the accurate extraction of peptide signals from LC-MS data and the tracking of these features across the measurements of different samples. We present here an open source software tool, SuperHirn,(More)
PURPOSE To characterize the quantitative properties of the optokinetic response (OKR) in zebrafish larvae as a tool to test visual performance in genetically modified larvae. METHODS Horizontal OKR was triggered in 5-day-old zebrafish larvae by stimulation with projected computer-generated gratings of varying contrast, angular velocity, temporal and(More)
MOTIVATION During evolution, functional regions in genomic sequences tend to be more highly conserved than randomly mutating 'junk DNA' so local sequence similarity often indicates biological functionality. This fact can be used to identify functional elements in large eukaryotic DNA sequences by cross-species sequence comparison. In recent years, several(More)
Selected reaction monitoring (SRM) uses sensitive and specific mass spectrometric assays to measure target analytes across multiple samples, but it has not been broadly applied in proteomics owing to the tedious assay development process for each protein. We describe a method based on crude synthetic peptide libraries for the high-throughput development of(More)
Chemical cross-linking of reactive groups in native proteins and protein complexes in combination with the identification of cross-linked sites by mass spectrometry has been in use for more than a decade. Recent advances in instrumentation, cross-linking protocols, and analysis software have led to a renewed interest in this technique, which promises to(More)
Selected reaction monitoring (SRM) is a targeted mass spectrometric method that is increasingly used in proteomics for the detection and quantification of sets of preselected proteins at high sensitivity, reproducibility and accuracy. Currently, data from SRM measurements are mostly evaluated subjectively by manual inspection on the basis of ad hoc(More)
The ability to analyze and understand the mechanisms by which cells process information is a key question of systems biology research. Such mechanisms critically depend on reversible phosphorylation of cellular proteins, a process that is catalyzed by protein kinases and phosphatases. Here, we present PhosphoPep, a database containing more than 10 000(More)
Adaptation to a steady background has a profound effect on both color appearance and discrimination. We determined the temporal characteristics of chromatic adaptation for appearance and discrimination along different color directions. Subjects were adapted to a large uniform background made up of a CRT screen and a 45x64 degrees wall, illuminated by(More)
The Hippo (Hpo) pathway is a central determinant of tissue size in both Drosophila and higher organisms. The core of the pathway is a kinase cascade composed of an upstream kinase Hpo (MST1/2 in mammals) and a downstream kinase Warts (Wts, Lats1/2 in mammals), as well as several scaffold proteins, Sav, dRASSF, and Mats. Activation of the core kinase(More)
How do the colors and lightnesses of surfaces seen to lie behind a transparent filter depend on the chromatic properties of the filter? A convergence model developed in prior work (D'Zmura et al, 1997 Perception 26 471-492; Chen and D'Zmura, 1998 Perception 27 595-608) suggests that the visual system interprets a filter's transformation of color in terms of(More)