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Budding yeast grown under continuous, nutrient-limited conditions exhibit robust, highly periodic cycles in the form of respiratory bursts. Microarray studies reveal that over half of the yeast genome is expressed periodically during these metabolic cycles. Genes encoding proteins having a common function exhibit similar temporal expression patterns, and(More)
The eukaryotic cell division cycle depends on an intricate sequence of transcriptional events. Using an algorithm based on maximum-entropy deconvolution, and expression data from a highly synchronized yeast culture, we have timed the peaks of expression of transcriptionally regulated cell cycle genes to an accuracy of 2 min (approximately equal to 1% of the(More)
Valosin-containing protein (VCP; p97; cdc48 in yeast) is a hexameric ATPase of the AAA family (ATPases with multiple cellular activities) involved in multiple cellular functions, including degradation of proteins by the ubiquitin (Ub)-proteasome system (UPS). We examined the consequences of the reduction of VCP levels after RNA interference (RNAi) of VCP. A(More)
An algorithm for evaluation of the crystallographic FFT for 67 crystallographic space groups is presented. The symmetry is reduced in such a way that it is enough to calculate P1 FFT in the asymmetric unit only and then, in a computationally simpler step, recover the final result. The algorithm yields the maximal symmetry reduction for every space group(More)
An algorithm for computing the discrete Fourier transform of data with threefold symmetry axes is presented. This algorithm is straightforward and easily implemented. It reduces the computational complexity of such a Fourier transform by a factor of 3. There are no restrictive requirements imposed on the initial data. Explicit formulae and a scheme of(More)
While genome-wide gene expression data are generated at an increasing rate, the repertoire of approaches for pattern discovery in these data is still limited. Identifying subtle patterns of interest in large amounts of data (tens of thousands of profiles) associated with a certain level of noise remains a challenge. A microarray time series was recently(More)
SUMMARY SCEPTRANS is designed for analysis of microarray timecourse data related to periodic phenomena in the budding yeast. The server allows for easy viewing of temporal profiles of multiple genes in a number of datasets. Additional functionality includes searching for coexpressed genes, periodicity and correlation analysis, integrating functional(More)
Modulators (Ms) are proteins that modify the activity of transcription factors (TFs) and influence expression of their target genes (TGs). To discover modulators of NF-κB/RelA, we first identified 365 NF-κB/RelA-binding proteins using liquid chromatography-tandem mass spectrometry (LC-MS/MS). We used a probabilistic model to infer 8349 (M, NF-κB/RelA, TG)(More)
Methylation is one of the most common chemical modifications of biologically active molecules and it occurs in all life forms. Its functional role is very diverse and involves many essential cellular processes, such as signal transduction, transcriptional control, biosynthesis, and metabolism. Here, we provide further insight into the enzymatic methylation(More)