Comprehensive Identification of Cell Cycle–regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization
Paul T. Spellman,Gavin Sherlock,Gavin Sherlock,Michael Q. Zhang,Vishwanath R. Iyer,Kirk R. Anders,Michael B. Eisen,Patrick O. Brown,Patrick O. Brown,David Botstein,Bruce Futcher +10 more
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TLDR
A comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle is created, and it is found that the mRNA levels of more than half of these 800 genes respond to one or both of these cyclins.Abstract:
We sought to create a comprehensive catalog of yeast genes whose transcript levels vary periodically within the cell cycle. To this end, we used DNA microarrays and samples from yeast cultures sync...read more
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Book ChapterDOI
Metal toxicity in yeasts and the role of oxidative stress.
TL;DR: A major role of free radical generation in the toxicities of many metals is discussed, and the evidence to date indicates that each of the major cellular macromolecules can be a target for metal toxicity.
Journal ArticleDOI
Dealing with missing values in large-scale studies: microarray data imputation and beyond
TL;DR: The imputation methods are first reviewed in the context of gene expression microarray data, since most of the methods have been developed for estimating gene expression levels, then they are turned to other large-scale data sets that also suffer from the problems posed by missing values, together with pointers to possible imputation approaches in these settings.
Journal ArticleDOI
Chitin synthesis in Saccharomyces cerevisiae in response to supplementation of growth medium with glucosamine and cell wall stress.
Dorota A. Bulik,Mariusz Olczak,Hector A. Lucero,Barbara C. Osmond,Phillips W. Robbins,Charles A. Specht +5 more
TL;DR: Chs3p-dependent chitin synthesis in S. cerevisiae is regulated both by the levels of intermediates of the UDP-GlcNAc biosynthetic pathway and by an increase in the activity of the enzyme in the plasma membrane.
Journal ArticleDOI
Penalized Generalized Estimating Equations for High-Dimensional Longitudinal Data Analysis
Lan Wang,Jianhui Zhou,Annie Qu +2 more
TL;DR: A penalized generalized estimating equations procedure for analyzing longitudinal data with high‐dimensional covariates, which often arise in microarray experiments and large‐scale health studies, and one important feature of the new procedure is that the consistency of model selection holds even if the working correlation structure is misspecified.
Journal ArticleDOI
A Bayesian system integrating expression data with sequence patterns for localizing proteins: comprehensive application to the yeast genome
Amar Drawid,Mark Gerstein +1 more
TL;DR: A probabilistic system for predicting the subcellular localization of proteins and estimating the relative population of the various compartments in yeast, based on a Bayesian approach, which gives better accuracy in determining relative compartment populations than that obtained by simply tallying the localization predictions for individual proteins.
References
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Journal ArticleDOI
Cluster analysis and display of genome-wide expression patterns
TL;DR: A system of cluster analysis for genome-wide expression data from DNA microarray hybridization is described that uses standard statistical algorithms to arrange genes according to similarity in pattern of gene expression, finding in the budding yeast Saccharomyces cerevisiae that clustering gene expression data groups together efficiently genes of known similar function.
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Real time quantitative PCR.
TL;DR: Unlike other quantitative PCR methods, real-time PCR does not require post-PCR sample handling, preventing potential PCR product carry-over contamination and resulting in much faster and higher throughput assays.
Journal ArticleDOI
Exploring the Metabolic and Genetic Control of Gene Expression on a Genomic Scale
TL;DR: DNA microarrays containing virtually every gene of Saccharomyces cerevisiae were used to carry out a comprehensive investigation of the temporal program of gene expression accompanying the metabolic shift from fermentation to respiration, and the expression patterns of many previously uncharacterized genes provided clues to their possible functions.
Book ChapterDOI
Getting started with yeast.
TL;DR: The yeast Saccharomyces cerevisiae is now recognized as a model system representing a simple eukaryote whose genome can be easily manipulated and made particularly accessible to gene cloning and genetic engineering techniques.
Journal ArticleDOI
A Genome-Wide Transcriptional Analysis of the Mitotic Cell Cycle
Raymond J. Cho,Michael J. Campbell,Elizabeth A. Winzeler,Lars M. Steinmetz,Andrew R. Conway,Lisa Wodicka,Tyra G. Wolfsberg,Andrei Gabrielian,David Landsman,David J. Lockhart,Ronald W. Davis +10 more
TL;DR: The genome-wide characterization of mRNA transcript levels during the cell cycle of the budding yeast S. cerevisiae indicates a mechanism for local chromosomal organization in global mRNA regulation and links a range of human genes to cell cycle period-specific biological functions.