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Open AccessJournal ArticleDOI

Comprehensive Identification of Cell Cycle–regulated Genes of the Yeast Saccharomyces cerevisiae by Microarray Hybridization

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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...

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Journal ArticleDOI

Replication Fork Stalling at Natural Impediments

TL;DR: This review describes the mechanisms and consequences of replication stalling at various natural impediments, with an emphasis on the role of replicationStalling in genomic instability.
Journal ArticleDOI

Kinetic Analysis of a Molecular Model of the Budding Yeast Cell Cycle

TL;DR: Using standard techniques of biochemical kinetics, a mechanism for the principal molecular interactions controlling cyclin synthesis and degradation is converted into a set of differential equations, which describe the time courses of three major classes of cyclin-dependent kinase activities.
Journal ArticleDOI

Systematic changes in gene expression patterns following adaptive evolution in yeast

TL;DR: In this article, the authors used DNA microarrays to compare genome-wide patterns of gene expression in the evolved strains and the parental strain and found that increased fitness is acquired by altering regulation of central metabolism such that less glucose is fermented and more glucose is completely oxidized.
Journal ArticleDOI

Fast optimal leaf ordering for hierarchical clustering.

TL;DR: This work presents the first practical algorithm for the optimal linear leaf ordering of trees that are generated by hierarchical clustering, and shows how optimal leaf ordering can reveal biological structure that is not observed with an existing heuristic ordering method.
Journal ArticleDOI

Analyzing time series gene expression data

TL;DR: This review is intended to serve as both, a point of reference for experimental biologists looking for practical solutions for analyzing their data, and a starting point for computer scientists interested in working on the computational problems related to time series expression analysis.
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.
Journal ArticleDOI

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

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.
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