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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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Citations
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Journal ArticleDOI

On Learning Gene Regulatory Networks Under the Boolean Network Model

TL;DR: This work proposes simple efficient algorithms that can be used to answer the Consistency Problem and find one or all consistent Boolean networks relative to the given examples and introduces a simple and fast way of finding all Boolean networks having limited error size in the Best-Fit Extension Problem setting.
Journal ArticleDOI

Mining the biomedical literature in the genomic era: an overview.

TL;DR: This paper surveys the disciplines involved in unstructured-text analysis, categorizes current work in biomedical literature mining with respect to these disciplines, and provides examples of text analysis methods applied towards meeting some of the current challenges in bioinformatics.
Journal ArticleDOI

Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.

TL;DR: MA-Networker, an algorithm that combines microarray data for mRNA expression and transcription factor occupancy to define the regulatory network of the cell, is presented, finding that, on average, 58% of the genes whose promoter region is bound by a transcription factor are true regulatory targets.
Journal ArticleDOI

Continuous Representations of Time-Series Gene Expression Data

TL;DR: This work presents algorithms for time-series gene expression analysis that permit the principled estimation of unobserved time points, clustering, and dataset alignment, and shows a specific application to yeast knock-out data that produces biologically meaningful results.
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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