Yeast genetic networks : methods and protocols / edited by Attila Becskei. — [Totowa, N.J.] : Humana, c2011. – (58.17/M592/v.734)

Contents

    CONTENTS
    
    Preface
    Contributors
    PART I EXPERIMENTAL ANALYSIS OF SIGNALLING IN GENE REGULATORY NETWORKS
    1 Global Estimation of mRNA Stability in Yeast 3
    2 Genomic-Wide Methods to Evaluate Transcription Rates in Yeast 25
    3 Construction of cis-Regulatory Input Functions of Yeast Promoters 45
    4 Luminescence as a Continuous Real-Time Reporter of Promoter Activity in Yeast Undergoing Respiratory Oscillations or Cell Division Rhythms 63
    5 Linearizer Gene Circuits with Negative Feedback Regulation 81
    6 Measuring In Vivo Signaling Kinetics in a Mitogen-Activated Kinase Pathway Using Dynamic Input Stimulation 101
    PART II MATHEMATICAL MODELLING OF NETWORK BEHAVIOR
    7 Stochastic Analysis of Gene Expression
    8 Studying Adaptation and Homeostatic Behaviors of Kinetic Networks by Using MATLAB
    9 Biochemical Systems Analysis of Signaling Pathways to Understand Fungal Pathogenicity 173
    10 Clustering Change Patterns Using Fourier Transformation with Time-Course Gene Expression Data 201
    PART III ANALYSIS OF NETWORK BEHAVIOUR BY QUANTITATIVE GENETICS
    11 Finding Modulators of Stochasticity Levels by Quantitative
    12 Functional Mapping of Expression Quantitative Trait Loci that Regulate Oscillatory Gene Expression
    PART IV EXAMINATION OF NETWORK BEHAVIOUR IN RELATED YEAST SPECIES Genetics 223
    13 Evolutionary Aspects of a Genetic Network: Studying the Lactose/Galactose Regulon of Kluyveromyces lacris 259
    14 Analysis of Subtelomeric Silencing in Candida glabrata 279
    15 Morphological and Molecular Genetic Analysis of Epigenetic Switching of the Human Fungal Pathogen Candida albicans
    16 Quantitation of Cellular Components in Cryptococcus neoformans for System Biology Analysis
    Index