METHODS IN ENZYMOLOGY: GUIDE TO YEAST GENETICS AND MOLECULAR BIOLOGY

By N. LUTIA

CONTENTS SECTION I: YEAST SYSTEMS BIOLOGY 1 YEAST SYSTEMS BIOLOGY: THE CHALLENGE OF EUKARYOTIC COMPLEXITY SECTION II: EXPERIMENTAL SYSTEMS BIOLOGY: HIGH-THROUGHPUT GENOME-WIDE AND MOLECULAR STUDIES 2 SACCHAROMYCES CEREVISIAE: GENE ANNOTATION AND GENOME VARIABILITY, STATE OF THE ART THROUGH COMPARATIVE GENOMICS 3 GENOME-WIDE MEASUREMENT OF HISTONE H3 REPLACEMENT DYNAMICS IN YEAST 4 GENOME-WIDE APPROACHES TO STUDYING YEAST CHROMATIN MODI?CATIONS 5 ABSOLUTE AND RELATIVE QUANTI?CATION OF MRNA EXPRESSION (TRANSCRIPT ANALYSIS) 6 ENRICHMENT OF UNSTABLE NON-CODING RNAS AND THEIR GENOME-WIDE IDENTI?CATION 7 GENOME-WIDE TRANSCRIPTOME ANALYSIS IN YEAST USING HIGH-DENSITY TILING ARRAYS 8 RNA SEQUENCING 9 POLYADENYLATION STATE MICROARRAY (PASTA) ANALYSIS 10 ENABLING TECHNOLOGIES FOR YEAST PROTEOME ANALYSIS 11 PROTEIN TURNOVER METHODS IN SINGLE-CELLED ORGANISMS: DYNAMIC SILAC 12 PROTEIN–PROTEIN INTERACTIONS AND NETWORKS: FORWARD AND REVERSE EDGETICS UBIQUITIN LIGASES 14 FIT-FOR-PURPOSE QUENCHING AND EXTRACTION PROTOCOLS FOR METABOLIC PRO?LING OF YEAST USING CHROMATOGRAPHY-MASS SPECTROMETRY PLATFORMS 15 THE AUTOMATED CELL: COMPOUND AND ENVIRONMENT SCREENING SYSTEM (ACCESS) FOR CHEMOGENOMIC SCREENING 16 COMPETITION EXPERIMENTS COUPLED WITH HIGH-THROUGHPUT ANALYSES FOR FUNCTIONAL GENOMICS STUDIES IN YEAST 17 FLUORESCENCE FLUCTUATION SPECTROSCOPY AND IMAGING METHODS FOR EXAMINATION OF DYNAMIC PROTEIN INTERACTIONS IN YEAST 18 NUTRITIONAL CONTROL OF CELL GROWTH VIA TOR SIGNALING IN BUDDING YEAST SECTION III: COMPUTATIONAL SYSTEMS BIOLOGY: COMPUTATIONAL STUDIES AND ANALYSES 19 COMPUTATIONAL YEAST SYSTEMS BIOLOGY: A CASE STUDY FOR THE MAP KINASE CASCADE 20 STANDARDS, TOOLS, AND DATABASES FOR THE ANALYSIS OF YEAST ‘OMICS DATA 21 A COMPUTATIONAL METHOD TO SEARCH FOR DNA STRUCTURAL MOTIFS IN FUNCTIONAL GENOMIC ELEMENTS 22 HIGH-THROUGHPUT ANALYSES AND CURATION OF PROTEIN INTERACTIONS IN YEAST 23 NOISE IN BIOLOGICAL SYSTEMS: PROS, CONS, AND MECHANISMS OF CONTROL 24 GENOME-SCALE INTEGRATIVE DATA ANALYSIS AND MODELING OF DYNAMIC PROCESSES IN YEAST 25 GENOME-SCALE METABOLIC MODELS OF SACCHAROMYCES CEREVISIAE METHODS IN ENZYMOLOGY 26 REPRESENTATION, SIMULATION, AND HYPOTHESIS GENERATION IN GRAPH AND LOGICAL MODELS OF BIOLOGICAL NETWORKS 27 USE OF GENOME-SCALE METABOLIC MODELS IN EVOLUTIONARY SYSTEMS BIOLOGY SECTION IV: YEAST SYSTEMS BIOLOGY IN PRACTICE: SACCHAROMYCES CEREVISIAE AS A TOOL FOR MAMMALIAN STUDIES 28 CONTRIBUTIONS OF SACCHAROMYCES CEREVISIAE TO UNDERSTANDING MAMMALIAN GENE FUNCTION AND THERAPY