METHODS IN CELL PHYSIOLOGY
CONTENTS PART I YEAST SYSTEMS BIOLOGY 1 YEAST SYSTEMS BIOLOGY: THE CONTINUING CHALLENGE OF EUKARYOTIC COMPLEXITY PART II EXPERIMENTAL SYSTEMS BIOLOGY: H IGH- THROUGHPUT GENOME-WIDE AND MOLECULAR STUDIES 2 CAPTURE OF RIBONUCLEOTIDES IN YEAST GENOMIC DNA USING RIBOSE-SEQ 1 3 METHOD FOR MULTIPLEXED INTEGRATION OF SYNERGISTIC ALLELES AND METABOLIC PATHWAYS IN YEASTS VIA CRISPR-CAS9 3 4 ULTRAHIGH-DENSITY SCREENS FOR GENOME-WIDE YEAST EMAPS IN A SINGLE PLATE 6 5 EPI-ID: SYSTEMATIC AND DIRECT SCREENING FOR CHROMATIN REGULATORS IN YEAST BY BARCODE-CHIP-SEQ 8 6 TRANSCRIPT PRO?LING ANALYSIS THROUGH PAIRED-END DITAG (PET) APPROACH COUPLED WITH DEEP SEQUENCING REVEALS TRANSCRIPTOME COMPLEXITY IN YEAST 9 7 RNA SEQUENCING BEST PRACTICES: EXPERIMENTAL PROTOCOL AND DATA ANALYSIS 1 0 8 ADVANCED METHODS FOR THE ANALYSIS OF ALTERED PRE-MRNA SPLICING IN YEAST AND DISEASE 1 2 9 PAT-SEQ: A METHOD FOR SIMULTANEOUS QUANTITATION OF GENE EXPRESSION, POLY(A)-SITE SELECTION AND POLY(A)-LENGTH DISTRIBUTION IN YEAST TRANSCRIPTOMES 1 3 10 MAPPING THE SACCHAROMYCES CEREVISIAE SPATIAL PROTEOME WITH HIGH RESOLUTION USING HYPERLOPIT 1 5 11 DATA-INDEPENDENT ACQUISITION FOR YEAST GLYCOPROTEOMICS 1 8 ´ 12 PROTEIN–PROTEIN INTERACTION PRO?LING IN CANDIDA ALBICANS REVEALED BY BIOCHEMICAL PURI?CATION–MASS SPECTROMETRY (BP/MS) 1 9 13 PROBING THE RNA-BINDING PROTEOME FROM YEAST TO MAN: MAJOR ADVANCES AND CHALLENGES 2 0 14 METABOLOMIC ANALYSIS OF YEAST AND HUMAN CELLS: LATEST ADVANCES AND CHALLENGES 2 2 15 MEASURING THE ACTIVITY OF PLASMA MEMBRANE AND VACUOLAR TRANSPORTERS IN YEAST 2 3 16 SELF-ESTABLISHING COMMUNITIES: A YEAST MODEL TO STUDY THE PHYSIOLOGICAL IMPACT OF METABOLIC COOPERATION IN EUKARYOTIC CELLS 2 5 PART III COMPUTATIONAL SYSTEMS BIOLOGY: D ATA MANAGEMENT AND MODELING THE CELL 17 DATA MANAGEMENT IN COMPUTATIONAL SYSTEMS BIOLOGY: EXPLORING STANDARDS, TOOLS, DATABASES, AND PACKAGING BEST PRACTICES 2 7 18 RATIONAL DESIGN AND METHODS OF ANALYSIS FOR THE STUDY OF SHORT- AND LONG-TERM DYNAMIC RESPONSES OF EUKARYOTIC SYSTEMS 3 0 19 GENOME-SCALE METABOLIC MODELING FROM YEAST TO HUMAN CELL MODELS OF COMPLEX DISEASES: LATEST ADVANCES AND CHALLENGES 3 1 20 NEXT-GENERATION GENOME-SCALE MODELS INCORPORATING MULTILEVEL ‘OMICS DATA: FROM YEAST TO HUMAN 3 3 21 ADVANCED MODELING OF CELLULAR PROLIFERATION: TOWARD A MULTI-SCALE FRAMEWORK COUPLING CELL CYCLE TO METABOLISM BY INTEGRATING LOGICAL AND CONSTRAINT-BASED MODELS 3 5 PART IV USING YEAST TO MODEL HUMAN DISEASES YEAST GENOME SCREENING AND METHODS FOR THE DISCOVERY OF METABOLIC PATHWAYS INVOLVED IN A PHENOTYPIC RESPONSE TO ANTICANCER AGENTS 3 7 23 ADVANCED YEAST MODELS OF FAMILIAL ALZHEIMER DISEASE EXPRESSING FAD-LINKED PRESENILIN TO SCREEN MUTATIONS AND ?-SECRETASE MODULATORS 3 8 24 FROM YEAST TO HUMANS: LEVERAGING NEW APPROACHES IN YEAST TO ACCELERATE DISCOVERY OF THERAPEUTIC TARGETS FOR SYNUCLEINOPATHIES 4 0