COMMENTARIES IN PLANT SCIENCE
CONTENTS PART I SYSTEMS BIOLOGY: AN OVERVIEW SYSTEMS BIOLOGY: PRINCIPLES AND APPLICATIONS IN PLANT RESEARCH INTRODUCTION NETWORK BIOLOGY EXPERIMENTAL APPROACHES FOR PLANT SYSTEMS BIOLOGY STRATEGIES FOR GENOMIC DATA INTEGRATION SYSTEMS BIOLOGY IN PLANT RESEARCH CONCLUSION AN OVERVIEW OF SYSTEMS BIOLOGY SYSTEMS THEORY AND BIOLOGY GRAPH ELEMENTS AND NETWORK ATTRIBUTES BUILDING BIOLOGICAL NETWORKS: IDENTIFYING NODES AND MAPPING INTERACTIONS BUILDING BIOLOGICAL NETWORKS: COMPUTATIONAL METHODS FOR NETWORK INFERENCE BIOLOGICAL NETWORK MODELS: DATA INTEGRATION BIOLOGICAL NETWORK MODELS: FROM NETWORK STRUCTURE TO DYNAMICS PERSPECTIVES PROKARYOTIC SYSTEMS BIOLOGY TYPES OF QUESTIONS A TYPICAL PROKARYOTIC SYSTEMS BIOLOGY PROJECT GLOBAL MODELS COMPARATIVE FUNCTIONAL GENOMICS OF PROKARYOTES REVIEW OF CORE TECHNOLOGIES FOR PROKARYOTIC SYSTEMS BIOLOGY CAULOBACTER CRESCENTUS BACILLUS SUBTILIS ESCHERICHIA COLI ANIMAL SYSTEMS BIOLOGY: TOWARDS A SYSTEMS VIEW OF DEVELOPMENT IN C ELEGANS WHY C ELEGANS AS A MODEL FOR DEVELOPMENTAL SYSTEMS BIOLOGY? DE?NING IN VIVO FUNCTIONS DURING DEVELOPMENT: TOWARDS A PHENOME MAP OF C ELEGANS EMBRYOGENESIS DATA INTEGRATION: TOWARDS A SYSTEMS VIEW OF EARLY EMBRYOGENESIS PART II PLANT SYSTEMS BIOLOGY: ENUMERATING AND INTEGRATING THE SYSTEM COMPONENTS SOFTWARE TOOLS FOR SYSTEMS BIOLOGY: VISUALIZING THE OUTCOMES OF N EXPERIMENTS ON M ENTITIES THE WORTHWHILE CHALLENGE OF INTERDISCIPLINARY WORK SUNGEAR DESIGN PRINCIPLES COMBINING VISUALIZATION TOOLS FOR PLANT SYSTEMS BIOLOGY MAPMAN GENEVESTIGATOR CYTOSCAPE VIRTUALPLANT THE PLANT GENOME: DECODING THE TRANSCRIPTIONAL HARDWIRING THE PLANT BASAL TRANSCRIPTIONAL APPARATUS PLANT TRANSCRIPTION FACTORS HARD WIRING OF REGULATORY SEQUENCES PLANT TRANSCRIPTIONAL REGULATORY MOTIFS, MODULES AND NETWORKS THE RNA WORLD: IDENTIFYING MIRNA-TARGET RNA PAIRS AS POSSIBLE MISSING LINKS IN MULTI-NETWORK MODELS SEQUENCING OF SMALL RNAS IDENTI?CATION OF MIRNAS IDENTI?CATION OF MIRNA TARGETS MICRORNA-TARGET MRNA PAIRS: MISSING LINKS IN MULTI-NETWORK MODELS? PROTEOMICS: SETTING THE STAGE FOR SYSTEMS BIOLOGY INTRODUCTION: THE NEED FOR PROTEOMICS IN SYSTEMS BIOLOGY DETERMINATION OF PROTEIN LOCATION IN THE CELL IDENTI?CATION OF DIFFERENT PROTEIN FORMS QUANTITATION METABOLOMICS: INTEGRATING THE METABOLOME AND THE PROTEOME FOR SYSTEMS BIOLOGY THE MOLECULAR HIERARCHY IN BIOCHEMICAL NETWORKS, THE CONCEPT OF SYSTEMS BIOLOGY AND FUNCTIONAL GENOMICS IN THE POST-GENOME ERA METABOLOMICS AND PROTEOMICS: POST-GENOME DISCIPLINES INTIMATELY BOUND TO MASS SPECTROMETRIC TECHNIQUES METABOLOMICS: GLOBAL ANALYSIS OF RAPID METABOLIC RESPONSES COMBINED WITH COMPUTER-AIDED ITERATIVE METABOLIC MODELLING APPLICATION OF METABOLOMICS IN MOLECULAR PLANT PHYSIOLOGY AND BIOCHEMISTRY MEASURING THE KEY PLAYERS: PROTEOMICS COMBINING METABOLOMICS, PROTEOMICS AND MULTIVARIATE DATA MINING: A SYSTEMS BIOLOGY APPROACH FROM THE IONOME TO THE GENOME: IDENTIFYING THE GENE NETWORKS THAT CONTROL THE MINERAL CONTENT OF PLANTS ANALYTICAL PLATFORMS FOR IONOMICS BIOINFORMATICS PLATFORMS FOR IONOMICS ARABIDOPSIS AS A MODEL SYSTEM FOR IONOMICS EVOLUTIONARY CONTEXT FOR IONOMICS DEVELOPMENT AND SYSTEMS BIOLOGY: RIDING THE GENOMICS WAVE TOWARDS A SYSTEMS UNDERSTANDING OF ROOT DEVELOPMENT ROOTS AND SYSTEMS BIOLOGY WHY STUDY ROOTS? ROOT DEVELOPMENT IN THE MODEL PLANT, ARABIDOPSIS THALIANA SYSTEMS BIOLOGY AT THE MOLECULAR LEVEL: MODELLING A ROOT TRANSCRIPTIONAL NETWORK IDENTI?CATION OF COMPONENTS COMPONENT MODELLING SYSTEMS BIOLOGY AT THE CELLULAR LEVEL: MODELLING ROOT GROWTH AND THE DYNAMIC BEHAVIOUR OF ITS COMPONENT CELLS SYSTEMS BIOLOGY: MODELLING THE ROOT PHYSICAL NETWORK FUTURE DIRECTIONS PERSPECTIVES ON ECOLOGICAL AND EVOLUTIONARY SYSTEMS BIOLOGY EMERGENT PROPERTIES OF SYSTEMS BIOLOGY, ECOLOGY AND EVOLUTION COMPLEX ENVIRONMENTS AND ECOLOGICAL SYSTEMS BIOLOGY GENE NETWORKS AND THE ECOLOGICAL TRANSCRIPTOME ANALYSIS OF SYSTEMS BIOLOGY DATA: THE ROLE OF ECOLOGICAL AND EVOLUTIONARY METHODS THE ECOLOGICAL AND EVOLUTIONARY CONTEXT OF MODEL ORGANISMS: THE EXAMPLE OF ARABIDOPSIS AND BEYOND NATURAL VARIATION IN GENOMES AND GENE NETWORKS THE FUTURE OF ECOLOGICAL AND EVOLUTIONARY SYSTEMS BIOLOGY