MicroRNA Cancer Regulation; Preface; Background; The Systems Perspective on microRNAs in Cancer; Scope of This Book and Target Audience; Structure; How to Read This Book; Biologists and Clinicians; Computational Scientists and Modellers; Acknowledgements; Contents; 1: MicroRNAs in Human Cancer; 1.1 miRNA Overview; 1.2 Methods for Studying miRNA Genetics and Expression; 1.2.1 miRNA Profiling; 1.2.2 miRNA Databases and Validation; 1.3 Mechanisms of Alteration of miRNA Levels in Malignancy; 1.3.1 General Principles of miRNA Genomic Organization 1.3.2 Alterations in Genomic miRNA Copy Numbers and Location1.3.3 Alterations in miRNA Transcriptional Regulation; 1.3.4 miRNA Biogenesis Pathway in Tumorigenesis; 1.3.4.1 miRNA Biogenesis; 1.3.4.2 Alterations in RNASEN/DGCR8 and DICER1/TARBP2; 1.3.4.3 Alterations in Other Pathway-Related RBPs; 1.4 Dysregulation of miRNA-mRNA Target Recognition; 1.4.1 miRNA Function/Mechanism; 1.4.2 Organization of miRNAs into Sequence Families; 1.4.3 miRNA-mRNA Stoichiometry; 1.4.4 Changes in the miRNA Targets; 1.5 Cancer Tissues Have Distinct miRNA Profiles; 1.5.1 miRNA Cancer Database 1.5.2 Tissue Heterogeneity1.5.3 miRNAs as Tumor Suppressors and Oncogenes; 1.5.4 miRNA-Regulated Pathways; 1.6 Alterations of miRNA Sequence; 1.7 miRNA Target Identification; 1.8 miRNAs as Diagnostics; 1.9 miRNAs as Therapeutics; References; 2: Bioinformatics, Non-coding RNAs and Its Possible Application in Personalized Medicine; 2.1 Introduction; 2.2 Background; 2.2.1 Types of ncRNAs; 2.2.2 miRNA Function; 2.2.3 miRNA Networks in Cancer; 2.2.4 miRNA Identification; 2.2.5 Deep Sequencing; 2.2.5.1 NGS Data Analysis; 2.2.5.2 NGS and ncRNAs; 2.3 miRNA Gene Prediction; 2.3.1 Prediction Factors 2.3.2 Prediction Methods2.4 miRNA Target Prediction; 2.5 miRNAs in Clinical Practice; 2.5.1 Cancer Predisposition and Development; 2.5.1.1 Diagnosis, Prognosis and Metastasis; 2.6 Conclusion; References; 3: MicroRNA Target Prediction and Validation; 3.1 Introduction; 3.2 Computational Methods to Identify microRNA Targets; 3.2.1 Thermodynamic Stability of the microRNA:mRNA Duplex; 3.2.2 Sequence Conservation of the Target Site Between Multiple Species; 3.2.3 Multiple Targets in the Same 3'UTR; 3.2.4 Functional Category of Targets; 3.2.5 Combining microRNA and mRNA Expression Data 3.2.6 Concluding Remarks Regarding Computational Methods3.2.7 Future Directions; 3.3 Experimental Identification and Validation of microRNA Targets; 3.3.1 Reporter Assays; 3.3.2 Proteomics Methods; 3.3.3 Biochemical Approaches; 3.3.4 Molecular Methods; 3.3.5 Concluding Remarks; References; 4: MicroRNA-Regulated Networks: The Perfect Storm for Classical Molecular Biology, the Ideal Scenario for Systems Biology; 4.1 Introduction; 4.2 Systems Biology in a Nutshell; 4.2.1 Network Construction; 4.2.2 Mathematical Model Construction; 4.2.3 Model Calibration; 4.2.4 Model Analysis 4.3 MicroRNAs as Components of Complex Network Motifs Preface -- 1 MicroRNAs in human cancer -- 2 Bioinformatics, non-coding RNAs and its possible application in personalized medicine -- 3 MicroRNA target prediction and validation -- 4 MicroRNA-regulated networks: the perfect storm for classical molecular biology, the ideal scenario for systems biology -- 5 The p53/microRNA network in cancer: experimental and bioinformatics approaches.-6 MicroRNAs in melanoma biology -- 7 MicroRNA in the lung -- 8 The E2F1-miRNA cancer progression network -- 9 Modeling of microRNA-transcription factor networks in cancer -- 10 Coordinated networks of microRNAs and transcription factors with evolutionary perspectives -- 11 Mathematical modeling of microRNA-mediated mechanisms of translation repression -- 12 Web resources for microRNA research -- 13 Discovery of microRNA regulatory networks by integrating multidimensional high-throughput data -- 14 Discovering the functional microRNA-mRNA regulatory modules in heterogeneous data -- 15 Elucidating the role of microRNAs in cancer through data mining techniques -- 16 Working together: Combinatorial regulation by microRNAs. . | 
