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BL
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| Record Number
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864766
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| Title & Author
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Theoretical and applied aspects of systems biology /\ Fabricio Alves Barbosa da Silva, Nicolas Carels, Floriano Paes Silva Junior, editors.
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| Publication Statement
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Cham, Switzerland :: Springer,, 2018.
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| Series Statement
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Computational biology,; volume 27
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| Page. NO
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1 online resource (xviii, 259 pages) :: illustrations (some color)
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| ISBN
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3030091171
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: 3319749749
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: 3319749757
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: 9783030091170
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: 9783319749747
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: 9783319749754
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3319749730
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9783319749730
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| Bibliographies/Indexes
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Includes bibliographical references.
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| Contents
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Intro; Preface; Foreword to Theoretical and Applied Aspects of Systems Biology; Contents; List of Editors and Contributors; Editors; Contributors; Part I Fundamentals; Bio-modeling Using Petri Nets: A Computational Approach; 1 Modeling Systems Biology; 2 Petri Nets; 2.1 Qualitative Petri Net (QPN); 2.2 Continuous Petri Net (CPN); 2.3 Stochastic Petri Net (SPN); 2.4 Hybrid Petri Net (HPN); 2.5 Colored Petri Net; 3 Model Analysis; 4 Tools; 5 Conclusion and Discussion; References; Modeling Gene Transcriptional Regulation: A Primer; 1 Introduction; 2 Gene Transcriptional Regulation in Prokaryotes.
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2.1 Basics of Gene Transcriptional Regulation2.2 The Lac Operon; 3 Computational Modeling of Transcriptional Regulation; 3.1 On the Modeling Approach; 3.2 Boolean Logic for the Lac Operon; 3.3 Network Motifs; 4 Discussion; References; Cellular Reprogramming; 1 Introduction; 2 What Is Cellular Reprogramming?; 2.1 Premise; 2.2 Meaning of Cellular Reprogramming; 2.3 Applications; 3 Reprogramming Methods; 3.1 Cellular Reprogramming Through the Overexpression of Transcription Factors; 3.2 Somatic Cell Nuclear Transfer; 3.3 Cell Fusion; 4 Modeling Cellular Reprogramming.
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2.1 Introduction to Taxonomic Binning2.2 Taxonomic Classification; 2.3 Functional Annotation; 2.4 Normalization; 3 Comparative Analysis; 3.1 Diversity Metrics and Distances; 3.2 Feature Representation and Dimensionality Reduction; 3.2.1 Feature Selection; 3.2.2 Feature Extraction; 3.2.3 Distance-Based Approaches for Feature Extraction; 3.2.4 Neural Network Approaches for Feature Extraction; 4 Diversity Metrics and Constrained Ordination; 5 Statistical Inference; 5.1 Multilevel Regression; 5.2 Multivariate Analysis; 5.3 Differential Abundance Analysis.
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4.1 A Data-Oriented Approach4.2 Ordinary Differential Equation; 4.3 Bayesian Network; 4.4 Boolean Network; 5 Cellular Reprogramming Using a Boolean Network; 6 Application of Cellular Reprogramming to Disease Control; 7 Conclusion; References; Metabolic Models: From DNA to Physiology (and Back); 1 Metabolic Models; 2 FBA: Predicting Metabolic Phenotypes; 2.1 Growth Prediction; 2.2 Gene Essentiality; 2.3 Octave Code with FBA Analysis; References; Analysis Methods for Shotgun Metagenomics; 1 Introduction to Metagenomics; 2 Sequence Quality and Identification.
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6 Machine Learning and its Application to Metagenomics6.1 Overview; 6.2 A General Machine Learning Review; 6.3 Taxonomic Classification and DNA Binning; 6.3.1 Naive Bayesian Classifier; 6.3.2 k-Nearest Neighbors; 6.3.3 Clustering; 6.4 Functional Annotation and Prediction; 6.4.1 Hidden Markov Model; 6.4.2 Logistic Regression; 6.5 Phenotype Prediction; 6.5.1 Random Forest; 6.5.2 Support Vector Machine; 6.5.3 Elastic Net; 7 Discussion and Conclusion; References; ANOCVA: A Nonparametric Statistical Test to Compare Clustering Structures; 1 Introduction; 2 The Silhouette Statistic; 3 ANOCVA.
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| Abstract
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Systems Biology is a rapidly expanding field and comprises the study of biological systems through mathematical modeling and the analysis of large volumes of biological data. This book presents the theoretical foundations of Systems Biology, as well as its application in studies on human hosts, pathogens and associated diseases. This book presents several chapters written by renowned experts in the field. Some topics discussed in depth in this book include: computational modeling of multidrug-resistant bacteria, systems biology of cancer, systems immunology, cellular reprogramming, bio-modeling using Petri nets, computational modeling of neuronal circuits, reconstruction and analysis of gene regulatory networks.
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| Subject
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Systems biology.
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Cellular biology (cytology)
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Life sciences: general issues.
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Medical equipment techniques.
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Molecular biology.
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NATURE-- Reference.
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Oncology.
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SCIENCE-- Life Sciences-- Biology.
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SCIENCE-- Life Sciences-- General.
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| Subject
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Systems biology.
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| Dewey Classification
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570.285
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| LC Classification
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QH324.2
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| Added Entry
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Alves Barbosa da Silva, Fabricio
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Carels, Nicolas
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Paes Silva Junior, Floriano
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